On Tatsumi Port Island in 1999, the Kirijo Group's experiments on the Shadows went disastrously awry, unleashing the most powerful shadow, Death. The Anti-Shadow Suppression Weapon Aigis pursued and battled Death, causing a car crash that killed Makoto's parents and left him the sole survivor. Aigis, unable to defeat Death, sealed a portion of its power in Makoto.
Ten years later, on April 6th, 2009, Makoto moves back to Tatsumi Port Island as a transfer student to Gekkoukan High School. Three days later, he enters the Dark Hour, a supernatural 25th hour where Shadows roam, is caught up in a Shadow attack on the Iwatodai Dormitory and awakens to the power of Persona, with the initial Persona Orpheus. Makoto learns that his dormmates are actually members of the Specialized Extracurricular Execution Squad (SEES), a group dedicated to fighting Shadows. Makoto is inducted into SEES and named their field commander due to his unique ability to control multiple Personas, the Wild Card.
Over the course of the next seven months, with the aid of the inhabitants of the Velvet Room - Igor and Elizabeth - Makoto leads SEES in battling the twelve fragments of Death in order to bring an end to the Dark Hour and exploring Tartarus, a massive tower that appears in place of Gekkoukan High during the Dark Hour. During this time, he re-encounters Aigis, who has lost her memories of their previous encounter due to damage sustained in the fight with Death. Eventually, SEES defeats the twelve fragments, but the Dark Hour is not destroyed. Makoto learns that SEES founder and former Kirijo Group scientist Shuji Ikutsuki had deceived them all; destroying the fragments will allow Death to return to its full power and summon the maternal being, Nyx, and bring about the Fall, the end of humanity. Ikutsuki is killed in a gunfight with SEES backer Takeharu Kirijo. Death manifests in the form of new Gekkoukan transfer student Ryoji Mochizuki, who offers Makoto a choice - kill him and allow SEES to live out the remainder of their lives in blissful ignorance, or let him live and make a futile attempt to delay the inevitable. In the bad ending, Makoto kills Ryoji and is last seen ignorantly singing karaoke right before the Fall. In the good ending, Makoto spares Ryoji. On January 31st, 2010, SEES ascends to the top of Tartarus and defeats Ryoji's true form, the Nyx Avatar, in battle, but are powerless to stop the Fall. Makoto ascends to face Nyx and expends all of his life force to create a seal to protect the Earth from her. Makoto spends the next two months living a peaceful life with his friends before dying peacefully in Aigis' arms on March 5, 2010.
After Makoto's death, Aigis inherits his Wild Card abilities. When the collective manifestation of SEES' grief over Makoto's death creates a new Shadow nest called the Abyss of Time, SEES investigates and learns that Makoto's soul is bound to a Great Seal in order to prevent Erebus, the collective manifestation of humanity's desire for death, from reaching Nyx and bringing about the Fall. After SEES defeats Erebus, Elizabeth departs the Velvet Room on a journey hoping to find a way to save Makoto from his fate.
