Makoto Yuuki is an orphan; his parents died ten years prior to the events of Persona 3, which sees him returning to the city he grew up in. He moves into the dorm in the introduction of the story, learning of his ability to summon a Persona when the dorm is attacked by Shadows during the Dark Hour. Mitsuru asks him to join SEES and he is later elected the team’s leader in combat.
Makoto is unique among his cohorts in that he has the ability to carry multiple Personas and switch between them during battle. He is also the only character with access to the Velvet Room.
The initial Persona of Makoto is Orpheus, although through Persona fusion and other means he has access to over 170 different Personas.
Soejima took longer to design the Main Character than any other character, as the game’s other characters would be made to complement his design. Soejima wrote in Art of Persona 3, “Initially, he looked more honest, like an ordinary, handsome young man. But, I worked to achieve greater ambiguity in his expression.”
In December we learn that a Shadow known as “Death” was sealed in Makoto as a child by Aigis, who was unable to defeat it herself. The Death Shadow was able to lead Makoto to twelve other greater Shadows; by defeating them, The Appriser was created, a being which summons Nyx to the world to bring about its destruction.
SEES battles The Appriser on the roof of Tartarus, but are not able to stop Nyx’s descent to Earth. Makoto enters Nyx and is able to seal it using the power of the Social Links he formed over the past year. While able to seal away Nyx from humanity, Makoto dies after the battle and his soul becomes the Great Seal.
In Persona 4, it is revealed that Igor’s assistant Elizabeth left her position to find a way to rescue Makoto from his fate as the Great Seal.
His true Persona is Thanatos of the Death Arcana and his Ultimate Persona is a fusion between Orpheus and Thanatos, known as Messiah.