Lelouch confronts Clovis about the murder of his mother, Marianne vi Britannia, before killing him. When he returns to Ashford Academy, he discovers that Kallen Kōzuki, one of the terrorists he helped in Shinjuku, attends the same school. The limitations to his newfound power are also revealed to him when he attempts to question her then erase her memory, so he creates a cunning deception to ease her suspicions of his identity. When the death of Prince Clovis is announced in the media, it is Suzaku Kururugi who is accused of the murder.

Kallen and Lelouch separately reflect upon the deaths of innocents in the Narita campaign. Shirley secretly follows Lelouch and witnesses the battle between the Japan Liberation Front and the Britannian Army, which Lelouch ends by detonating the Japan Liberation Front freighter as the Britannian Knightmares begin to board it, killing all personnel on board and giving the Black Knights the element of surprise. Suzaku attacks Lelouch, easily overpowering his weaker Burai with the Lancelot, forcing him to eject. He crash-lands near Shirley and is knocked unconscious. Shirley prepares to kill him to avenge her father, but hesitates when his mask falls off, revealing to her that Zero is Lelouch.

The aftermath of the Avalon's arrival inexplicably leaves Lelouch, Euphemia, Kallen, and Suzaku on the island of Kaminejima. Suzaku encounters Kallen while Euphemia is found by Zero. Suzaku learns Kallen is a Black Knight and pilot of the Guren Mk-II, and in turn tells her about how he killed his father. Euphemia confirms her suspicions that Lelouch is Zero. Schneizel, Lloyd, and Cécile Croomy survey the island's ancient ruins. When Lelouch, Kallen, Suzaku, and Euphemia suddenly fall into the ruins, Lelouch and Kallen steal the prototype Knightmare Frame Gawain to escape. Elsewhere, the exiled Japanese government from seven years ago launches a full-scale assault on Kyūshū with the help of the Chinese Federation.