The Purist faction within the Britannian Army scapegoats Suzaku for Clovis' death, planning to use him as an excuse to rid the army of Honorary Britannians. Lelouch concocts a plan to save his childhood friend, with some help from Kallen and Kaname Ohgi, leader of Kallen's resistance group. Announcing himself publicly as Zero, Lelouch declares it was he who killed Clovis, and uses his power on Jeremiah Gottwald to force him to assist in Suzaku's rescue. In private, Lelouch offers Suzaku the opportunity to turn against Britannia for falsely accusing him, but Suzaku refuses, wishing to change the Empire from within.

To Lelouch's surprise, C.C., the girl who gave him his power, is alive and now living in his residence. Suzaku, having been acquitted of all charges, accidentally meets Third Princess Euphemia li Britannia and ends up intervening in an internal Purist faction struggle. Meanwhile, Second Princess Cornelia li Britannia endeavors to take charge of Area 11 as Viceroy and bring Zero, now the Empire's number one enemy and most wanted man, to justice.

Cornelia sets a trap for Zero at the Saitama Ghetto as she begins to clear another resistance cell. Despite C.C. trying to stop him, Lelouch takes the bait and goes to the aid of the Saitama resistance. His plan falls apart from a combination of Cornelia's superior tactics and the resistance cell's dissimilar motivations. Lelouch is cornered and nearly discovered, but C.C. dons his Zero costume and distracts the Britannian Army, allowing Lelouch to escape. Lelouch blames his defeat on the undisciplined rebels and resolves to build something better than a mere resistance unit.

The Black Knights' assault on the Britannian Army in Narita proves successful, and Cornelia is cornered by Kallen and Lelouch. The army is pinned down by the Japan Liberation Front when they attempt to assist her. At Euphemia's request, Suzaku rushes onto the battlefield in the Lancelot to rescue Cornelia. He saves Cornelia and manages to corner Lelouch. C.C. comes to Lelouch's rescue by mentally traumatizing Suzaku, but is injured when Suzaku begins firing wildly. As he takes care of her, Lelouch inadvertently learns her real name. The Black Knights retreat from the conflict in victory, leaving the Japan Liberation Front and the Britannian Army to fight amongst themselves.