Following a series of attacks that have left teachers and students alike sapped of their magic, headmistress Liza Quillyn decides to seal off the College, rendering it impossible to enter or leave the premises. As a result, Philomela Sargant is unable to comply with her grandmother Lizbeth's order to withdraw from the school.

Trapped inside the College, Chise Hatori and her classmates begin to adjust to their novel and stressful circumstances. But as time goes on, Philomela's condition only gets worse—both mentally and physically. Meanwhile, details about the tragic past of Chise's roommate, Lucy Webster, continue to resurface. As Chise grapples with worries about her friends and with her evolving self, the identity of the mysterious magic-draining culprit plaguing the College may finally come to light.