Convicted for a crime she didn't commit and haunted by mysterious Shadows, Lucinda Price is sent to Sword and Cross, an isolated correctional facility; there, she meets Daniel, who feels they've met before, and Cam, who knows why she's there.
After her solitary punishment, Luce questions her memory of what happened to Cam; she tries to retrieve his medical records, but Daniel refuses to help; Cassie, the only one to escape, encounters a nightmarish creature.
Luce suspects Howson is controlling their memories and steals photos of her and others undergoing medical procedures; while on a hike, Howson learns of Cassie's attack and brings her to Sword and Cross.
Luce learns Daniel hasn't aged in over twenty years; determined to expose the truth, she plans a breakout with Daniel as proof; Howson is tipped off, and the Outcast injures Daniel; Luce finds the body of another Lucinda Price.
Miss Miriam hunts the Outcast while Howson fights to save Daniel; Luce and the others try to escape, but the creature pursues them; Luce learns who betrayed them to Howson and why; Daniel fades as he recalls a past life with another Luce.
Miss Miriam reveals some secrets of Sword & Cross; Luce faces her own struggles, fearing she'll die if they stay together; Luce has a vision of Penn's death and tries to prevent her from leaving, but someone is waiting for Penn with deadly intent.
Luce believes she was murdered; Daniel confronts Miss Miriam, and Cam faces Howson; Luce seeks answers from Miss Sophia; Daniel saves her, and they reconcile; Luce faces a violent end that could change humanity's future.