The Persona 3 FES disc will contain an "enhanced" version of the original game, plus a 30-hour episode where gamers play as Aigis. Aigis is described as "a humanoid weapon whose personality matrix allows her to use a Persona. She is no longer bound by her programming, but still has strong ties to her companions." The new episode will feature an original story and 17 new music tracks.

The Atlus RPG sees a group of students studying in a Japanese high school during the day, where their actions count towards building up their "personas." At night, they explore the tower Tartarus and use their personas to battle the sinister shadows that lurk within. The new game will continue on past the final battle that ended the original, and it will show "the aftermath of the final battle and the students' struggle to find meaning in their new lives."

The original Persona 3 game will get new personas and cutscenes, extra quests and events, a weapon synthesis system, a hard difficulty mode, and new outfits for the main characters.