Plot:Shin Megami Tensei IV: Apocalypse

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This is a complete summary of Shin Megami Tensei IV: Apocalypse’s plot and multiple endings. Be warned that spoilers are detailed below.

Beginning

It is the year 2038 A.D. in Tokyo. The city and its populace are caught in an escalating war between the angels led by Merkabah and the demons led by Lucifer. Humanity has placed their entire hope into a single man named Flynn, a Samurai originally from the Eastern Kingdom of Mikado above the Firmament, who has liberated Tokyo from its warring syndicates and is now fighting to stop the angels and demons.

In his sleep, the young Hunter cadet Nanashi dreams of a shadowed figure calling him "Akira" and beckoning to join him in saving humanity. He awakes to the voice of Asahi, his adoptive sister and fellow Hunter cadet. Both Nanashi and Asahi admire Flynn and aspire to become heroic Hunters like him, but are powerless without smartphones to summon demons with; a privilege given only to full-fledged Hunters. Their instructors, Nikkari and Manabu, shortly return from clearing out demons in Downtown Ginza. Nikkari has the cadets go searching for salvageable Relics in the area. While looking, Nanashi happens to find a smartphone and Asahi leaves to inform the men. She comes back with Manabu, who realizes that the phone's data is too corrupted to use the Demon Summoning Program. He nonetheless lets Nanashi keep the phone until he can receive another.

The three report back to Nikkari afterward. He asks the cadets their age and remarks they are close–but not quite–to becoming Hunters. He decides to give the cadets a history lesson on the current state of Tokyo: 25 years ago, demons had suddenly invaded Tokyo. In the ensuing chaos, the world's nations were destroyed in nuclear warfare, but Tokyo had survived the onslaught by the sacrifice of a young man and the guardian deity, Masakado. The pair transformed into the stone ceiling covering Tokyo, shielding the city from the missiles. Rumors circulated that the catastrophe was caused by the angels and it became known as "God's Plan". However, while the Firmament trapped the populace inside with the demons, the sudden and mysterious distribution of the Demon Summoning Program allowed them to fight back and control the demons. Nikkari adds that he also had assisted the JSDF in digging a tunnel through the Firmament via the Sky Tower. They succeeded after several years of digging, but were immediately repelled by angels protecting the people already living there. Despite the soldiers' attempts to fight back, they were outmatched and forced to retreat back to Tokyo. With no other hope of escape, the people of Tokyo had split off into disparate factions, the Ashura-kai, the Ring of Gaea, and the Hunter Association.

With their work done for the day, the team return home to the underground district of Kinshicho. Nikkari informs the cadets there will be an announcement by the Hunter Association next morning and advise they attend. Nanashi and Asahi shortly return home for the night. Nanashi has another dream where he is again called Akira. In his dream, a panic ensues over an incoming ICBM and one of the JSDF's men missing. Akira then spots the missing soldier, a man closely resembling Flynn, on the Ginza monitor screen. He helplessly watches as the man unsheathes Masakado's Katana to summon the guardian deity, sacrificing himself in the process just as the Firmament appears over Tokyo. The dream abruptly ends at Asahi's urging for Nanashi to wake up. He explains his dream to her, surmising that the man resembling Flynn had committed suicide. Asahi suggests he share this dream with their instructors and they leave together to attend the assembly at the Kinshicho Hunter Association bar.

Asahi asks her father if he has seen Nikkari, to which he rebukes her for not calling him Boss while at work and nudges the cadets off. They shortly find Nikkari and Manabu in the crowd waiting on the assembly. Nanashi tells the men his dream, which earns him their suspicion and Nikkari's order never to mention the dream nor the name Akira again. The men explain that Akira was a soldier who worked for Fujiwara and Skins, the founders of the Hunter Association, but had betrayed the Hunters by abandoning Tokyo. They end the topic there and turn their attention to the bar monitor as the assembly begins airing. Fujiwara and Skins address the audience with the announcement of worsening conditions: Merkabah's angels have taken over the Sky Tower while Lucifer has built a stronghold at Camp Ichigaya. Both factions are planning to soon intercept each other, which would catch Tokyo in-between as collateral. However, they also announce that Flynn intends to take out both adversaries. To that end, all Hunters are now ordered to provide Flynn their aid in any way they can and will soon be issued tasks from the Association.

With their next tasks pending, Nikkari takes the cadets to Kinshi Park to gather food as their morning assignment. As they arrive, Nikkari decides it is time for the cadets to learn the basics of combat. He leaves Manabu to instruct them and waits at the park fountain. The cadets shortly report back to Nikkari with their success, however the team suddenly find themselves surrounded by a group of demons led by Adramelech, Lucifer's sworn knight. The demon Horde came to watch Merkabah's descent from the Sky Tower and are left hungry from their travels. The team engage the demons in battle, but find their attacks are ineffective. Both Manabu and Nikkari perish while shielding Asahi and Nanashi from Adramelech's flames. Nanashi soon follows as he also dies to the demons.

Nanashi awakes to find himself in a suspended world haunted by ghosts. A voice beckons him to come to its center. There Nanashi is approached by the god Dagda, who informs him they are in Yomotsu Hirasaka and that he is dead. However, Dagda offers to revive him in exchange for his complete servitude.

If Nanashi responds with his name, his pact with Dagda is sealed and he is bestowed with new strength. Dagda states that henceforth Nanashi is now his Godslayer and puppet. Nanashi is revived back in Kinshi Park in an aura of green energy that seals his wounds and repairs his smartphone, which Dagda now inhabits. Asahi attempts to fend off the demons by summoning from Nikkari's phone, but her access is blocked. Dagda speaks to Nanashi from his phone and tells him that he can now summon demons with it. By Dagda's order, Nanashi enters the battle, to the astonishment of both Asahi and Adramelech. Nanashi overpowers the demon horde this time and Adramelech falls back after sensing a godly power backing him.

After recomposing herself from the experience, Asahi uses Nikkari's phone to send the Association a report and determines they should return to Kinshicho and inform Boss directly. Once back, Asahi asks her father to make them official Hunters so they can honor Nikkari and Manabu. Her father refuses to allow this and Asahi angrily leaves, holding onto Nikkari's phone. In their determination to prove themselves capable, the cadets come up with the plan to recruit their own demons at the southern shopping district outside Kinshicho.

The pair succeed in scouting their own demons and Asahi shortly after receives a quest on Nikkari's phone to rescue a Hunter at the Sky Tower. She decides they should take the quest and hurry to the tower through Kinshi Park. There they find a pair of Hunters quarreling with an Angel and a Power, who have deemed the Hunters as transgressors and should be executed. Nanashi and Asahi fight the Angel while the other Hunters face the Power. Although the Hunters are victorious, they are soon after intercepted by Aniel who overwhelms Nanashi and his demons. However, a woman's voice tells them not to give up and two figures–Flynn and his partner Isabeau–join the battle. Together, Nanashi and the Samurai defeat Aniel.

Isabeau asks the cadets to help her and Flynn carry the wounded back. Regardless if Nanashi accepts or declines, the group return to Kinshicho. Boss is furious with Nanashi and Asahi for flagrantly rushing into danger and scolds them. However, both Flynn and Isabeau interrupt to commend the cadets for their camaraderie and accomplishments, adding that more lives would be lost if not for their aid. Boss gives in to their recommendation and decides to finally make Nanashi and Asahi official Hunters. While Boss registers them with the Association, Nanashi spots a green ghost hovering around Flynn, but whom no one else seems to notice. Flynn and Isabeau leave some time afterward to see Masakado at Ginza, promising the new Hunters they will see each other again soon.

Fairy Forest

With Nanashi and Asahi now officially Hunters, Asahi looks for new quests to take. However, all of the available quests are too high-ranked for them to take, except for one: an unusually written and vague request to stop a fight by a client named Nozomi. The new Hunters decide to accept it anyway and head for Ameyoko Way at Ueno.

Along the way, Nanashi once again spots the ghostly figure from before, bemoaning how no one can see him. He suddenly realizes that Nanashi can see him. Overjoyed, the ghost introduces himself as Navarre, a former Samurai of the Eastern Kingdom of Mikado up until his death. He claims to have fought alongside Flynn and decides to join Nanashi's party out of his own accord.

At Ameyoko Way, the party are approached by a woman with an unusually small voice, introducing herself as their client Nozomi. She vaguely explains that there is a fight at the Fairy Forest and that the only way to reach it is through a Terminal. She offers to let the party borrow her phone to reach the forest's Terminal, as only registered Terminals can be freely used. Although uncertain about their client's strange mannerisms, the party decide to accept her request anyway and follow her to Ueno's Terminal. Using Nozomi's phone, the party transport to Yoyogi where the Fairy Forest is located, which has otherwise been barricaded by a boulder blocking the road.

The group are amazed to discover that the Fairy Forest is a dense woodland of cherry blossom trees. Suddenly, another woman closely resembling Nozomi appears, asking about the visitors. The Hunters' client transforms back into a Napaea, having disguised herself to lead them there. The woman reassures the party that the forest's Fairies are harmless and only want to live there peacefully. She introduces herself as the real Nozomi, the leader of the Fairies as their queen, a title she inherited from their previous queen. Navarre expresses skepticism of her, to which Nozomi retorts back and reveals that she can also see him. The exchange brings Asahi awareness that Nanashi is being haunted, however she still cannot see Navarre.

Napaea asks Nozomi about the state of the Fairy Forest. A fairy has taken over the forest's spring, which Nozomi had planned to address herself until she lost her phone; Napaea had secretly borrowed her phone to seek more help and bring Hunters to the forest. During talks, a spectral figure manifests from Nozomi's body: Danu, the mother of the Tuatha De and the source of Nozomi's fairy queen powers. She directly addresses Nanashi, sensing that he is being possessed by her son Dagda. Nozomi however interrupts the confrontation, stating that the forest's situation still needs to be addressed. Danu apologizes and leaves the group to their task. Nozomi accompanies the Hunters to the spring, briefly joining Nanashi's party.

En route to the spring, the party encounters Oberon and Titania quarreling amongst themselves. Oberon has created a spectral blade called the Jade Dagger, which allows souls to have power in the physical world. He insists he created the dagger to aid the souls who died to the angels and demons, but which Titania believes is part of a ruse to play tricks on them. Nozomi attempts to break up their fighting by taking the Jade Dagger, but finds that it slips through her hands as only the dead can wield it. Oberon then notices Navarre and offers him the Jade Dagger as the only one who can use it. With the Jade Dagger in hand, Navarre helps the party reach the forest's spring by clearing the Wraith Walls blocking the way.

The party discover that a King Frost is the culprit behind the seized spring. King Frost asserts that by taking control of the spring, all the Fairies will have to follow his command and help him look for the forest's treasure. However when asked what the treasure is, King Frost admits that his informant gave him no details. He refuses to explain further and attacks the party, but is defeated and reverts back to a single Jack Frost who surrenders. A shadowy figure is then spotted attempting to leave which Nozomi corners. The figure, a Preta, swears that he was under orders to steal the forest's treasure and attempted to trick the Fairies into finding it. He leaves the party with no further details other than a god from the Divine Powers had sent him. Despite the suspicious activity, Nozomi feels there is no need for concern.

With the quest resolved, Danu once again appears to confront Nanashi about Dagda's power. Dagda answers her this time, appearing before the group. Danu demands he explain his plot, but Dagda refuses to elaborate and merely tells her that his answer will become clear in time, before disappearing again. Nozomi decides it is wise to keep Dagda's presence to themselves for the time being and thanks the Hunters for their help. She leads them back to the forest entrance and bids them farewell, leaving the party. Nanashi, Asahi, and Navarre all return to Kinshicho.

Kanda-no-Yashiro

Asahi asks her father if there are any more large jobs she and Nanashi could take, but leaves disappointed upon finding there are none available to their current ranking. An old man then approaches the pair, overhearing their dissatisfaction and offering them a job. Although uncertain of his claim, the party follow him to the train platform and discover an ethereal entrance in the store room. They find the old man in a room on the other side, revealing himself to be Odin. He assures the Hunters that he means them no harm and only intends to guide them, so that they may become strong enough to fight alongside Flynn. Odin instructs the party to go to Kanda-no-Yashiro to find an Ark within its depths and unseal the Demon inside it, explaining that the Demon's strength would become a great aid to humanity in the war. Persuaded by his words, Nanashi and Asahi accept Odin's quest.

Near Ueno, the party finds the well leading into Kanda-no-Yashiro and descend down. They shortly find an angel and a demon inside arguing amongst themselves, each insisting they are here on orders to protect the shrine. Another angel interrupts them, reminding the angel of their orders to protect the shrine's crest. Asahi realizes the shrine must be significant for both angels and demons to be protecting it and is convinced of Odin's claim. Drudging through the shrine's caverns, the party defeat the angels and demons guarding its crests: the Mallet Crest, the Mirror Crest, and the Horse Crest, each opening another section of the shrine.

The final crest opens a passage to the farthest depths of the shrine, where the party discover an enormous room with a stone sphere in the center, identifying it as the Ark. As they approach it however, they are immediately intercepted by its guardian, Sukuna-Hikona. He warns the Hunters that the shrine is where the Kunitsukami have imprisoned a dangerous foreign deity and tells them to leave. Nanashi refuses and Sukuna-Hikona engages the party in battle, but is felled.

Odin emerges and congratulates the party on their efforts. He tells them to open the Ark, becoming more demanding each time. If Nanashi refuses to break the seal, Dagda forces him to by taking possession of his body. The Ark's seal is broken as a brilliant pattern of light shines across the room and releases Krishna, the leader of the Divine Powers. Krishna leaves with Odin to find Flynn, declaring that he is not the party's enemy and promising he will bring them salvation. Asahi realizes they have been manipulated and that Flynn is in immediate danger. The party leave for Ginza to find him.

They find Flynn and Isabeau at Downtown Ginza, moments from summoning Masakado from his giant boulder. The pair are stopped when they are suddenly approached by demons allied with the Divine Powers. Krishna appears to Flynn and reassures that he is neither allied with Merkabah nor Lucifer, but claims he intends to save humanity. When pressed by Isabeau, he adds that the world being ruled by a creator who claims to be the one true god and has enslaved humanity and other deities alike. Flynn refuses to join Krishna and Odin responds by attacking him with a lightning bolt, which Flynn dodges. However, Flynn then realizes that Asahi has been taken hostage by Maitreya, another god of the Divine Powers. Left with no other choice, Flynn surrenders and is repeatedly struck by Odin until he is rendered unconscious.

Krishna seizes Flynn and instructs Maitreya to release Asahi. Droves of reinforcement Hunters then arrive to rescue Flynn, to which Krishna demonstrates his power by releasing Shesha, a gigantic, demonic snake that crashes a hole through the Firmament and unveils the sky above. Krishna tells the people of Tokyo that anyone who wishes to be saved should come to Tsukiji Konganji; he gives them time up until the next full moon to decide, when a new universe will be created. The Divine Powers then enter Shesha's mouth with Flynn and disappear in a spatial rift, leaving behind Masakado's Katana which Isabeau takes.

New Moon

The following morning, an emergency conference is held by the Hunter Association to report on the latest developments: with the Divine Powers having now captured Flynn and entering the war, the power of balance in Tokyo has shifted considerably. Lucifer and his forces have extended their control across Camp Ichigaya, Shinjuku, and Shibuya; Merkabah now controls the Sky Tower, Kinshicho, Ueno, and Ikebukuro; while the Divine Powers have seized control of Ginza and Tsukiji Konganji—however, Shesha's emergence has put the war in favor of the Divine Powers. Flynn's capture has also brought the Hunters' morale significantly down, however Fujiwara and Skins insist they must keep up Tokyo's defenses and rescue Flynn at all costs. The broadcast ends in an uproar among the Hunters, with many losing hope or considering siding with the Divine Powers.

Nanashi and Asahi receive supplies for a resupply run to Shinjuku. As they enter the ward, they encounter a ghostly young girl. She is followed by the sudden entrance of Stephen, who cryptically comments on the girl's interest in the party and that the future's fate must now be up to them. He also adds that Shesha has already devoured many people, but disappears without further elaborating. As soon as he leaves, the Hunters receive an emergency quest that Shesha has been spotted at the Metropolitan Government Office near Shinjuku and that all Hunters converge there to defeat the serpent. The party decide to join and, as they enter Shinjuku's underground tunnel, realize the truth in Stephen's words as they discover that many people inside have been eaten by Shesha.

After delivering the supplies, the party hurries to the government office and engage Shesha, but find their attacks inflict very little damage upon it. Midway into the battle, a Power and Adramelech then arrive, each under orders from their respective leaders to defeat Shesha. Adramelech acknowledges the group's common goal and suggests they team-up, which Asahi furiously refuses in her grief over Nikkari and Manabu. Adramelech nonchalantly responds they can settle matters after Shesha has been killed and Asahi agrees begrudgingly. The group all fight Shesha together, but it coils itself and recovers from all the damage it received before escaping into a spatial rift.

Having now repelled Shesha, Asahi challenges Adramelech, but the demon has no interest in fighting her; expressing that his orders were merely to destroy Shesha alone. The Power likewise expresses this and the entities tensely part ways from the Hunters. The party returns to Kinshicho for the night.

1/8 Moon

The next morning, another conference broadcast is held. The angels and demons have agreed to hold a conference with the Hunter Association, with Isabeau as the mediator. Two Samurai men join the meeting, whom Isabeau introduces as Jonathan and Walter, the Samurai who had sacrificed their lives to become Merkabah and Lucifer, respectively. The men then take their true forms as the aforementioned entities and begin negotiations; Lucifer proposes a ceasefire between them so that they may focus on the Divine Powers. Merkabah agrees under the terms that they help each other in defeating the faction and states he will send his elite Samurai to Tokyo. Lucifer in turn states he will lead the people of Tokyo, adding that only humans are capable of destroying gods and demons—known as Godslayers. As the Divine Powers intend to use Flynn as their own Godslayer, it is imperative to all other parties that Flynn be rescued. The Hunter Association are left in no position to argue and the broadcast ends in high tension. Dagda reminds Nanashi that he already has him as his own Godslayer and instructs him to side with the humans against the Divine Powers.

Asahi receives a pair of quests from the Association, one to retrieve the rumored Ame-no-Habakiri in the Fairy Forest, and another to work alongside the resurrected Ashura-kai in retrieving materials to construct the Shesha Radar. The first quest taken is left up to Nanashi.

Ame-no-Habakiri

The Hunter Association has gathered intel that a weapon capable of defeating Shesha, known as Ame-no-Habakiri, may be found in the Fairy Forest. Nanashi and the others return to the forest, but to their shock find it has been attacked and left in scorched ruins. They find Nozomi near the entrance, unhurt but in deep anguish over the discovery. Dagda suspects the Divine Powers had intercepted the request and raided the forest in search of the weapon. Nozomi recognizes Ame-no-Habakiri as Excalibur and accompanies the Hunters in finding it.

They proceed to the forest's Central Gate, also finding it completely destroyed. Napaea then arrives and confirms the destruction to be the Divine Powers' doing. Nozomi informs that the sword is located in Northern Lake Hill, but to get there the party must pass through the Maze Garden, adding that there is a chest nearby containing the Scroll of Guiding with instructions on navigating the maze. Nozomi stays behind to tend to the Fairies, promising she will reconvene with the party soon. The Hunters make their way through the Maze Garden and arrive at the hill's lake just as the Divine Powers' Titan is about to take Ame-no-Habakiri. They defeat him and claim the sword. Nozomi rejoins the party at that point, having now moved the Fairies to a safer location.

Danu shortly reappears again to ask the group if they know of the Divine Powers' true goal. She plainly states that their ultimate goal is to conquer the universe, suspecting this to be a plot of revenge after the Creator God had defeated the ancient deities and wrestled dominion over the universe and humanity. Dagda then emerges to add that the Divine Powers plan on destroying the current universe and take humanity's souls to the next, which will inevitably lead to the deaths of mankind. Danu asks Dagda if he is among the Divine Powers; he responds they are only more pawns to him and reveals his goal: to wrest control of the Divine Powers' recreated universe and regain his true form. The news horrifies Danu and she disagrees, asserting that there is still beauty in the universe worth protecting together in spite of the Creator God's control. However, Dagda tells Nanashi to ignore her and states he will help him attain true freedom without dependencies in his new universe, while also taunting him that he has little else choice but to cooperate or accept death. His words bring the party the realization that Nanashi is dead and is no longer human in his resurrected state. The revelation deeply upsets and terrifies Asahi.

Danu threatens Dagda of one day stopping him herself, before they both disappear. Nozomi comforts Asahi amid fears that Nanashi would have to be killed for his role in Dagda's plans. She decides to join the party henceforth to make sure that risk will never come to pass.

As the party exit the forest, they once again encounter the ghostly girl and Stephen from before. Stephen explains that although Danu and Dagda's views differ, their positions are nonetheless in opposition to the angels and demons and are a neutral path, but adds that there is still another path and encourages Nanashi to choose his own. He states that he will continue to watch over him and shortly leaves with the girl.

Shesha Radar

The Hunters are tasked with salvaging supplies needed to construct the Shesha Radar, a device that can pinpoint the next exact location of Shesha. The party head to Kasumigaseki to report to the Hunter Association's new headquarters, stationed in the old Counter-Demon Force Base, for a secret meeting among the Hunters in Professor Matsuda's laboratory. As they enter the laboratory, they overhear a couple Hunters discussing the quest and its client, the resurrected Ashura-kai. One of the Hunters suspects the partnership is a ploy for the Ashura-kai to regain traction after their former leader, Tayama, had gone missing. Rumors also claim that the Ashura-kai are being manipulated by Lucifer.

Professor Matsuda finishes his preparations and turns the Hunters' attention to a transmission from Fujiwara and Skins. The Hunter Association explains that Hunters will be divided into teams for the salvage mission, with each assigned an area to collect parts for the Shesha Radar, while also reminding them that they will be working alongside the Ashura-kai for this task. Matsuda also stresses that the Hunters must keep the mission a secret from the Divine Powers. The party then receive their assignment to locate a sensor in the Sky Tower.

At the Sky Tower, the party are immediately stopped by its sentry angels; they are unaware of the mission and refuse to let them inside. The group are then approached by an Ashura-kai man, his demons, and a silver-haired boy. The man introduces himself as Abe, the new leader of the resurrected Ashura-kai since Tayama's disappearance. He also orders his accomplice to greet the party as well, who timidly introduces himself as Hallelujah. While Abe leaves to negotiate with the angels, the party talk with Hallelujah and learn that he was taken into the Ashura-kai at a young age since his mother's disappearance. Hallelujah also speaks highly of Abe, adding that he is the reason why the Ashura-kai are still in operation; on the opposite end, he views Flynn negatively for his role in damaging the Ashura-kai, but notes that Abe has been fixated on him.

Abe shortly returns, having successfully driven off the angels and orders the party into the tower. They enter what used to be Medusa's domain before her defeat by Flynn's hands. Abe explains that the sensor should be in the Excavation Workers' Quarters further above and hurries the party along. They arrive at the observation deck next, but are shortly attacked by a Rukh that causes a panic among the Hunters. Despite the surprise, Nanashi and the others defeat the demonic bird and Hallelujah is left impressed by their tenacity. He, however, expresses little confidence in himself, which prompts Abe to yell at him. Spurred by the demand, Hallelujah joins the party to prove his capability.

Arriving at the Excavation Workers' Quarters, the party finds a storeroom and begin scouring it for supplies. Amid Abe's continued demands, they find the sensor. However, just as the party leave, Abe secretly informs Hallelujah they are splitting and that he is to now accompany the party and keep a close watch on them. A loud commotion interrupts their conversation and the party exit the room, finding that the angels from before have been turned to stone. The party are confronted by the revived Medusa, now allied with the Divine Powers. Abe decides to leave the Hunters and Hallelujah to Medusa, claiming he will report the encounter to Lucifer. Medusa is defeated in the battle.

Hallelujah expresses his desire to join the party. However, Dagda emerges to state that he is working as a spy for the Ashura-kai, to which Hallelujah admits that he has been assigned to watch them and ensure they do not endanger Tokyo. Regardless of Nanashi's decision on the matter, the party allow Hallelujah to accompany them. They leave together to deliver the sensor to the Hunter Association.

2/8 Moon

Overnight, Nanashi once again has another dream as Akira. He finds himself talking with Skins in a green field on the Firmanent’s surface. Skins expresses they have made little progress since their arrival due to the onslaught of angels. In a moment of doubt, Akira contemplates giving up, but quickly reassures that will not happen. The dream then suddenly shifts to the tunnels of Naraku beneath the Firmament, where the JSDF have been cornered against another wave of angels. Skins reluctantly retreats the group further into the tunnels. The dream again shifts to a scene elsewhere in Naraku where a group of archangels approach the denizens of Tokyo. Sister Gabby, the human form of Gabriel, explains that only those chosen by God are worthy to set foot upon the surface and all else shall be purged; however, she adds that God has shown mercy and has allowed the denizens a chance to join them. Before she can give the conditions, the dream abruptly ends.

Second Battle with Shesha

That morning, the elite Samurai sent by Merkabah arrive in Tokyo. The Hunters are assigned to meet with them at Ueno and escort them to Kasumigaseki. The five chosen Samurai, collectively known as the Crusaders, are led by their appointed captain, Gaston. Navarre immediately recognizes the man to be his younger brother, yet Gaston cannot see him.

Gaston confidently announces that once the Crusaders have defeated Shesha, they will take Flynn back to the Eastern Kingdom of Mikado to be judged by Merkabah. Hallelujah is skeptic that the group can defeat Shesha, while Gaston's subordinates concern that their leader's disdain is fostering ill-will to their new allies; however, Gaston remains certain of his assured success and position, adding that he has been chosen personally by Merkabah and bestowed the Spear of Michael, a weapon capable of damaging Shesha. Hallelujah quips that Gaston's arrogance is identical to Navarre, bringing Gaston to a surprised pause before quickly asserting that he no longer has a brother, to Navarre's distress. Gaston demands to be immediately escorted to Kasumigaseki and joins the party.

Upon their arrival, Gaston dismisses the party and descends into the Counter-Demon Force Base. At that very moment, the Hunters receive a quest to ready themselves for Shesha's next attack. They report back to Professor Matsuda to receive the completed Shesha Radar, which Nanashi attaches to his smartphone. Immediately the radar detects Shesha approaching Shibuya's Miyashita Park. As the party wonder how they can pierce Shesha's defenses, Nozomi is certain that Ame-no-Habakiri will be able to. They decide then to leave for Shibuya themselves; however, as they leave Kasumigaseki, they find Gaston waiting for them. He invites the party to accompany him to Shesha's location, claiming that he made a tactical decision to part ways with the other Crusaders—though Hallelujah suspects they had in actuality abandoned their captain. Gaston demands the party lead him to Shesha, adding they are to stand aside while he faces the serpent alone.

Arriving at Miyashita Park, the party engage Shesha head-on. True to his word, Gaston's Spear of Michael proves to be effective against it. Shesha once again attempts to recover itself by coiling around, but is attacked before it can succeed, either by Gaston alone or him and Nanashi working together. They weaken the serpent enough where Gaston impales its face with his spear. Despite the severe blow, Shesha is still standing, leaving Gaston unable to retrieve his spear. Nanashi is encouraged by Dagda to finish off Shesha with Ame-no-Habakiri and finally defeats it.

Gaston is humiliated by the turn of events, furiously insisting that he was meant to slay Shesha. He then switches to insulting Asahi's worth during their argument. A new broadcast announcement interrupts the party's arguing, so they head back to Kinshicho to attend. Gaston decides to accompany them, intent on proving himself the true victor.

Tsukiji Konganji

During the broadcast, Lucifer praises the Hunters for defeating Shesha. Merkabah in turn commands the Hunters to head for Tsukiji Konganji next to rescue Flynn before he can become the Divine Powers' Godslayer. Although the conference ends in good cheer, Asahi is left visibly upset from her earlier argument with Gaston and worries that she is holding the party back. While comforting her, Nozomi and Hallelujah incidentally ask Navarre what led to his death. He ashamedly admits that he slipped and drowned in a river while watching a female Hunter bathe.

The Hunters receive their next assignment: all Hunters are to descend onto Tsukiji Konganji and defeat the Divine Powers and rescue Flynn. As Nanashi and the others prepare to head out, they are approached by Isabeau asking to join them on their mission. Together they head for the temple but are stopped by a pair of demons, permitting entry only to those who have embraced the Divine Powers' ideology and are willing to sacrifice themselves. Realizing they cannot use the main entrance, the party leave to search for another point of entry.

In Downtown Ginza, the party encounter a pair of Gaeans who recognize them as the ones that Ladies Mii and Kei, their leaders, were discussing. The Gaeans explain that the Ring of Gaea has split into opposing factions between those who continue to follow the deceased Lady Yuriko's teachings and those who have defected to Maitreya. To aid the party in reaching Tsukiji Konganji, they tell them to follow the underground path in Harumi Way to find Ladies Mii and Kei in the Silver Prison Room, who know of another passage into the temple.

The party meet with Ladies Mii and Kei at the promised destination. The old women are willing to confide another passage into the temple on the condition that their apprentice—a young girl wearing a mask named Toki—be escorted inside. Toki has been ordered by the women to assassinate both Maitreya and Flynn, as revenge for fragmenting the Ring of Gaea and for the death of Lady Yuriko, respectively. Although the party are wary of this arrangement, they are left with little other choice but to let Toki guide them into the temple—though Isabeau stresses they will not allow her to kill Flynn. Toki does not respond and instead keeps to her orders as she leads the party into a hidden, underground passageway near Tsukiji Konganji.

Entering the main temple, the party realize that Tsukiji Konganji is being heavily guarded and they are forced to resort to stealth. They encounter a dying Gaean woman who informs that Flynn is being kept in the underground treasury while Maitreya's location is unknown. She hands them the Corridor Key to the treasury before passing away. The party proceed ahead, fighting Maitreya-aligned Gaeans along the way, and enter the Lapis Lazuli Passage. They face Zhong Kui of the Divine Powers at the end and defeat him.

Once inside the treasury, the party finds Flynn being crucified. Toki immediately darts in to strike him, but her attacks are parried by Isabeau. Toki decides to face the party herself then, but they triumph over her. Their fight is interrupted as Krisha's voice enters the room and commands Maitreya to strike the girl. Toki's mask falls off, revealing her true face, and she collapses on the verge of death. Krishna, Maitreya, and Odin show themselves and surround Flynn. The party confronts the Divine Powers on their true motives, yet Krishna is unfazed and asserts that humanity must reject their living bodies to find true freedom and salvation. He adds that come the full moon, a new universe will hatch from the Cosmic Egg and Shesha will lead humanity to it. Gaston calls on Krishna's bluff, but the deity informs that Shesha is immortal and will soon return. He vows that the Cosmic Egg will soon hatch and sends Odin to fight the party.

Caught between arguing amongst themselves, the party are defeated by Odin. Dagda is called out into the open and Krishna brands him a traitor. Dagda denies ever siding with the Divine Powers and asserts that their goals differ. Odin attempts to persuade him to their cause by stating their universe will be equal with all souls divided evenly between the ancient gods, yet Dagda persistently refuses and declares that none shall stand in his way. Krishna mocks Dagda by calling Nanashi his doll—a revelation that shocks the party as they are forced to again confront that Nanashi is a reanimated corpse. Krishna continues to stoke doubt by crediting his freedom from Kanda-no-Yashiro to him. During this exchange, Toki awakes and threatens Nanashi for her defeat. She turns to the others and advises they escape while she distracts the Divine Powers with a flash bomb, swearing that she will return to finish her mission. The party quickly make their escape.

Toki splits from the party while the others safely arrive back at Tsukiji Konganji's entrance. Gaston immediately confronts Nanashi for lying to them about Dagda and accuses him of being a spy for the Divine Powers. Nozomi also admits that she will file a report of the occurrence to the Hunter Association, despite Asahi's pleas that she and Nanashi were manipulated. Nozomi asserts that the young Hunters need to take responsibility for their actions, but reassures them they still have her support. As the party begin to leave, Hallelujah and Navarre offer Nanashi their sympathies and support. Isabeau meanwhile takes her leave from the party and extends her well wishes.

3/8 Moon

Nanashi awakes to Nozomi the next morning. Both he and Asahi have been summoned to Cafe Florida in Shinjuku by the Hunter Association on suspicion of treason. Nozomi promises to support them and encourages the young Hunters to stay positive.

At the cafe entrance, Nozomi shows the guard the proof of membership—a matchbox—and takes the party inside. They find Fujiwara, Skins, and a group of vindictive Hunters waiting for them. Tensions rapidly escalate as arguments and accusations are flung during the tribunal. However, in acknowledgment of Nanashi and Asahi's explementary work alongside their mistakes, Fujiwara and Skins allow them a second chance with the Hunter Association. Their announcement stokes more fury among the Hunters until a violent tremor interrupts the crowd and an enormous mandala of light shines over Tokyo. Reports soon afterward come in that demons have begun raiding Shinjuku.

Fujiwara decides to let this be an opportunity for Nanashi to prove his loyalty with the Hunters and is made to swear an oath to never betray them. Regardless of his response, the party exit the cafe to eliminate the raiding demons. However, once outside, they discover that neither their phones nor Gaston's Gauntlet are able to use the Demon Summoning Program anymore. Nanashi is unaffected by the issue, suspected to be because of Dagda's powers. With Nanashi as Tokyo's sole remaining demon summoner, the group hurry to Shinjuku and learn it was the Divine Powers behind the raid and the program's jamming. After saving a civilian, they run into Isabeau again leading a group of Hunters. She warns that demons have also infiltrated Kinshicho and advises they make for the district. The party are forced to head there on foot as the Terminals have also ceased operation.

They arrive to find Kinshicho's guardsman mortally wounded by Maitreya-faction Gaeans. Following a battle with them, the guard explains that the angels protecting Kinshicho have been killed and the district turned into a warzone. Asahi realizes the danger her father is in and runs ahead into the underground tunnels alone. The party hurry after her and hear her scream coming from the Hunter Association bar. Inside, they find her father bloodied and hunched over her unconscious body after shielding her from an attack. Quetzalcoatl of the Divine Powers fights the party and is defeated. Asahi awakes to discover her father grievously wounded. He asks Nanashi to watch over his daughter before succumbing to his injuries. Reinforcement Hunters then arrive and escort a distraught Asahi out of the bar. Hallelujah offers his sympathies to Nanashi by relating his own family, explaining that he has never known his father and his mother had disappeared when he was young.

Suddenly the monitor in the bar along with everyone's phones turn to a transmission from Krishna. He and Maitreya explain that the Divine Powers have set up a barrier over the entirety of Tokyo, called the Tokugawa Mandala, and have jammed the Demon Summoning Program through it. Furthermore, Krishna adds that Shesha will soon return and eliminate the demons opposing the Divine Powers. Abe enters the bar as the broadcast ends to deliver an urgent report: the party are now tasked with destroying the Tokugawa Mandala and must find a demon named Tenkai for information on the phenomena. Abe explains that Tenkai is located in Midtown near Ginza as a boulder and hands the party Myoko's Disc, the demon's medium.

Tenkai is called from his boulder with the medium. The demon, one of the National Defense Divinities, agrees to assist the party as part of his pact with Flynn. He explains that the Tokugawa Mandala draws strength from jars placed in each of the five Fudo Temples located across Tokyo, which siphon enormous amounts of Aether—otherwise known as Magnetite—from the Expanse and prevent demon summoning. In order to destroy the barrier, the party will need to seal the jars; however, Tenkai cautions that the amount of Aether is dangerously high and could ravage the party's minds. Only a person of "virtuous heart" may be able to resist the Aether long enough to seal the flow. As the party discuss amongst themselves the possibility of having to sacrifice one of their own, Toki suddenly appears offering to be their sacrifice. She explains that her training has honed her mind and that she should have resistance to the Aether, adding that this task is a nonvoluntary, direct order from Ladies Mii and Kei. Although distrustful of her, the party allow her to accompany them to the Fudo Temples. Tenkai sends their locations to their phones.

Each of the Fudo Temples are guarded by one of five Kishin: Bishamonten, Jikokuten, Koumokuten, Zouchouten, and Marishiten; each one of them defeated by the party. As Toki approaches each Aether jar, she is briefly overcome by strong emotions and desires, but manages to resist them long enough to seal each jar. Though party worry about her constitution, they press on. As the final jar is sealed, the Tokugawa Mandala shatters in another tremor and operation is restored to the Demon Summoning Program and Terminals. Toki collapses from mental exhaustion. A shadow calling herself Inanna suddenly emerges from her body as a result of the Aether. Inanna demands that Danu return her power and fights the party for it. They thwart Inanna and she attempts to possess Toki in a final attempt for control, but Gaston strikes the shadow before she can succeed and she fades away. Toki shortly awakens and, to the surprise of everyone else, has seemingly changed by responding respectfully to them. She denies there is anything unusual however.

Maitreya emerges into the room shortly afterwards, furious with the party's perceived selfishness in destroying the mandala and returning Tokyo to the demons. They kill the deity and Toki almost collapses again from exhaustion; she is caught by Nanashi which flusters her. The group then decide to return to Kinshicho for rest, while Toki separates from them again. As the party arrive back in Kinshicho, Fujiwara and Skins contact them to thank their efforts and to declare that Nanashi has redeemed himself, adding that some Hunters have already forgiven him and are now calling him their new Champion. They also formally allow the party to access the Hunter headquarters in Kasumigaseki any time they want.

The party reunite with Asahi in her room, who has since regained her composure and is already aware of the party's celebrated achievements. However she is left despondent, admitting to her recklessness in wanting to make a name for herself as a Hunter and how she has put the party in danger. She realizes that protecting others is more important and asks the party to allow her to fight alongside them again. Gaston refuses, yet again criticizing her worth, and Hallelujah punches him in the face in retaliation. Asahi breaks up their arguing and admits she is inadequate without Nanashi's help, but is nonetheless determined to make up for her shortcomings. The rest of the party accept her back and they retire for the night.

Half Moon

The Shesha Radar abruptly rouses the party that next morning, detecting Shesha at Ikebukuro's Sunshine Front. They leave immediately and reach Shesha on the Metropolitan Highway, discovering the serpent has radically transformed in appearance since its last encounter. Shesha is able to speak now and recognizes the party as the ones who previously killed it. The group manage to kill Shesha again, and as it dies, it threatens it will keep returning and kill Nanashi the next time they meet.

Shortly after the battle, Gaston receives a message from the angels on his Gauntlet whilst a messenger from Lucifer approaches the others. With Shesha now repelled a third time, Merkabah and Lucifer have both independently staged another assault on Tsukiji Konganji and droves of angels and demons are now en route to the temple. At the same time, the Hunters are issued a quest to head there themselves and rescue Flynn before either entities can reach him first. The party find Tsukiji Konganji in the middle of an all-out war. Isabeau spots them and joins the group into the temple. While inside, they realize that Tsukiji Konganji is unusually devoid of Maitreya's Gaeans. Another group of Hunters suspect they have committed mass suicide by allowing themselves to be devoured by Shesha.

Reaching the temple's inner chamber, the party discover Flynn free of his bounds and fighting against Odin. He deftly parries the deity and triumphs over him, seemingly defeating Odin as he vanishes. The party are overjoyed to find Flynn safe, albeit wounded from the fight. Isabeau offers him Masakado's Katana, but to her surprise, he refuses the weapon and shortly collapses from his injuries. Krishna then reveals himself, unfazed by Odin's defeat and fixated squarely on Flynn. The party step in to Flynn's defense and face Krishna in battle, defeating him. Krishna accepts his defeat without resistance and vanishes afterwards.

Certain that the Divine Powers have now been defeated, the party briefly celebrate, but Dagda reminds Nanashi that Lucifer and Merkabah are still at large. They are suddenly approached by a pair of angels, demanding that Flynn be handed over to them to become their side's messiah. Gaston denies them, stating that Flynn's apprehension was ordered to the Crusaders and refusing to give up Flynn nor allow him to be killed. The angels are thwarted and the party immediately leave to make their escape with Isabeau carrying Flynn. They are confronted by more of Merkabah's subordinates along the way as well as Lucifer's minions, also demanding that Flynn be given up as their messiah. The party overcome them as well.

At the temple's entrance, they are stopped by the remaining Ring of Gaea, led by Ladies Mii and Kei. The women summon Toki and order her to kill Flynn. But Toki refuses to obey, declaring that she is no longer theirs to control and is joining Nanashi's side. Toki argues that the Ring of Gaea no longer behold their original values of pursuing individual strength, but instead have degraded to clinging onto a new order. The women sic their followers on the party, but they are felled by them. Mii and Kei are unfazed by their defeat, stating that Toki has always been expendable to them and leave her to her own devices while they depart to reclaim Tsukiji Konganji. Toki decides to join the party henceforth and is welcomed by the team, yet Asahi deep down feels insecure over the thought of her and Nanashi becoming close.

Upon exiting the temple, the party are then approached by Adramelech. He has also come to take Flynn to Lucifer, adding that the Ashura-kai have also agreed to this arrangement. The party fight and kill Adramelech, avenging Nikkari and Manabu while also eliminating the last wave of their pursuers. Isabeau proceeds to bring Flynn to the Hunter headquarters for medical treatment, assuring everyone they can now manage from there on. Having now accomplished their mission, the party feel a strengthened bond of togetherness and all return to Kinshicho.

5/8 Moon

The following morning, Nanashi awakes to Toki watching him in his sleep. She admits to feeling drawn to him and is troubled by the fact. Before she can confess her thoughts, Asahi walks into the room and demands to know why the other girl is here. Their bickering ends when the rest of the party arrive, reminding them of that morning’s conference. Gaston believes that he and Hallelujah will soon be parting ways, now that Flynn is safe and the Hunters, Samurai, and Ashura-kai no longer have a common goal. They head into the local bar to watch, finding it packed with crowds of elated Hunters. During the wait, Gaston receives a message on his Gauntlet that the Eastern Kingdom of Mikado have sealed themselves off and are ordering that all dispatched Samurai return at once; the Crusaders have also been dissolved as well along with his position as captain. The news hits Gaston hard as he falls silent.

Fujiwara delivers the conference from the new Hunter headquarters' briefing room. Flynn appears to announce his return and to thank the Hunters for rescuing him, vowing that he will in turn save all of Tokyo. Flynn informs that the Kingdom of Mikado have adopted a strict isolationist policy and are refusing to allow the people of Mikado and Tokyo to work together, but he asserts they should cast aside prejudices and come together for the sake of humanity. He likewise calls upon the Samurai to think for themselves and for the people of Tokyo to accept the immigrant Samurai as one of their own. The conference ends with roaring applause from the audience.

Gaston is suddenly surrounded by his fellow former Crusaders and is berated for the abuse he had put them through. They remind him that he is no longer their captain and leave to return to Mikado. Dejected, Gaston refuses Hallelujah's suggestion to stay in Tokyo and decides he will also leave for Mikado as well, leaving the party behind.

The remaining party members receive a top secret assignment from Fujiwara and are ordered to report back to the Hunter headquarters. Fujiwara and Skins meet with them in the briefing room, explaining that the Divine Powers have left them with fewer firepower and that they cannot simply ignore the Samurai's retreat. They ask the party to sneak into Mikado and gather intelligence. The group are shortly joined by Isabeau, who is to accompany the party, along with Flynn and Professor Matsuda. The professor explains that the Sky Tower and Mikado are presently separated by a Domain, called Purgatorium, which can only be bypassed by those permitted by the angels. To aid the party's infiltration, he has created replicas of the Gauntlets to use as fake IDs while the party disguise themselves as returning Samurai. Skins stresses that as this will be a reconnaissance mission, they will be going alone with no backup and must be especially careful. Another team will be sent to investigate Lucifer's side. Asahi asks Flynn if he will also be accompanying them, but he responds that it would be too dangerous for him and that he has no way of hiding his appearance from Merkabah. Asahi questions how they will adequately disguise themselves for the mission, knowing that Samurai must be at least 18 to serve and reminding the party that most of them do not look old enough to pass. They realize they can use props and makeup to aid their disguises. After finishing, they leave to climb the Sky Tower.

In the Hall of Grief, the gateway between the Sky Tower and Naraku, the party find an angel guard inspecting the returning Samurai individually and checking their Gauntlets. They successfully pass by the angel without heavy suspicion and enter Naraku, proceeding further onward until they reach the surface where the Kingdom of Mikado lies. Isabeau tours the party around the area; she points out the toppled monument of King Aquila, the kingdom's ancient founder, while adding that legend claims he used to be called Akira. Asahi recalls the name as the one that Hunters hate. A patrolling Samurai then approaches the group, informing they are too early for the plaza's meeting. Isabeau decides to show the party the rest of the city's immediate area while they wait for the meeting as well as to gather more information.

During their tour, the party visit the monastery where the monks keep archives of Mystic Relics and data. Believing this to be an ideal place to gather information, they quietly search through the archives but only find records of the Firmament's emergence. Hallelujah finds an old, broken Gauntlet in storage. Recalling Navarre's earlier explanation that anyone who can activate a Gauntlet becomes a Samurai, Hallelujah goads Nanashi to try touching it. If Nanashi agrees to do so, his touch activates the Gauntlet and brings the immediate attention of a nearby monk, surprised that he was able to engage it when none have been able to. Hallelujah also tries activating it himself, but it does not respond to him. The monk condemns them for touching a valued treasure and demands they leave at once.

In the Luxurors' district, Isabeau explains to the party how the kingdom used to have a caste system until recently, between the Casualry working class and the Luxuror upper class. Realizing that Gaston came from a Luxuror family, the party decide to ask around for his whereabouts—though this agitates Navarre and he asks the party to quickly finish. They overhear a pair of Luxurors gossiping about Gaston and learn that he has labored to clear his family's name after Navarre had tarnished it. The men, however, do not know of Navarre's whereabouts and express that his family have since disowned him. Heartbroken, Navarre confesses he had failed to live up to his family's lofty expectations and had abandoned his post as a Samurai. He recognizes how hard Gaston must have worked to regain that honor.

At Lake Mikado, Nanashi has the option to take a nap on its shore. If he chooses to do so, he hears an unfamiliar man speak in a dream. The man recollects his days at the lake and laments waking from his last nap there whilst making a cheeky remark to whomever he is speaking to. He then says to hurry but his sentence is interrupted by Asahi's voice, who echoes his sentiment and tells Nanashi to wake up. Upon awakening, Nanashi finds a fishing hook in his hand as a ghostly voice implores him to give the item to Flynn.

Towards the end of their tour, a messenger sends for all Samurai to immediately attend the emergency meeting in Aquila Plaza and the party leave to participate. The meeting was to be chaired by Abbot Hugo, but he is interrupted by the sudden arrival of Merkabah in the form of Jonathan who takes over. Merkabah reveals his true form to all the Samurai and informs that the time of Armageddon—where Lucifer and the people of Tokyo shall be purged—has arrived. He instructs that they will seize control of the Yamato Perpetual Reactor in Camp Ichigaya and with it create a black hole that will swallow all of Tokyo. Merkabah recognizes the party's presence and unveils them as infiltrators. They are immediately arrested and Nanashi is knocked unconscious in the scuffle.

Nanashi has another dream as Akira. He tells a young Fujiwara and Skins that he is staying behind on the Firmament with the angels. The dream then shifts to an earlier scene of Sister Gabby and the archangels addressing Tokyo's denizens. She outlines the conditions for joining them on the Firmament: the people must make a covenant with God and abandon civilization to become His servants, emphasizing this to be their one and only chance to live on the surface. The dream returns to Akira as Skins argues over his decision. But Akira stays committed, stating that he is willing to use any opportunity to save the people of Tokyo. He intends to outsmart the angels and build a country on the surface where humans can live in peace–calling this his middle path. Fujiwara and Skins come to agree and choose to remain in Tokyo to maintain order there. The three men agree to meet each other again once they have each found a middle path that benefits all. The dream ends with Akira watching Fujiwara and Skins leave through the gate before its doors close behind them.

Nanashi awakes to find everyone, sans Isabeau, imprisoned in a cell and all of their possessions confiscated. They are soon visited by Gaston, informing them that Isabeau is being interrogated while the rest of them are going to be executed. Gaston is powerless to help them beyond confiding that their equipment is in the monastery. He turns to Nanashi and reminds him that even without his phone, he alone should still be able to summon demons and break free. Gaston leaves the prison dejectedly, refusing to elaborate on his current status. Nanashi summons his demons and breaks through the cell’s bars. During the jailbreak, he finds a discreetly hidden sword and takes it with him.

Outside, Nanashi is forced to fight off waves of angels alone as the sole equipped fighter while the rest of the party encourage him. They make their way to the monastery for their gear, but are stopped by Azrael inside. Nanashi again fights alone but Azrael overwhelms him by summoning angel reinforcements, turning the situation dire. Left with no other choice, Hallelujah steps forward and reveals his true identity as a half-human, half-demon hybrid. He unleashes a blast that eliminates the angel horde and joins Nanashi as they together fight Azrael and defeat him.

Hallelujah confesses his heritage to the party, explaining that his mother used to tell him his father was a demon. But he feared the truth coming out and hid his demonic powers from public eye. The party accept him for who he is. Toki locates their equipment while Nanashi becomes fixated on the broken Gauntlet from earlier. He chooses whether to take it with him or leave it behind.

The party then realize that even if they escape into Naraku, they will not be able to pass the guardsmen there. They decide to use Mikado's Terminal instead, but when Nanashi attempts to use his fake Gauntlet to bypass its ID check, he is rejected. A pursuing angel then enters the Terminal, explaining they had downloaded the confiscated phones' data and used them to reprogram the Terminal. Suddenly Gaston arrives and strikes the angel down. He sadly confesses that he is no longer recognized nor wanted in his own country and asks the party to take him with them to Tokyo, saying he will use his Gauntlet to assist them. They safely teleport to Kasumigaseki's Terminal.

The party report back to Fujiwara and Skins to share their findings. The men are disappointed with their findings, but stay determined for the battle ahead. They advise the party go rest in preparation. If Nanashi brought the broken Gauntlet, the men deliver it to Professor Matsuda for inspection.

6/8 Moon

Another war conference is held between the Hunters, Merkabah, and Lucifer. Merkabah formally ends the ceasefire and states that his Godslayers, the Samurai, are en route to Tokyo to bring forth Armageddon. Lucifer has no intention of giving up the Yamato Perpetual Reactor and agrees to end the ceasefire. Merkabah encourages Tokyo's citizens to join his cause with the promise of a place above the Firmament; Lucifer calls his bluff and swears he will destroy him along with YHVH. Fujiwara states that the Hunter Association remains committed to Flynn, but adds that each individual's decision to fight is their own. The conference ends with some Hunters choosing to remain with Flynn while others consider defecting to Merkabah.

At the same time, Hallelujah receives a text from Abe that the Ashura-kai will be joining Lucifer. The arrangement leaves him conflicted between wanting to help Flynn and his loyalty to the Ashura-kai. Regardless of Nanashi's thoughts, Hallelujah decides to accompany the party. As they leave for Camp Ichigaya, they are approached by the ghostly girl and Stephen again. Stephen explains that the girl is actually the Goddess of Tokyo, whose power has diminished over the citizens becoming divided. He adds that the city is now at a critical point and its future lies squarely in the party's choices. The pair leave with Stephen encouraging the party to make their own decision.

The road to Camp Ichigaya is hindered by waves of angels and demons along the way. When the party finally reach the facility, they find Isabeau there with a group of Hunters. She reassures that she is safe and was released on probation to assist Merkabah's crusade—however, her loyalty lies with the people of Tokyo and she rejoins the party. Meanwhile, a Hunter reports to Skins that Tokyo's populace have become equally divided between the Hunters, Merkabah, and Lucifer. Flynn then arrives and rallies the remaining Hunters for the upcoming war. He presses on ahead to infiltrate a separate route alone. The other Hunters all descend after him into the burning Camp Ichigaya.

The party briefly notice that Abe is also in Camp Ichigaya as well, but they are unable to descend further into the facility's core—where the reactor is located—due to a magic barrier and are forced to take another route. They eventually come across a portal and enter the Hall of Eternity in the Chaos Realm, Lucifer's stronghold. The party defeat Belial there, opening another route in Camp Ichigaya. Following this route, the party encounter the Ashura-kai and the Ring of Gaea (who have also chosen to side with Lucifer) arguing over who fights Merkabah. Hallelujah breaks up the altercation, whose command impresses the party. The route leads to another portal to the Chaos Realm. There the party find a pile of unconscious Hunters; Nanashi can choose to either carry them back to the entrance or leave them behind. Lucifuge challenges the party in the realm and his defeat eliminates the barrier to Camp Ichigaya's depths.

Isabeau and Gaston witness their former commander, Hope, lead a group of Samurai into the facility's depths. They follow them and reach a third portal that sends them to the Hall of Eternal Light. Abe's bodiless voice criticizes Hallelujah for going against his orders and he urges him to come see him further inside, saying he will reveal the truth then. The party find Abe at the hall's end. He reveals himself to be Samyaza, a name Hallelujah recognizes from his mother. The demon confirms he is Hallelujah's father and goads his son into joining Lucifer's side. The revelation overwhelms Hallelujah, but with Gaston's encouragement, he refuses his father and resolves to make his own decisions. Samyaza fights the party and is defeated, destroying the last barrier in Camp Ichigaya in the process.

The party reach the reactor's steel doors and find the entrance strewn with corpses of Hunters, angels, and demons. Determined to finally bring the war to an end, they march inside and find that all parties have already gathered for the final face-off.

Over the course of the following events, Merkabah and Lucifer each offer Nanashi the chance of joining their cause. If Nanashi accepts, the game will proceed to the Law or Chaos Ending, respectively. Refusing them continues the remainder of the story.

Merkabah makes the first move, commanding his Samurai to strike Lucifer and, to the people of Tokyo, promising them a place above the Firmament if they join him. Some Tokyo citizens willingly volunteer, but a group of Hunters refuse and are instantly vaporized by Merkabah in retaliation. The sight leaves the Tokyo citizens and Samurai further conflicted and divided among each other, which Flynn uses as an opportunity to encourage his troops. Merkabah turns to address Nanashi and offers to free him from Dagda if he joins his cause. His party members refuse and Dagda and Danu emerge to state that humanity cannot submit to the wills of angels or demons. Dagda reiterates his desire for a universe where humanity can transcend to true freedom and orders Nanashi to destroy Merkabah.

If Nanashi chooses to fight Merkabah, the entity commands Gaston to impale Nanashi with his spear, adding that he will forgive all of his transgressions in aiding the party. But Gaston refuses, affirming his decision to side with the people. He breaks the Spear of Michael in half and an Awakened Power courses through him. As this happens, Flynn flashes a twisted smirk towards his direction. The party face Merkabah and weaken him. Flynn commands his Hunters to altogether charge in and finish the entity. Merkabah kills more of the Hunters one by one, but Flynn persists in encouraging the Hunters' attack. Nanashi can choose to either take advantage of the opportunity or attempt to stop the Hunters' charge. Attempting to stop them earns Nanashi their ire in misunderstanding, believing that he is trying to protect Merkabah.

The party land the final blow on Merkabah and destroy him. Lucifer praises their victory and encourages the people to join him in fighting YHVH next. Flynn refuses and smirks again as the Hunters rally behind him. Unfazed, Lucifer attempts to persuade Dagda and Danu instead. When they refuse, he turns to Nanashi and offers to give him new life in exchange for siding with him.

If Nanashi chooses to fight Lucifer, the Ashura-kai begin to panic at the prospect of losing their leader. Hallelujah chastises them and swears he will take over the Ashura-kai. The men are doubtful of him at first but become impressed after hearing he has removed Abe. Hallelujah's confidence bestows him Awakened Power. As the party engage Lucifer, Flynn mobilizes his troops into another charge and more of them are killed in the scuffle. During the fight, Flynn approaches Nanashi and asks him to distract Lucifer while he sneaks up from behind. If Nanashi agrees, the plan is successful and Flynn delivers a critical strike upon Lucifer, but it is not enough to defeat the entity.

The battle continues until the party destroy Lucifer, thereby finally ending the war between humans, angels, and demons. The survivors are left with a mixture of joy, anger, and grief. As they all leave Camp Ichigaya, the party return to Kinshicho for the night.

7/8 Moon

Asahi eagerly awakes Nanashi to prepare for a victory celebration at the Hunter headquarters. While the party discuss the coming event, Gaston passingly remarks that he can now see Navarre since the day prior. The brothers share a heart-to-heart moment as Gaston admits he had hated Navarre for tarnishing the family name, but now understands his struggles and has realized his own arrogance. Hallelujah meanwhile has fully committed to rebuilding the Ashura-kai, stating he will do it in his own way.

The party arrive at the headquarters to find the celebration already underway with a large crowd of attendees. The crowd immediately recognize Nanashi and the others as Tokyo's saviors and cheer them on. Fujiwara, Skins, and Isabeau also commend the party's efforts. Unexpectedly, Flynn approaches the podium for an impromptu speech to the crowd. Flynn declares that with the war's end, humanity can finally move forward towards the future, but adds that the heavy toll of surviving the last 25 years has left their progress stagnant. He encourages that only through working together will humanity regain their lost freedom. Flynn's speech incites a raucous applause from the crowd. But when the party next realize, almost everyone in attendance suddenly collapses into a catatonic state one by one. The only ones left unaffected are the party, Fujiwara, and Skins.

Flynn takes ownership for the occurrence, stating that he has devoured the crowd's souls through their faith. His face suddenly changes into a green serpentine visage and the party realize that the Flynn they rescued is actually Shesha. Shesha assures them the real Flynn is safe and with Krishna; the Divine Powers' seeming defeat was actually a staged act to trick the Hunters. This scheme was made possible through Shesha's continuous evolution each time it resurrected. Shesha has now devoured enough souls to become the Cosmic Egg.

Having sworn to kill Nanashi the next time they meet, Shesha attempts to devour him in front of the group. But Asahi jumps in to protect him and is devoured instead, body and soul, leaving behind only her goggles and a pool of her blood. Grief-struck, the party swear to destroy Shesha, but it taunts them that its constant resurrection makes that impossible. Shesha leaves to become the Cosmic Egg outside. The party chase after Shesha and witness it leap into the air and transform into the Cosmic Egg, forming a massive, pulsating egg in the center of Tokyo.

Krishna and Odin, along with the real Flynn still affixed to a cross, appear to address the party. Krishna thanks them for destroying Merkabah and Lucifer and reminds them that the Cosmic Egg will hatch during tomorrow's full moon. He also reassures that the souls Shesha ate are inside of the egg and will be reborn along with the new universe. The entities disappear into the Cosmic Egg with Flynn. Fujiwara calls the party shortly afterward, urgently asking them to meet him in the Hunter headquarters.

The party brief Fujiwara and Skins on the development. They acknowledge that both the Divine Powers and Cosmic Egg must be destroyed and Flynn rescued, however, Fujiwara regretfully states that most of his Hunters are left in a catatonic stupor, leaving the party as the only ones who can stop the Divine Powers. If Nanashi had brought the Broken Gauntlet from Mikado before, Fujiwara also adds that Professor Matsuda has finished inspecting it and confirms it to be Akira's Gauntlet. He comments that Nanashi reminds him of Akira and explains how he and Skins had made a promise with Akira to find a middle path in saving Tokyo. The men entrust Akira's Gauntlet to Nanashi and ask him to follow the same path they chose.

As the party leave for the Cosmic Egg, they are surrounded by the Divine Powers' demons, who have come to collect Tokyo's remaining souls. The demons claim that people all over Tokyo are also doing the same and attempt to force the party to surrender. The party fight off some of the demons and prepare to face another wave, when suddenly the remaining demons are felled one by one by arriving members of the Ashura-kai. The men volunteer to protect Tokyo from the demons. Their arrival is followed by a surprise phone call from Ladies Mii and Kei, who vow that the Ring of Gaea will also support the city. They are joined by groups of the remaining Hunters and Samurai volunteering to do the same. The four groups agree to momentarily set aside old grudges to work together for the sake of Tokyo, allowing the party to advance to the Cosmic Egg unhindered.

Odin confronts the party outside the Cosmic Egg. He is aware of Dagda's ability to resurrect souls and, knowing the threat it poses to the Divine Powers, engages the party in a fight to the death. This time the party triumph over Odin, destroying the deity and leaving behind only his spear, Gungnir. Gaston, now vindicated from his earlier defeat by Odin, takes the spear as a victory spoil. As the party wonder how to get inside the Cosmic Egg, Nanashi notices a pillar sticking out of it. He pulls it out, which opens an entrance into the egg.

Inside, the group discover an enormous, otherworldly dimension with rising columns of the countless souls Shesha ate. Krishna reveals himself to the party, but has no intention of fighting them and instead has come for Toki. As he points to her, the girl suddenly writhes in pain as the Aether accumulated inside her releases. She spontaneously transforms into the resurrected Inanna, who has taken possession of Toki's body since the last Fudo Temple. Inanna madly demands Danu's power and Nanashi's attention as Toki tries to fight for control. Krishna informs that, through Inanna, Toki is to become the mother of all the reborn souls in the next universe. He implants a wayward soul into Inanna's body which is then reborn as the resurrected Maitreya. The deity undergoes a transformation of rebirth, becoming Mitra-Buddha. He creates a mandala over the Cosmic Egg that prevents Dagda from reviving the souls inside, including Nanashi's own. The Divine Powers then escape further into the Cosmic Egg, taking Inanna with them.

Chasing after them, the party face several demons allied with the Divine Powers along the way, including Baal, Apsu, and Seth. The party realize that, through Inanna, the Divine Powers can be reborn infinitely and progressively become stronger each time, making the search for Inanna that more urgent. They also find more pillars throughout the Cosmic Egg that open to other sectors, eventually assembling nine pillars altogether.

Inanna is eventually found and Danu confronts her. Inanna once again demands that Danu relinquish her power to her. Nozomi defies the deity, swearing on her dedication to the Fairies and determined to prove her capability as the fairy queen. Nanashi can choose to either immediately fight Inanna or attempt to talk her down; in the latter he tries to reach out to Toki's consciousness as she struggles against Inanna. Regardless of the decision made, a battle occurs and Inanna is defeated in the end, reducing her to a lingering shadow as Toki regains control of her own body and mind. Danu absorbs the trace remains of Inanna and bequeaths her power to Nozomi, filling her with new Awakened Power. Nozomi is confident that with Inanna's power safely inside her, the deity can no longer harm Toki again. Toki plainly thanks Nanashi for saving her and admits that she was not strong enough to resist Inanna. The rest of the party point out that her behavior has changed and is closer to when they had first met her. Toki also has no recollection of her earlier attachment to Nanashi, though her own feelings for him begin to naturally form.

Pressing on ahead, the party reach Mitra-Buddha next. During the confrontation, he enlightens them that Flynn is the reincarnation of the man who fused with Masakado to become the Firmament, while Nanashi is the reincarnation of the Akira who founded Mikado and became King Aquila. He adds that humanity's continuous cycle of reincarnation is a hindrance to the Divine Powers' plan on bringing them salvation. Through the creation of the Cosmic Egg's mandela, he has resolved to pause this cycle. The party in turn swear they will continue to defeat the Divine Powers no matter how many times they reappear. They destroy Mitra-Buddha and weaken his mandala, though its effects still linger for a little while yet. The battle leaves Toki realizing that she has been trying desperately to hide her weakness, but through her journey, has learned that true strength is the ability to change. She swears that she will continue to grow stronger through change and gains Awakened Power.

As the party advance to Krisha and Flynn's location, Dagda stops Nanashi midway and appears before the group. He informs them that it is now dusk and the full moon will soon rise. He demands that Nanashi now make his final decision on the Cosmic Egg: either destroy it and preserve the old universe, or side with him and use the egg's power to create their new universe. Danu emerges to rebuke Dagda and states that the Cosmic Egg must be destroyed for humanity's sake. The rest of the party all agree with her. Dagda reminds Nanashi that he will have true freedom in their new universe and urges him to not allow the group to hold him back. He demands again that Nanashi make his decision. This choice will determine the game's ending route.

Alignment Split

Bonds Route and Ending

The Bonds route, also referred to as the Peace route in the localization, occurs if Nanashi chooses to destroy the Cosmic Egg, thereby siding with his friends and preserving the old universe.

Nanashi's decision infuriates Dagda and he decides to take away the life he gave him, inflicting great pain and injury upon the boy. Nanashi attempts to fight back but is unable to control his demons as efficiently without Dagda's power. As the party panic over their dying friend, Danu asks them to keep Dagda distracted while she devises a plan. After some time, she declares that with Inanna's power she shall remake Dagda anew. Danu unleashes her power and another Dagda emerges, who gives Nanashi's life back along with his will. He implores that Nanashi, now his Godslayer, destroys the old Dagda. Towards the end of the battle, the old Dagda resigns to his defeat at the hands of his Godslayer and is destroyed. The victory bestows Nanashi with Awakened Power as a human. At the same time, the lingering effects of Mitra-Buddha's barrier comes to an end.

Danu asks the reborn Dagda to revive all of the souls trapped in the Cosmic Egg. He sends out motes of light which envelop the souls and carry them to their original bodies outside. A mote lands in front of the party and takes shape into the revived Asahi. She apologizes for worrying the party, but also admits that sacrificing her life for Nanashi had also eased her own worries of burdening them. Navarre interjects to speak to her, despite believing himself to still be invisible, and commends her selflessness. Asahi admits that she can see Navarre now, shocking him, and thanks him for his kindness. She promises to henceforth recognize her limitations with good grace. Nanashi hands Asahi her goggles and, as she puts them back on, she gains Awakened Power.

Dagda and Danu point out that the group still need to confront Krishna and rescue Flynn. With renewed resolve, the party press onwards. They find Krishna and Flynn at the heart of the Cosmic Egg. Although Krishna's plans have been foiled for the time being, he remains determined and states there will still come another time when he will bring his salvation. Krishna explains that humans repeatedly reincarnate as ordained by the Axiom, but it was YHVH who had created the universe to be used as a crucible for humanity's suffering. YHVH's covenant claims that humanity will be saved through submission to him; to that end, he had created Lucifer to deceive humanity and to prolong their suffering. This has created an endless loop where humans are bound to their dependency, submission, and suffering. But Krishna insists that YHVH's covenant is not the only means of salvation and swears that he will never give up on saving humanity. He intends to end the cycle of reincarnation and bring humanity together as a great singularity. Krishna then proceeds to merge himself with Flynn, becoming a Godslayer called Vishnu-Flynn. Krishna swears through him that he will destroy all who get in his way and engages the party.

During the battle, Krishna confesses his belief that humans cannot be trusted and that this trust led Dagda to his downfall. At another point, Vishnu-Flynn's body briefly stops moving as a result of Flynn fighting back. Nanashi can ask his partner to call out to him or do it himself, however the words fail to reach Flynn as Krishna resists and morphs Vishnu-Flynn into another form wielding quadruple swords. However, Flynn continues to resist Krishna, eventually overwhelming the deity and forcing the two to separate.

Flynn collapses and Isabeau runs to his side. Though impressed with Flynn's tenacity, Krishna continues to wildly insist that he will save humanity. A twisted smirk crosses his face, to which Navarre urgently calls out to Isabeau to give Masakado's Katana to Flynn. Isabeau suddenly realizes that she can see Navarre and is briefly stunned, but is urged again to quickly hand Flynn the sword. She does so just as Krishna is about to jump back into Flynn's body. Flynn leaps up and slashes Krishna with the sword. He states that humanity will save itself before sealing away Krishna with another strike.

Flynn thanks the party for saving him and admits he feels remorse for allowing himself to be captured. Navarre relates to his guilt, stunning Flynn as he notices the ghost. Navarre confesses that he did not want to be seen out of shame for his past actions and suspects his guilt had unknowingly hidden his presence until now. He has since come to acknowledge his guilt and, as a result, has become visible to the whole party. If Nanashi has the fishing hook from Lake Mikado, he can give it to Flynn, who will recognize it as belonging to Issachar and thank Nanashi for doing so.

The full moon finally rises, but with the souls now returned, the Cosmic Egg turns stagnant. Danu instructs Nanashi to pierce the egg's heart with Ame-no-Habakiri. As he does, the egg begins to violently tremble and the party leave to escape. The Cosmic Egg is destroyed and the remaining Divine Powers are forced to retreat. Demons remain in Tokyo but have turned to hiding.

Sometime later, Flynn and the group gather around Masakado's boulder to revive the deity and destroy the Firmament. Flynn unsheathes the deity's katana, however, neither it nor the boulder react. Masakado's bodiless voice responds that Tokyo no longer needs his protection now that the people of Tokyo and Mikado have learned to coexist, and thus the Firmanent's destruction is no longer necessary. He entrusts the future to Flynn and Nanashi and bids them farewell, at which point a column of light rises from the boulder and flies away through the hole in the Firmament.

YHVH's Universe

A few days following Masakado's departure, Nanashi experiences a dream where he finds himself alone in a Monochrome Forest and is approached by Stephen. The man reveals that he has secretly been helping Nanashi all this time while in the disguise of Professor Matsuda. Stephen proceeds to explain the mission that the Axiom has left humanity: humans are able to observe the universe and give answers to otherwise unexplainable phenomena. These answers form faith followed by truth, which in turn can either invigorate or kill deities. But as deities cannot observe the universe themselves, they resort to deceiving humanity into observing things that benefit them and hence why they fight over humanity. Stephen recognizes that Lucifer, Merkabah, and Krishna's defeats have brought the world peace, but adds that YHVH continues to exist in humanity's observations and will inevitably repeat the cycle of suffering. He presents Nanashi with two choices: either continue to live in fear of God and accept the universe's false freedom, or destroy God and attain true freedom. Stephen promises that he will aid Nanashi again and leaves him with the instruction to meet at Masakado's boulder after making his decision. Nanashi awakes as is joined by the other party members, including Isabeau, as they enter his room. They realize they have all had the same dream and agree to destroy YHVH together.

They arrive at Ginza to find that a crowd of Hunters have already gathered around Masakado's boulder. Flynn steps out from the crowd, recognizing that the party have also come to slay YHVH and wishes to accompany them. The Hunters behind him all volunteer to assist as well. Stephen arrives at that point to address the crowd and instructs Nanashi to offer the boulder the nine pillars obtained from the Cosmic Egg. As Nanashi lines up the pillars, they begin to glow and are absorbed into the boulder, transforming it into a massively tall Monolith. Stephen explains to the party that the Monolith is the gateway into YHVH's Universe and touching it will take them there. As Nanashi and the others proceed to do so, they are instantly transported to the dimensional realm.

If Nanashi had brought back the Broken Gauntlet from Mikado earlier, the party observe its screen activate. The device transmits data to the party's smartphones, bequeathing them two Light Grimoires and Heavy Grimoires each. The reasoning is unknown, but Nozomi believes the Gauntlet is lending them its help.

The party venture further into YHVH's Universe as Flynn closely follows Nanashi and helps to repel the demons along the way. At some point, Flynn spots in the distance the lingering spirit of Walter. Walter recognizes Flynn and responds that he had found himself in YHVH's Universe after regaining his own consciousness. However, he still feels Lucifer's yearning and vanishes to find his purpose. Shortly afterward, the party encounter Beelzebub and Lucifuge again. Nozomi notices they lack cognizance and are more akin to dolls. The demons are shortly after followed by a doll-like Lucifer. After defeating the demons, Stephen suddenly appears to inform the party that what they fought were actually illusions created by YHVH. He adds that YHVH is able to recreate past battles through the party's observations and cautions them there will likely be more illusions further ahead. He then disappears.

Soon after, the party come across Jonathan's wandering spirit. Like Walter, he is also lost in YHVH's Universe and is being called by Merkabah's yearning. He also vanishes to find his purpose. Just as before, the party encounter illusions of Azrael and Aniel before finally facing Merkabah's illusion.

Further into the realm, the party are confronted by Metatron, an unfamiliar angel who was sent by YHVH to purge them. Just as the party believe they have defeated him, a horde of Metatrons suddenly spawn and respond that God will create as many of them as needed. The Metatron Army are defeated and the party press onwards, though more Metatron Armies continue to appear throughout YHVH's Universe as common encounters.

Eventually the party find an giant stairway leading to what appears to be a dead end. There they find the spirits of Walter and Jonathan again. The Samurai declare they have now found their true purpose: Lucifer and Merkabah are to become one and regain their original form. As they transform into their respective entities, they fuse together and become Satan, the ancient angel and arbiter. Satan informs the party that the universe is constantly in flux and that the old will inevitably give in to the new as the law of all things. He recognizes that eliminating YHVH and ushering in a new governance aligns with this law and adds he will guide the party to YHVH's throne, but first challenges them to deem if they are worthy. After overcoming his various tests and weakening him, the party prove themselves as Satan concedes they have passed his judgment.

The party are taken to a corridor with a series of towering doors leading to the throne. As they approach the first set of doors, a domineering voice calls out to them and beckons they turn back or else face destruction. The party choose to open the doors and each time are threatened by the same voice. As they open the final set of doors, they find themselves in a pitch black space where YHVH directly confronts them—soon after revealed that many more copies of himself exist around the space. YHVH claims that defeating him would lead humanity astray and that humans are weak without his guidance. But the party state they believe in their bonded strength and swear they will triumph. Satan appears to judge YHVH's right to rule and separates himself, which momentarily resurrects Walter and Jonathan who join the fight. Flynn, Isabeau, Walter, and Jonathan together form their own party, creating a Double Party between both Nanashi's and Flynn's parties. YHVH retorts that once he has destroyed them all, he will replace all of humanity with another, more obedient one.

Throughout the battle, Nanashi's allies talk down YHVH, highlighting his hypocrisy and manipulation. Their defying words break through YHVH's defenses and gradually eliminate his copies. Dagda realizes this is the power of human understanding; by refusing YHVH as the One True God, they weaken him and negate his invincibility. YHVH is eventually weakened to a point where his supreme form diminishes, radically transforming his appearance into a multi-headed, snake-like entity. The party continue to fight YHVH as he grows increasingly more desperate. Dagda and the rest of the party encourage Nanashi to land the finishing blow himself. As YHVH perishes, he swears that although he will slip from human memory for now, humanity will inevitably lose their way again whereupon he shall return and the party will regret their actions. He disappears in a flash of white light.

Nanashi and the others awake to find themselves back in Downtown Ginza on the other side of the Monolith. Isabeau realizes that Walter and Jonathan are gone. The men's voices echo as they respond they cannot return to the world as Satan was a part of YHVH and thus they must return to the Axiom. They promise to meet with Flynn, Isabeau, and Navarre again in their next lives before fading away. Stephen and the Goddess of Tokyo then arrive, the latter stating that humanity no longer needs to live in fear of God. The Goddess of Tokyo thanks the party as she regains her former power and form as that of a young woman. She adds that the Axiom is the universe's binding force and will at times bestow two messiahs, recognizing them as Nanashi and Flynn. Stephen and the Goddess then depart, entrusting humanity's future to the party and reminding them to not give in to the deception of gods and demons.

Having now defeated YHVH, the party decide to finally part ways. Gaston intends to return to the Kingdom of Mikado and help rebuild it; Hallelujah recognizes Tokyo will also need rebuilding and pledges to do his part as the leader of the Ashura-kai; Asahi decides to retire from Hunter duties and instead follow her father's footsteps in supporting the Hunters; Navarre admits that he has moved past his guilt and almost disappears into the great beyond, but quickly reappears as he decides he does not yet want to leave; Toki resolves to resume her training to become stronger and reiterates she no longer needs the Ring of Gaea; while Nozomi, Danu, and Dagda pledge they will leave for the Fairy Forest. Dagda tells Nanashi that he no longer needs him as his Godslayer and fully restores his life and humanity. The party say their farewells but promise they will still be in contact.

At a later, unspecified time, Nanashi receives a text from Asahi asking to come with her to the Kingdom of Mikado for an event. Tokyo's rebuilding is now underway as both humans and demons work together. Dagda narrates the ending as he thanks Nanashi for bringing humanity and gods together and that his goal will now be to rebuild fairykind alongside Danu. Later on, Nanashi reunites with the rest of the party at Aquila Plaza to watch the unveiling of its new monument—a large statue of both Nanashi and Flynn as the world's messiahs. Dagda thanks Nanashi again and bids him farewell.

Massacre Route and Ending

The Massacre route, also referred to as the Anarchy route in the localization, occurs if Nanashi chooses to side with Dagda and use the Cosmic Egg to create their new universe.

The rest of the party is appalled by Nanashi's betrayal since they all have reasons to protect and nurture the current universe. Dagda tells Nanashi to ignore their words, calling them delusional for trying to uphold what they believe is correct. As his former allies stand in the way, Dagda encourages Nanashi to kill them and use their souls as the foundation of the new universe. One by one, they each fall, uttering their final words before Dagda snags their souls. Danu also dies at the hands of Dagda when she struggles to maintain her form without Nozomi.

With his former friends lying dead at his feet, Nanashi gains Awakened Power as a Godslayer. Dagda gifts him the Destiny Stone and has him pick up Masakado's Katana. If Nanashi has the Broken Gauntlet from Mikado, he discards it at Dagda's suggestion, severing his ties to his former life as Akira. The two then leave to confront Krishna and claim the Cosmic Egg for themselves, finding him in the heart of the Cosmic Egg alongside the crucified Flynn. Krishna assumes the two share his goal of creating a new universe, since Dagda did not use his powers to revive the souls fueling the Egg. Dagda laughs at the insinuation, stating that the new universe will be his and Nanashi's alone. Krishna bemoans the inevitability of their respective Godslayer fighting the other. After promising to rescue Flynn from his suffering at the hands of YHVH, Krishna merges himself with Flynn's body to become a being called Vishnu-Flynn, citing it as the true form of a Godslayer. He vows to stop Dagda and Nanashi from claiming the Cosmic Egg then battles the two.

During the fight, Krishna notices Nanashi's lack of companions, deducing that the boy has abandoned his humanity which galvanizes his belief that only he can bring salvation to humanity. As Nanashi whittles away at Vishnu-Flynn, Krishna is shocked by the boy's strength. Dagda mocks him for believing himself equal to Nanashi, angering Krishna and causing Vishnu-Flynn to transform into a new form that wields four swords. However, Nanashi eventually triumphs over Vishnu-Flynn, separating the entity and killing Flynn in the process. As Krishna breaks down at the loss of Flynn and his ruined plans, Nanashi seals him away with a strike from Masakado's Katana.

Once the full moon rises, the Cosmic Egg's heart transforms into a throne, to which Dagda directs Nanashi to sit on, transforming the room's interior into a celestial space. Dagda assures him that their preparations are complete and he will soon become god of the new universe. Dagda then suggests Nanashi takes a nap to prepare himself for the final battle, leading to him falling asleep on the throne.