The player wakes up having lost their memory and finds themselves transported into the past, wearing the uniform of Gakuen Alice — which means everyone treats them as a student whether they know anything about the school or not. Traveling through time with the teacher Noda-sensei, they gradually piece together why they are there: to protect the entire school from a threat brought by a boy known as Anti-Alice. Between major story beats, the player selects study partners, takes part in activities, and participates in weekly mini-game events.