The person you saved isn't the person who comes back. Noir's memory return doesn't feel like a victory, it feels like a loss wearing a familiar face, and Kanata has to keep fighting alongside someone who treats him like a mistake she's correcting. The show understands that some battles end with you standing next to a stranger wearing your ally's body, searching for a city that might not exist just to find one moment of the person you actually knew.

Kanata and his friends come home victorious from a dangerous fight, yet they have in a way lost their amnesiac magus Noir. Having recovered part of her memory, she has returned to her earlier self, Mystere, who treats her master Kanata with condescension. Mystere recalls picking up a signal from Histoire, a mystical city, back when she was an artificially intelligent magus. Meanwhile, Tokio disappears from Rock Town while pursuing ghosts of his past, and his search leads toward shocking discoveries. Kanata, his childhood friend Ellie, and the magus diva Ciel set out for Histoire, but a hostile group called Ideal sends assassins after them. To have any chance at his dream, Kanata must learn uncomfortable truths about Ideal and about some of the people closest to him. This second cour of the mecha drama continues the science fiction story.