GrimGrimoire allows players to take on the role of Lillet Blan, a young magician who is admitted to a prestigious and mystical magic school; however, on the fifth day of school, everyone mysteriously vanishes. Lillet awakens the next day to discover she is once again living out the first day of school; but her memories from the previous days are intact, giving her the opportunity to solve the mystery behind the disappearances and prevent the tragedy from occurring.

Lillet Blan arrives at the Tower of Silver Star to begin her schooling. During her first five days, she meets her teachers and fellow students. On her fifth evening, Lillet wakes to find the Tower under attack from Calvaros's released spirit, who has killed the other teachers and is seeking the Philosopher's Stone. Before he can kill her, the clock strikes midnight and she is sent back to the beginning of her first day at the Tower. During the next three loops of time, Lillet learns more about the Tower's inhabitants and her own situation.