Fuuka is a shy junior who is known for being sickly. Unlike the other members of SEES, she does not have any fighting abilities, nor do her Personas. Instead she takes Mitsuru's place as the team's tactical support. Fuuka's role is to forecast where upcoming bosses can be found, analyze the weaknesses of various enemies, and provide commentary on the battles. She also provides information on the medical status of the team.

A few months into the school year, Fuuka goes missing for several days. Yukari, Junpei, and the Main Character decide to investigate after strange things start happening to girls who once bullied Fuuka. It turns out that the girls locked Fuuka up in the school gymnasium, where she accidentally became trapped in Tartarus. SEES takes part in a dangerous mission to rescue her.

In Tartarus, Fuuka is awakened to the reality of her Persona power. At the same time, Natsuki, one of the girls who bullied Fuuka, wanders into the school to see if Fuuka is alright. Fuuka who ends up saving Natsuki in spite of all that Natsuki did to her, and they both become fast friends afterwards even though Natsuki has no memory of the incident. Under Natsuki and SEES' influence, Fuuka changes from a shy and isolated girl into a strong-willed, compassionate young woman. Both her Persona and her hacking skills manifest her desire to always be connected to her friends.

Fuuka is one of the girls that the Main Character can date over the course of the game. Since dating Fuuka involves tasting her horrible cooking, Main Character must maximize his courage statistic before he can ask her out. If the Main Character makes the correct choices, Fuuka will fall in love with him, and he can help her to become more comfortable with being an "unfeminine" computer geek.