Persona 3 begins with the Main Character returning to the city after ten years. He is quickly brought into SEES when his awareness of the Dark Hour is revealed and that he can summon multiple Personae into battle. With their help, SEES is able to explore Tartarus further and defeat Greater Shadows that appear every full moon, believing that by killing all twelve of them, they will be able to end the appearance of the Dark Hour. However, SEES learns they have been misled; by destroying the Greater Shadows, they have freed parts of a being called Nyx who will bring about the end of the world if it is fully restored. It is revealed that the Kirijo Corporation was attempting to do this ten years ago, but Nyx was released prematurely in a laboratory accident that also created the Dark Hour and Tartarus. Aigis, a robot designed to fight Nyx, battled the being but was unable to fully defeat it, instead dispersing parts of it into the Greater Shadows, and installing the last part into that of a young boy nearby, revealed to be the Main Character.
SEES encounters Ryoji, a teenage boy who tells him he is Death incarnate and that if they do not kill him by December 31, he will unwillingly usher in Nyx and the end of the world. The player is given the option to kill Ryoji at this point; if taken, the game explains that members of SEES lose memories of the last year, and show them leading normal lives until inevitably the end of the world occurs. If Ryoji is spared, then the game continues, and on January 31, SEES climbs to the top of Tartarus to face Ryoji, now in his true form of the avatar of Nyx. Though they defeat it, the avatar is able to still call forth Nyx; the moon splits open revealing a strange device that begins to kill people across the Earth. The Main Character uses all of his Social Links gained from SEES and other friends to create a seal to lock Nyx away forever, though sacrificing himself to do so.
The world returns to normal, though the memories of the past year are lost to the SEES members. As they finish school, they come to realize that they each promised to gather on the school's roof should they make it to graduation day. There, they find the Main Character lying in Aigis' lap, smiling at the brief reunion with the other SEES members before he dies.