Despite returning victorious from a dangerous struggle, Kanata and his friends have, in a sense, lost a key ally, the amnesiac magus Noir. Having partially recovered her memory, Noir reverted back to her former personality: that of Mystere, who acts in a patronizing manner toward her master Kanata. However, Mystere remembers detecting a signal from Histoire, a mystical city, during her former life as an artificially intelligent magus.

Meanwhile, Tokio disappears from Rock Town while hunting down the ghosts of his past; however, shocking revelations await the deeper his search goes. As Kanata, his childhood friend Ellie, and the magus diva Ciel set out for Histoire, a hostile organization named Ideal sends assassins after them. If Kanata wants to stand a chance at accomplishing his dream, he must uncover the unpleasant truth about Ideal—and some of his closest allies.