On August 10, 2010, a.t.b., Japan was conquered by the Holy Empire of Britannia. Seven years later, teenage student Lelouch Lamperouge finds himself pulled into a battle between anti-government terrorists and the Britannian Army in the Shinjuku Ghetto. In the midst of the conflict, a mysterious, green-haired girl saves him from death by granting him "the power of the king", which allows him to compel others to do his bidding.

Using his newfound power, Lelouch hijacks an enemy Sutherland and leads the rebels in a counterattack against the Britannian army, forcing Viceroy Clovis la Britannia to call for the release of an experimental Knightmare Frame, the Lancelot, piloted by Suzaku Kururugi. The Lancelot proves to be far superior to the previous Knightmare Frame models and Lelouch is forced to change his plans. Just as the Britannian Army corners the terrorists, Prince Clovis orders an immediate cease-fire, as he is being held at gunpoint by Lelouch.

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.

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.

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.