Aegis is controlled using the phone's directional pad. 0 is used to attack, and enter causes Aegis to jump. Pressing jump twice allows Aegis to perform a double jump. The right software key summons Palladion. The left software key is used to bring up the menu. Aegis gains experience and money by defeating Shadows. The experience allows her to grow stronger and the money is used to purchase items from the laboratory.
Aegis may use three weapons: guns to shoot faraway multiple targets, the grenade launcher for a single target and the drill for melee. Aegis may also summon Palladion, which has four abilities learned by leveling up. Two are physical attacks on enemies that are impervious to Aegis' normal attacks, while the third one includes a "stun" attack, and the fourth ability is an escape ability, allowing Aegis to escape from battles or the dungeon to return to the Kirijo Laboratory.
The storyline follows Aegis, an Anti-Shadow weapon transported to the Kirijo Ergonomics Research Laboratory in Yakushima Island. On the course of six days there, Aegis meets Yuu Kimijima, the chief scientist who regards Aegis, despite being a weapon, as a human being. Aegis learns that despite Yuu's warm demeanor, she struggles with an inner conflict over life and humanity.
The game concludes with the confrontation between Aigis and Death on the Moonlight Bridge as seen in Persona 3.
- Aegis (アイギス, Aigisu) - the humanoid Anti-Shadow weapon developed by the Kirijo Group.
- Yuu Kimijima (君嶋夕) - the scientist who took over from her predecessor as Aegis' development chief. She is friendly and treats Aegis like a human being, and the one who gave Aegis the red ribbon.
- Souta Aizawa (相沢総太) - Aegis' head instructor with an unlikeable attitude, and at times at odds with Kimijima.
- Eiichiro Takeba (岳羽詠一郎) - one of the researchers, and Yukari Takeba's father.
- Kyouka Sayama (狭山京香) - a bespectacled girl who is in charge of Aegis' equipment and items.
- Mitsuru Kirijo (桐条 美鶴) - daughter of the head of the Kirijo Group.