Plot:Shin Megami Tensei IV

	This article covers a complete plot summary.
	The contents within will contain major spoilers. Reader discretion is advised.

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

Beginning

Flynn has a series of strange dreams in his sleep. In his first dream, he is taunted by bodiless voices warning him that his decisions henceforth will bear consequence and create a new world. In the second, Flynn awakes to a burning city where a shadowed figure named Walter coaxes to join him in ushering a world of unrestrained freedom. In the third dream, Flynn then finds himself in a barren desert where another shadowed figure named Jonathan insists on maintaining a world of everlasting peace. Lastly, Flynn is approached by a young girl who begs him to revive her.

Flynn awakes to his childhood friend Issachar at Lake Mikado, where they had fallen asleep earlier. Both men are Casualries in the Eastern Kingdom of Mikado who have left their home village to participate in the Gauntlet Rite at Mikado Castle, a required coming-of-age ceremony where all participants are tested if they are worthy of becoming Samurai, the kingdom’s soldiers. They hurry to Mikado Castle and are met with disdain by the city’s Luxurors, the kingdom’s affluent upper class, while seeking directions to the Rite. The pair eventually arrive at Aquila Plaza where the ceremony is being held beneath the giant statue of King Aquila, the founder of the kingdom and Samurai order. Each participant is instructed to wear a Gauntlet with a screen, which if their touch successfully engages, deems them as worthy of becoming a Samurai. Issachar is rejected during the Rite while Flynn passes the test, separating the two men as Flynn is whisked away to live his new life as a Samurai in Mikado Castle.

The following morning, Flynn meets the other new prentices: Isabeau, a strong-willed yet reserved Luxuror; Jonathan, a Luxuror who is docile and kind-hearted; Walter, a rough yet good-natured Casualry; and Navarre, an arrogant and hostile Luxuror. Both Jonathan and Walter faintly recall seeing Flynn in their dreams but do not pursue the matter. Commander Hope issues the prentices their training exercise: everyone is to descend into Naraku, an underground dungeon complex that lies beneath Mikado and is plagued by demons, and to complete a series of tasks there. Flynn is then shortly introduced to Burroughs, his Gauntlet’s navigational AI. With Burroughs’s guidance, Flynn completes all his training exercises and is declared the victor for having first completed the final task as a contest. While the other prentices all congratulate him, Navarre is humiliated and swears vengeance before storming off.

The next day the prentices are called to K's Tavern to receive K's lesson on Challenge Quests. Following a prior argument, Navarre proposes a challenge to see who can first complete all of the day's Challenge Quests. Flynn finishes all of the quests, however as he returns to the tavern, he is approached by a suspicious Samurai who informs that Navarre has gone missing in Naraku and asks Flynn to covertly find him. During his search, Flynn is attacked twice by a hooded man and his demons. Jonathan and Isabeau come to Flynn's aid after deducing that the hooded man is actually a Samurai in leagues with Navarre to humiliate the Casualry prentices. Joined by Walter, the party follow Navarre's trail to a Demon's Domain he had mistakenly fallen in. Inside they come across the young girl from Flynn's dream as well as a man named Stephen, who cryptically comments on the girl's interest in the Samurai and their future roles. The Samurai find Navarre in the heart of the Domain and rescue him from the demon Alraune, eliminating the Domain in the process. Navarre loses his sanity from the experience and shortly retires from duty.

The Samurai are given a holiday following the incident. Jonathan suggests to Flynn and Walter that they visit the local bakery for breakfast. The baker there fervently raves to them about literature, which has started to suddenly appear in Mikado and has grown popular with the Casualry class. Rumors circulating between the Casualries and Luxurors speak that a figure known as the Black Samurai has been showing up all over the kingdom and distributing books. The Samurai are indifferent to the books and head to Lake Mikado to eat, where they meet Issachar about to head back home to Kiccigiorgi with a souvenir. The rest of the day passes without incident; however, at night the Samurai order awake to news that a fire has broke in the direction of Kiccigiorgi Village. The prentices beg Commander Hope to allow them to accompany the brigade as Kiccigiorgi is also Flynn's hometown, which Hope permits. They arrive by morning to find the entire village engulfed in flame after being raided by demons. Flynn and the others head into Kiccigiorgi Forest to look for survivors and learn that the village youth had been holding Sabbaths to discuss literature and were transformed into the demons attacking the village. As they rescue the last of the survivors, Hope informs them that the Black Samurai has been spotted in the forest and orders for their immediate capture.

The Samurai run into Issachar during their search, who has grown embittered by his rejection at the Rite and the Luxurors' oppression. He reveals that he has also been turned into a demon and attacks Flynn. The party defeats him and continues their search deep into the forest where they finally find the Black Samurai, realizing that she is a woman clad in unusual armor. She offers the Samurai her books and affirms that she is only spreading knowledge and wisdom to the kingdom. When they refute her offer, the Black Samurai tells them to go "to the underground" before making her escape by siccing her horde of Lilims, which manage to subdue the men with their Charm. Flynn blacks out during the fight and dreams of a barren wasteland where he again encounters Stephen and the young girl, who once again begs Flynn to revive her. He awakes to the other prentices and they return to Mikado Castle.

Flynn is once again visited by the shadowed Walter and Jonathan in his dreams that night. Walter again asks Flynn to join him and urges that he hurry to the underground, while Jonathan insists that Flynn persevere and stay. The next morning, the Samurai order are called to an emergency meeting led by Hugo, the Abbot of the monastery; and his right-hand, Sister Gabby. Hugo announces the monastery's suspicion that the Black Samurai is in leagues with the "Unclean Ones", those said to dwell deep underground and who once attempted to invade Mikado in ancient times before being repelled by King Aquila. The Samurai are thereby ordered to venture into the Unclean Ones' country, believed to lie in the depths of Naraku, and capture the Black Samurai. The announcement causes a stir as entering the farthest depths of Naraku is forbidden and, as the Unclean Ones' country is also said to have many valued Mystic Relics, Isabeau suspects the monastery has an ulterior motive for the order. Despite their doubts of the mission, Flynn, Isabeau, Jonathan, and Walter all volunteer to find the Black Samurai.

As the party descends into Naraku, they encounter and fight the Minotaur, an ancient demon appointed by King Aquila to guard the depths. The caverns eventually lead the Samurai to the top floor of the Sky Tower which, to their surprise, overlooks a lit cityscape below while a vast ceiling of stone looms high above. After defeating Medusa, who guarded the tower's lower deck, the party lands in the city streets where some men run away in terror after mistaking them for Angels. A transmission from Abbot Hugo informs the Samurai that they have reached Tokyo, the Unclean Ones' country. To help the Samurai collect their bearings, he issues them a quest to find the Counter-Demon Force Base where more information may be gleaned.

Search for the Black Samurai

As the party begin their search for the Black Samurai and the Counter-Demon Force Base, they find their way to Ueno where they discover that Tokyo's civilians have taken refuge in underground train stations from the demons above. There the Samurai are introduced to the Hunter Association, an organization of Demon Hunters who take on various errands for pay. They also overhear murmurs about the Ashura-kai, another organization keeping Tokyo's districts safe from the demons and maintaining order in exchange for large payment sums. Flynn receives a tip from one of the Association's patrons of the Force Base's location in Kasumigaseki; yet the way has become inaccessible due to the river bridge's destruction. The patron, however, suggests that Flynn exterminates the Peallaidh that has taken over Shinobazu Pond after ousting the Kelpies there. The Samurai defeat Peallaidh and bring his head back to the grateful Kelpies gathered at the river, who then form a bridge for them to cross.

Advancing to Kasumigaseki, the party gains entry to the Counter-Demon Force Base below ground, finding it long abandoned and in disarray. Walter is startled to discover sets of armor identical to the Black Samurai's, which Burroughs identifies as the Demonica armor that the Counter-Demon Force once wore. Burroughs's data banks further yield that the Counter-Demon Force were active 25 years ago in an effort to combat the demons that suddenly appeared in Tokyo, but cannot ascertain whether the Black Samurai was among its roster. She accesses additional data from the base's briefing room and sends it to Mikado's monastery. A call from Sister Gabby passes along a message from Hugo that the Samurai are now formally tasked with collecting Tokyo's Mystic Relics, much to Walter's chagrin. Having scoured the base for all information, the Samurai leave to resume their search for the Black Samurai.

Flynn and the Samurai arrive at Shinjuku where they are approached by a girl named Hikaru, recognizing them as the rumored "angels" said to have come from above. Hikaru knows of their search for the Black Samurai and passes a tip that she may be found in the Juraku Bookstore in Ikebukuro, but does not elaborate why she is helping the Samurai other than out of interest. Ikebukuro, however, is presently blocked by a barrier that requires the Jirae Talisman to dispel.

While investigating Shinjuku, the Samurai discover that the Ashura-kai have been subduing demons by distributing pills known as Reds. But while the pills pacify the demons, rumors claim that the pills also turn people into demons. In Shinjuku Park, Flynn also finds the remains of a giant Cocoon; one of the vessels that the Angels used 25 years ago to whisk away Tokyo's children to the sky. Flynn accepts a job from the local Ashura-kai branch to exterminate the Corpses in East Shinjuku. As he defeats the last one, the party are then confronted by a furious Demon Hunter. Outraged by the Ashura-kai oppressing the people with their strict control, the Hunter ingests a Red and transforms into Dullahan. She is either killed or spared depending on Flynn's choice. Having finished the job involving the Corpses, the Ashura-kai hand Flynn a new request: kill Kuebiko, who has taken residence in the Metropolitan Government Office. The Samurai accept the job with the promise of the Jirae Talisman as reward. However as they arrive, they turn conflicted as Kuebiko challenges the Ashura-kai's right to force demons to leave. Depending on Flynn's choice, he either fights Kuebiko or turns on the Ashura-kai and fights their Harpy horde. Regardless of his choice, the party receives the Jirae Talisman afterward.

At Ikebukuro, the party meets a woman named Kaga, a member of the Ring of Gaea which follows a philosophy of absolute strength and survival-of-the-fittest. Kaga and the other Ring members have been unable to reach Ikebukuro due to Xi Wangmu's barrier around the city. Flynn dispels the barrier with the Jirae Talisman, which impresses Kaga, but she tells the group to stay out of their business as she and the other members leave to wrest Ikebukuro from Xi Wangmu. The Samurai follow suit into Xi Wangmu's Demon Domain and confront the demon, but their attacks prove ineffective against her and her magic barrier. The Ring of Gaea then pour in and join the fight; their attacks likewise also fail to pierce and they are each devoured by Xi Wangmu. Kaga approaches last and shows the demon no fear, swearing that she and the Ring of Gaea will never yield and continue to struggle against all odds. She is also devoured; however, through the Ring of Gaea's continued struggle inside Xi Wangmu's stomach, they manage to weaken the demon enough for the Samurai to fight back. Xi Wangmu's defeat frees Ikebukuro from her influence and the Samurai are left impressed by Kaga's tenacity.

Resuming their search, Flynn and the others finally find the Black Samurai in Juraku Bookstore. She shows them no resistance and casually asks what they now think of Tokyo, comparing it as a mirror of Mikado, which deeply offends Jonathan. The Samurai apprehend her and immediately take her back to the Kingdom of Mikado. Their triumphant success earns them the recognition of King Ahazuya and awards them the Third Order of Merit. Abbot Hugo congratulates the Samurai following the ceremony, but boasts for having suggested the award ceremony. Confident that the people of Mikado will no longer succumb to the Black Samurai's influence, he tasks the Samurai with finding more Mystic Relics. Walter angrily objects to the order but is stifled by Commander Hope. Hugo then excuses himself to prepare for the coming public execution of the Black Samurai at the Obelisk Plaza. Word around Mikado Castle adds that the Casualries are encouraged to attend, as part of a coordinated scheme that the Black Samurai's death will quell further unrest.

At the crowded execution, Hugo permits the Black Samurai to give her final words. She addresses the crowd before her and states they will find no love from God. Her words infuriate Hugo and he orders for her immediate execution. But as her mask is removed, her face is revealed to be identical to Sister Gabby's and starts an uproar. The Black Samurai laughs that the Samurai have already realized the kingdom's bias and swears she will resurrect as often as she is needed. She is then executed afterwards. Her parting words stay with the populace and encourages them to hold more Sabbaths.

Rescue at Kagome Tower

The following morning, Sister Gabby summons Flynn and the other Samurai to the monastery for a confidential matter. Although wary of her striking resemblance to the Black Samurai, they nonetheless arrive to hear her request. Gabby implores that the Samurai hurry to Shinjuku Park where three of their allies are being held captive, adding that they are vital to the kingdom's future.

The party make their way into Shinjuku Park and dispel its barricade with the Hexagram Rosary that Gabby entrusted them. They find Kagome Tower on the other side, a stronghold heavily-guarded by the Ashura-kai and demons. The captives are located inside the tower, imprisoned in birdcages and each being guarded by a powerful demon: Murmur, Gemori, and lastly Asmodeus. The Samurai defeat the demons and free each of the prisoners, finding them badly enervated and wearing masks that blot out their memories, but which can only be removed by a kindred spirit. Jonathan, Walter, and Isabeau each carry a prisoner back to the Kingdom of Mikado.

Back at the monastery, Gabby gives the party her thanks and assures that the rescued men will recover in time. She still does not divulge their identities and merely explains they were inconvenient to the demons, but again reassures that they are of great importance to the kingdom. She urgently switches the topic to inform the party that the Black Samurai’s body had suddenly disappeared while they were away, claiming that eyewitness saw her resurrect and flee for Tokyo. Gabby asks that the Samurai yet again return to Tokyo and find her, this time with the express order to kill her. As the party prepare to leave on their next mission, they are suddenly approached by a Samurai with a summons from the leader of the Ashura-kai, Tayama. Jonathan concludes that this turn of events is opportune to ask about the Black Samurai.

Black Samurai's Resurrection

The Samurai make their way to Shibuya, where Tayama requested them. Immediately upon their arrival to the district, they receive a transmission from the man himself. Tayama reveals that he has taken a Samurai hostage as ransom and tells the party to head for Club Milton in the heart of Shibuya to hear their next task. The revelation deeply infuriates Jonathan as he worries for his fellow’s safety.

They arrive at Club Milton and meet its manager. He tasks the Samurai with killing Koga Saburo inside the club, who has been blocking the distribution of Reds in the district. They defeat Koga Saburo and the manager leaves to phone Tayama of their success, later informing them that Tayama has agreed to meet them in-person in the Hills building at Roppongi. The manager nonchalantly jokes about the unknown state of the hostage, prompting Jonathan to angrily grab and threaten him.

In the opulent Hills building, the party finally meets Tayama and find the hostage alive and well, though terrified. Tayama wants the Samurai to do him one more favor by killing Yuriko, the Ring of Gaea’s leader. He explains that Yuriko has been vying for control of the Yamato Perpetual Reactor, which supplies electricity to all of Tokyo. To further persuade the Samurai to his cause, he shows them the "future of Tokyo" on a monitor: a group of children the Ashura-kai have been raising as part of a project to bring a utopia to Tokyo, adding that their safety would be threatened if the electricity was lost. Tayama further adds that the party will likely find the Black Samurai among the Ring of Gaea as well. Although uncertain whether to trust the Ashura-kai, the Samurai take the job with little else choice.

The group head to Ginza, where the Ring of Gaea are stationed. Flynn earns respect from the guard by beating him in a fight and is advised to take the Ring's entrance test at Tsukiji Hongwanji. At the temple, each of the Samurai are given a lit candle and are instructed to make their way to the temple's sanctum alone without letting their candle go out. Flynn and the others successfully pass the trial, but as they enter the inner sanctum, their plot to kill Yuriko is uncovered and they are dropped through a trap floor. They find themselves in the Passage of Ethics and are told, through Yuriko's mercy, that they are permitted to meet her. As they move through the passage, the group are confronted by split paths and a pair of voices asking them questions they must answer through the paths they choose. Walter and Jonathan are able to easily make their choices, though Isabeau falls to Flynn's decision and worries that Yuriko is attempting to divide them.

At the end of the Passage of Ethics, the Samurai are shocked to discover that Lady Yuriko is actually the Black Samurai. She shows them her true identity as the demon Lilith. Jonathan swears to kill her for having cursed the kingdom, to which Lilith claims that it was not her books that transformed the people into demons but the natural result of them suppressing their desires. She asserts that they should instead turn their hatred onto the kingdom’s stifling control and expresses her wish to restore humans to their natural order. Her words causes strife between Jonathan and Walter which quickly escalates in them crossing swords. Walter asks Lilith how to bring in her ideal world and she tells them to go beneath the Hills building in Roppongi, where they will find "true evil" in an underground facility. Walter implores that the party leave Lilith alone until he has seen this evil for himself and departs.

Outside, the group find Walter speaking with Hikaru before taking off. Hikaru explains that she was telling him about Fujiwara at Cafe Florida in Shinjuku, who knows more about Roppongi's underground. She slips a Matchbox into Flynn's hands before leaving, adding that it is the cafe's proof of membership. The party find Walter outside the cafe unsuccessfully demanding to be let in; they are all permitted entry after Flynn shows the Matchbox. Inside they meet Fujiwara and his partner Skins, who both lead the Hunter Association, as well as Hikaru again. Fujiwara is pleased to finally make the Samurai's acquaintance and asks them how they traversed Naraku. He also asks if they believe the people of Mikado and Tokyo could coexist, leading to his admission that they are considering emigrating to Mikado and asks the Samurai to tell their leaders when the time comes. Fujiwara gives a tip that a passage leading to Roppongi's underground can be found in Midtown. Skins warns them that the Ashura-kai have a demon guarding the building, which brings Jonathan and Walter to a truce in banding together again.

At Midtown, Flynn fights Tenkai, one of the National Defense Divinities under the Ashura-kai's control, who tests his resolve. The party also meets the angel Mastema on the top floor, who was assigned to guard the building from thieves looking to steal the Reds; he opens the passage to their objective. The passage leads the Samurai to Reverse Hills, the upside-down mirror image of Tayama's Hills building, where they discover people–many of them children–are being held. As they make their way further in, they are horrified to realize that the people are being kept to harvest their brain cells used to make the Reds. The Samurai then run across Yaso Magatsuhi, a National Defense Divinity used to spread a sedative gas around the facility. They are overcome by its gas and hallucinate before blacking out, later reawakening in Tayama’s office. Tayama berates the Samurai for their trespassing and justifies his project as a necessity for Tokyo's continued survival. He allows the Samurai one last opportunity to kill Yuriko.

A transmission arrives from Abbot Hugo informing the party they are to urgently return to Mikado and make for its holy land, Shene Duque. When they arrive, they find a giant Cocoon there much like the remains found in Shinjuku Park and Sister Gabby waiting for them. She invites them into the Cocoon and introduces the new leaders of Mikado: the Heralds Michael, Uriel, Raphael, and finally herself as her true identity of Gabriel. Through the Samurai's earlier efforts at Kagome Tower, the archangels have finally been reunited and their power restored. Gabriel explains that she was assigned by God to watch over the people of Mikado as Sister Gabby and, through the archangels' power, have now cleansed the kingdom of corruption. She refuses to listen to Fujiwara's request and asserts that the party must not succumb to the Unclean Ones' temptation; instead they are to resume their task of killing the Black Samurai.

Party's Separation

The entire experience cements Walter's beliefs and he refuses to kill Lilith, reasoning that the kingdom's leadership is no different from Tayama's tyranny. He decides to leave Mikado behind and tells Flynn he will wait at the barracks should he decide to join. Isabeau declines to join either side, worried for Fujiwara's and Skins's safety and leaves to check on them. Jonathan keeps to the archangels' order and waits at the entrance to Naraku.

Flynn can choose to side with either Jonathan or Walter. Whichever side he joins, Isabeau will decline to accompany them.

Siding with Jonathan

If Flynn chose to side with Jonathan, they leave together for Tsukiji Hongwanji and arrive to find a fatally injured Ashura-kai man, having been sent by Tayama to kill Yuriko in the Samurai's stead. In his dying breath he instructs the pair to take the temple's hidden passage through a secret manhole. Flynn and Jonathan make their way to Lilith's Demon Domain and fight off her followers who transform themselves into demons. Lilith is unsurprised by the pair's arrival and engages them in battle. As the Samurai land the final blow upon her, Lilith utters that it is now all over for them, as a friend of theirs has already left to open the Expense. She dies without another word. Jonathan recalls Tayama telling them about Yuriko's vying for the Yamato Perpetual Reactor and suggests they head there. They hurry for Camp Ichigaya, where the reactor lies, finding a wake of dead Ashura-kai men and demons along the way.

They arrive to the reactor's room just in time to witness the demon Yamato Takeru's death and Tayama's lifeless body sprawled on the floor. Walter then approaches the pair, revealed to be the one responsible for the trail of death. He tells them his plan to open the gate to the Expanse using the reactor and bring in another wave of demons, and thus create a world where only the strong can reshape it. He then activates the reactor which absorbs everyone inside the room.

Siding with Walter

If Flynn chose to side with Walter, they leave to see Lilith at Tsukiji Hongwanji. Lilith is pleased to see them and instructs they are to head for Camp Ichigaya where the Yamato Perpetual Reactor is found, which they will use to open the gate to the Expanse and summon a new wave of demons to Tokyo. Doing so will destroy the present world's order and those who survive shall have the strength to reshape the world as they see fit. Lilith warns them that Tayama's National Defense Divinities will be guarding the stronghold and so accompanies them, though this only unlocks her for Special Fusion.

Flynn and Walter head for Camp Ichigaya and are confronted by the Ashura-kai and their Defense Divinities along the way, including a revived Koga Saburo, Omoikane, and Michizane. When they finally reach the reactor's room, they are confronted by Tayama holding the remote to the reactor. He chastises them that if the Expense were to open, Tokyo would be flooded with far too many demons than they could handle and the world at large would be thrown into chaos. His words fail to sway Walter, to which Tayama summons Yamato Takeru to fight the pair. They overcome the demon and Tayama frightfully relinquishes the remote without any more resistance. Flynn is handed the remote and Walter urges him to press it while Tayama panics and pleads him not to. Regardless of whether or not Flynn presses it, the reactor is activated and absorbs everyone inside the room.

Blasted World

Whichever side that Flynn chose, after the events at the Yamato Perpetual Reactor, he awakes alone in a blank space where is approached by four white phantoms closely resembling K, Issachar, Hugo, and Isabeau–collectively known as the White. The phantoms speak of the futility of revolt and preservation, and to demonstrate this to Flynn, they send him off to witness an alternate world of possibility.

When Flynn next awakes, he finds himself in the Counter-Demon Force Base's briefing room in the company of Jonathan and Walter. Both men have been arguing that Flynn chose to accompany him and mention having also dreamt of the White. Outside, the group are devastated to find a vast and barren desert instead of the city of Tokyo. Jonathan notices that the ceiling overhead is also gone and worries what had become of the Eastern Kingdom of Mikado. The trio band together to find answers.

The party find and enter an underground shelter where they are immediately confronted by a band of cloaked men. In their panic and confusion, the men draw their weapons at the Samurai but notice the Gauntlets on their arms. They immediately call for a man named Kiyoharu while another escorts the Samurai to a locked room. There the trio are called by a voice asking about their "Demonicas" and to demonstrate their Demon Summoning Programs. Whether or not Flynn complies, Kiyoharu–the owner of the voice–excitedly enters the room. Kiyoharu is overjoyed that his prayers have finally been answered and instructs the men to free the Samurai before leaving to tell Akira the news.

Flynn and the others meet with Akira and learn of the situation: the Samurai have landed in an alternate world of Tokyo that was destroyed 25 years ago by God's Plan. The survivors have been agonized by an adversary called Pluto the Tormentor, whose poison has made the air outside lethal to breathe and has forced the people underground. Kiyoharu has been fervently praying to God to send them Messiahs who can defeat Pluto. Akira explains he was recently visited by the White in his dreams, telling him that Messiahs would soon arrive and seek this world's Yamato Perpetual Reactor, and awoke with its remote in his hand. Akira believes the Samurai to be the Messiahs and promises them the remote if they can defeat Pluto. They accept his conditions and are told to head to Pluto Castle.

The Samurai infiltrate the castle and fight its legion of robots, which Burroughs identifies as Pluto Soldiers. They soon after discover that Pluto is also a robotic entity that was sent by God to exterminate the survivors with its poison. They destroy Pluto, which clears the air, and return to high praise and renewed hope among the survivors. As promised, Akira entrusts the Samurai the reactor's remote and asks them if it is true that it can open the gate to the Expanse; he explains his goal to summon demons to rebuild Tokyo and live in harmony with them. He adds that if they succeed in rebuilding, he will name this world the Eastern Kingdom of Mikado in honor of the Messiahs.

With the remote in their possession, the Samurai make their way into the ruins of Camp Ichigaya and are again absorbed into the activated reactor. Flynn is once again approached by the White, informing him that the world he has seen is one possible outcome if he chooses to pursue preservation. They proceed to send him into another alternate world.

Infernal Tokyo

Flynn, Jonathan, and Walter once again awaken to find themselves in the Counter-Demon Force Base's briefing room. A strange man notices them and runs out shouting for Akira upon seeing their Gauntlets. Outside the room, the Samurai discover that the base is inhabited by Demonoids, people who have fused with demons; as well as their Neurishers, those enslaved by the Demonoids to feed on their emotional energy. The party then meet this world's Akira, a Demonoid himself, who immediately enlists their aid. Akira wants the Samurai to join him in killing Kenji, the King of Tokyo, so that they can become its new rulers. He adds that Kenji received a prophecy from the White that he will be killed by "Intruders", making the Samurai prime suspects and targets; however, Akira claims that he will keep them safe from the tyrant. Although reluctant, the Samurai agree to accompany Akira with little else choice. But before making for Kenji, Akira tells the trio they will first wrest control of Shinjuku.

Outside, the party discover that the Tokyo of this world has been turned into a burning city rife with violence and ruled by might. They follow Akira to Shinjuku where a guard, a Vetala, stops them to pay the toll. Walter foils Akira's plan of sneaking in by encouraging that he stands up for himself; instead, the Demonoid hides behind his bodyguards and has them fight the guard. The Samurai obey, but realize that this world's Akira is cowardly and weak. Having infiltrated the district, the group then proceed into Mahamayuri's Demon Domain and challenge him for rulership of Shinjuku. Akira once again has the Samurai fight off the demon and his Yaksa horde. With Mahamayuri's death, Akira lays claim to Shinjuku and his followers from Kasumigaseki shortly move into the district. Once things settle, Akira explains that he had also received a prophecy from the White that Messiahs from another world would arrive and seek the Yamato Perpetual Reactor. He is disheartened that the Samurai will leave him soon, knowing that he will be killed in their absence, but understands their urgency and accompanies them to Camp Ichigaya where Kenji is guarding the reactor.

Jonathan asks Akira what he plans to do upon becoming Tokyo's next king, to which Akira admits that he wants to bring back order to Tokyo where everyone – Demonoids and Neurishers alike – can all live equally. He leaves the Samurai to their task. Flynn and the others make their way to the heart of Camp Ichigaya, learning along the way that the stronghold is being used to turn people into either Demonoids or Neurishers by choice. They find Kenji in the reactor's room and defeat him, thereby making Akira the new King of Tokyo and the Samurai earning control of the reactor. They once again activate it and are absorbed inside.

The White approach Flynn and explain that the worlds he has seen are both possible outcomes in pursuing preservation or upheaval, respectively, but will inexorably lead humanity to destruction either by God's will or through their own hubris. As such, the White claim that humans are forever bound to the will of God. However, they propose Flynn a third choice: to free humanity and become their true Messiah by reducing the world to nothingness. They then urge him to make his choice: either bring the world to nothingness, or choose to preserve or destroy the world's order. This choice, along with Flynn's final Alignment score, will determine the game's ending route.

Nothing Ending

The Nothing End occurs if Flynn chooses to bring the world to nothingness. The White show him the Yamato Perpetual Reactor's Control Device, explaining that they were its creators and originally intended it to be a particle accelerator for creating black holes. They instruct him to destroy the reactor's Control Device so that it may run amok and create a massive black hole big enough to swallow the world whole.

Flynn attacks the device with Burroughs lending him support. She swears to follow him through to the end, though her resolve and trust in him wavers overtime. Flynn lands the finishing blow, destroying the reactor's final safeguards as it begins to malfunction. The White blissfully thank Flynn and hail him as their true Messiah before disappearing one by one. Alone, Flynn watches the blank space be decimated in the growing black hole which soon swallows him as well. The black hole continues to grow in mass as it overtakes Tokyo, Mikado, and finally the entire world at large. Everything from that point ceases to exist.

Monochrome Forest

If Flynn chooses to preserve or upheave the world's order, the White turn furious and trap him in the Monochrome Forest, a fabricated space where he is sentenced to die. From there, depending on his final Alignment score, he will meet certain people there who will aid him. If his Alignment score ultimately aligns with Law, he meets Jonathan and Gabriel there. If his score aligns with Chaos, he instead finds Walter and Hikaru; the latter revealed to be Lucifer. If Flynn's final score aligns with Neutral, he is aided only by Stephen and Burroughs, who are revealed to know each other.

Regardless of the route, Gabriel, Hikaru, or Stephen explain to Flynn that he is trapped within the Expanse and that it and the White are both aggregates of people's thoughts. He must defeat the four White in order to break their influence over this space and return him to his present world. If Flynn is on the Law or Chaos routes, he is accompanied by Jonathan or Walter, respectively.

Flynn finds and defeats the White's lookalikes of Hugo, K, Isabeau, and Issachar, in that order. Upon defeating the last White, Gabby, Hikaru, or Stephen appears before him and congratulates his efforts, adding that while the White have only been momentarily destroyed, their influence shall not presently interfere any longer. They then return Flynn (and any accomplice) to his present world. From there the story significantly diverges.

Alignment Split

Law Route and Ending

Flynn and Jonathan awaken to find themselves inside Shene Duque's Cocoon beneath the watch of the archangels. Gabriel welcomes them to the Cocoon as the kingdom's new holy castle. The other archangels explain they have ridden the last of Mikado's "Filth", but the kingdom is still under threat as the gate to the Expense has been opened and Tokyo's order lost in the ensuing chaos. Though the archangels have sealed Naraku, legions of demons will inevitably try to penetrate their defenses. Gabriel then implores Flynn and Jonathan to aid them in completely annihilating Tokyo using the Yamato Perpetual Reactor, which will create a black hole they call the "Great Abaddon" and swallow everything in its wake. Uriel adds that the Demon Lord Lucifer has also been resurrected and will pose an obstacle to them; thus the archangels beseech that one of the two Samurai fuse with them to bring forth God's chariot. But in doing so, that man will also perish in the process. Although Jonathan is initially overwhelmed by the fear of death, he steps up to elect himself as Mikado's martyr and fuses with the archangels. Merkabah emerges from the light and leads Flynn to the Yamato Perpetual Reactor.

However, as the pair enter Camp Ichigaya, they are stopped by Isabeau. Having been told by Walter of Flynn's plan to annihilate Tokyo, she refuses to let him carry out this genocide and engages him in battle alongside her demons. She is unable to defeat Flynn and, unwilling to let his hands be stained with her blood, she takes her own life. Merkabah nonchalantly remarks they must remain vigilant lest more people become a victim to Tokyo's filth just as Isabeau had.

Flynn and Merkabah are transported to the Hall of Eternity in Lucifer Palace, where they challenge the Demon Lord's generals along the way. In the heart of the palace they find Lucifer, born from Walter's sacrifice, and triumph over each of his forms; his death dispels the palace and the pair find themselves right in the reactor's room.

Having now secured the reactor, Merkabah comments that the time for Tokyo's demise has finally come and all shall be swallowed by the Great Abaddon. But he adds that even they will not be spared from the black hole, for they have also been brushed by filth and stained in their blood. Merkabah presses the remote and summons a black hole from the reactor's core that quickly grows and consumes its surroundings. Both Flynn and Merkabah watch in silence as they too are swallowed by it. The black hole continues to gain mass until it overcomes all of Tokyo.

The ending is then narrated by Jonathan's voice as he shows the future that Flynn's sacrifice has guaranteed the Eastern Kingdom of Mikado. The kingdom is now a world of everlasting peace populated only by the innocent as God intended. The statue of King Aquila has since been replaced by one in Flynn's likeness and he is now hailed by all as the Messiah who brought them this peace.

Chaos Route and Ending

Flynn and Walter awaken back at their world's Yamato Perpetual Reactor alongside Hikaru. She explains that demons have now flooded Tokyo through the opened Expanse and destroyed the city's order, turning it into a place that the strong can reshape. However, victory is not yet theirs; the archangels of the Eastern Kingdom of Mikado are preparing to strike back and bring God's chariot to the war. Hikaru implores that if she were to fuse with one of the Samurai, she will regain her full power equal to God's as the Demon Lord. But in doing so, the one who fuses with her will also lose their individual consciousness and in essence die. Regardless of Flynn's choice, Walter willfully steps up to be the sacrifice and fuses himself with Hikaru. Emerging as the resurrected Demon Lord Lucifer, the entity joins Flynn to scale Naraku and strike down Mikado.

Before they can leave Camp Ichigaya, Isabeau confronts them. Jonathan has told her of Flynn's decision to wage war with the Kingdom of Mikado and this she cannot abide by, certain that if a new regime were to be installed, another violent rebellion will inevitably occur. Unwilling to let Flynn be the cause of a never-ending war, she engages him and Lucifer in battle alongside her demons. Isabeau is unable to triumph over Flynn though and, refusing to let his hands be stained with her blood, takes her own life. Lucifer spares her no sympathy and urges they hurry to Mikado.

Flynn and Lucifer make their way through Naraku and are transported to Purgatorium, a realm the angels have created to protect the kingdom from intruders. Together they slay the waves of seraphs along the way until they finally reach the center where they meet God's chariot, Merkabah, born through Jonathan fusing himself with the archangels. Merkabah falls to Flynn and Lucifer, which destroys Purgatorium and scatters the forces of law without a leader.

Lucifer changes back to the form of Hikaru, now that there are none left to oppose them, and marches with Flynn to the now defenseless kingdom. Demons start pouring in from Naraku and attack the populace or coerce them into becoming demons. Lucifer suggests to Flynn they watch the kingdom's end from the castle rooftop. As they watch the kingdom burn down, Hikaru recognizes Flynn for giving free will to the people of Tokyo and Mikado, but adds that the people will inevitably destroy each other if left unchecked and yearn for a new king. She asks if he will rise as their new ruler.

Neutral Route and Ending

Before Flynn is returned to his world, Stephen reveals that the young girl he had met in his dreams is actually the Goddess of Tokyo and that, in order to revive her, he must remove the stone dome dividing Tokyo and Mikado. For that task, he informs that Flynn will need to return Masakado – the guardian deity of Tokyo who is also the dome itself – back to normal.

Flynn awakes to a girl's voice and finds himself back in his world's Counter-Demon Force Base at Isabeau's side. She is greatly relieved to see him awake, but adds that Jonathan and Walter have since gone missing. She informs Flynn that war has broken out in Tokyo; demons have flooded in through the opened Expanse while the angels of Mikado are preparing to annihilate them along with all of Tokyo. Unable to reach anyone else, Isabeau had been searching all over for Flynn's whereabouts and begs to accompany him.

Flynn and Isabeau head to Cafe Florida to consult Fujiwara and Skins, however, even they are uncertain what to do in the situation. Burroughs chimes in to remind them of the guardian deity of Tokyo, which catches Skins's attention and he urgently asks Flynn if he knows the deity's name. Flynn responds with Masakado and is made to hold the katana that Skins has been safeguarding, realizing that he is able to unsheathe it. Relieved, Skins explains that during the Counter-Demon Force's days, he had slayed Masakado together with a young man. That man and Masakado had turned themselves into the stone ceiling covering Tokyo in order to shield the city from an onslaught of ICBMs launched during God's Plan. Skins was entrusted with Masakado's Katana, which is also the medium used to control him, but no one since has been able to unsheathe the blade until now. Fujiwara adds they had been biding their time for the right person to appear by founding the Hunter Association. They give Flynn the katana and encourage him to revive Masakado at Ginza, whose power would surely be enough to end the war between the angels and demons.

Flynn unsheathes the sword at the giant boulder in Ginza, turning the stone back into the floating, severed head of Masakado. The deity recognizes Flynn as the reincarnation of the young man he once aided and realizes Flynn's intention to return Tokyo its rightful form by removing the ceiling. Isabeau is overjoyed to have finally found the answer to reuniting the people of Tokyo and Mikado. Unfortunately, Masakado's body had left him to become the ceiling above, and as such he presently has no power to help them. However, he adds that there is still another way by reuniting the souls of Tokyo into becoming one Great Spirit of Hope. Flynn is given the Chalice as a vessel to gather the people's hopes in.

The Samurai pair visit the Hunter Association and learn of their latest initiative to boost the Demon Hunters' morale: the Association has decided to host a tournament to see which Hunter can complete the most Challenge Quests around Tokyo and become its champion. The barkeep encourages Flynn to participate too, adding that he would become a beacon of hope to all the people if he won.

After completing all of the necessary Challenge Quests and touring the districts of Tokyo, Flynn and Isabeau find renewed hope and cheer among the people, who now regard Flynn as their champion. Their hope fills the Chalice as light until it is full, when the light takes shape as the Great Spirit of Hope. The pair hurries this light to Masakado and restores some of his power. However, Masakado still cannot return to his body, as the Great Spirits of Goodwill and Spite have grown too powerful and have become obstacles in pursuit of preservation and upheaval. Masakado explains that the Great Spirit of Goodwill has turned into God's chariot while the Great Spirit of Spite has taken shape as the revived Demon Lord and both are vying for the people's hope. These Spirits must be regained by slaying their entities. Isabeau urges that they make for Naraku first, realizing they must also evacuate the people of Mikado before the ceiling falls. Masakado joins the party.

As the group head into Naraku for Mikado, they are instead transported to Purgatorium – a realm constructed by the angels to protect the kingdom from intruders. The pair advance to its center, fighting off waves of seraphs along the way, until they find themselves in a dark room where they hear Jonathan's voice. The voice is revealed to no longer be of Jonathan's, but of God's chariot Merkabah, who was born out of Jonathan's sacrifice in fusing himself with the archangels. Flynn and Isabeau together defeat Merkabah's forms, thus dispelling Purgatorium and freeing the Great Spirit of Goodwill. Isabeau proceeds ahead to persuade the kingdom to evacuate, telling Flynn they will reconvene at Cafe Florida once they have both finished their final tasks.

Flynn returns to Camp Ichigaya to find the Demon Lord next and is transported to the Hall of Eternity in Lucifer Palace, where he is condemned to wander its maze-like corridors endlessly. Flynn fights Lucifer's generals and traverses through the Hall of Eternal Light until he finds Walter waiting for him. The Samurai is instead revealed to now be Lucifer, after Walter had sacrificed himself to Hikaru so that she could regain her full strength as the Demon Lord. Flynn defeats Lucifer as well and the palace disappears, thereby freeing the Great Spirit of Spite. A transmission arrives from Isabeau informing that she has succeeded in evacuating the people of Mikado, who are now en route to Shinjuku, and asks Flynn to meet her there.

At Cafe Florida, Flynn reunites with Isabeau, Fujiwara, Skins, Commander Hope, K, and Hugo, who are all in good cheer and hopeful for the future. Flynn and Isabeau shortly leave to return Masakado to his true form; he congratulates the pair for returning Tokyo to humanity's hands, but warns that humanity will inevitably repeat its same mistakes again. Flynn relinquishes the Great Spirits of Goodwill and Spite, which returns Masakado's full power as he flies up to the ceiling in a column of light. The Samurai watch as the ceiling crumbles away and sunlight finally returns to the city as Masakado, in his true form as an enormous demon, towers overhead.

Flynn next appears at a shoreline reminiscent of the wasteland where he had met the young girl, the Goddess of Tokyo, in his dreams before. She appears before him and emerges as her true self – a woman closely resembling Burroughs – and thanks him for restoring her and Tokyo.