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.

A group from the Japan Liberation Front takes a hotel and its occupants hostage, including most of the Ashford Student council and a disguised Princess Euphemia. As such, Princess Cornelia cannot make a move against the hostage takers, which Lelouch realizes and takes advantage of. He mounts a rescue with Ohgi's resistance, using his knowledge of Euphemia to barter his way past Cornelia's blockade. As Lelouch speaks with the hostage takers, Suzaku sinks the floating hotel using the Lancelot. Using explosives set up by the resistance fighters, Lelouch derails any rescue efforts by the army so he can take credit for their rescue. Broadcasting publicly to the nation, he announces the creation and purpose of his Order of the Black Knights, "allies of justice" who will judge the world and protect the weak from "those with power".

Cornelia and the Britannian Army heads to Narita, hoping to destroy the remnants of the Japan Liberation Front. Lelouch has his Knights follow her in the hope of capturing her alive so he can question her about his mother's death. As the Britannian forces close in on the Front's headquarters, Kallen utilizes her new Knightmare Frame, the Guren Mk-II, to cause a massive landslide that takes out much of the Britannian forces.

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.

C.C. explains her history with Mao, and how his inability to turn his Geass off drove him insane. An injured Villetta wakes up in Ohgi's apartment and he discovers she has selective amnesia. C.C. leaves Lelouch to take care of Mao herself, but Mao gains the upper hand when he incapacitates her. Lelouch utilizes his intellect to fool Mao and rescue C.C. from him, using the Britannian Police to surround and shoot Mao. Safe on a rooftop away from the scene, Lelouch affirms his contract with her, promising to not fall victim to his power as Mao did.

An inauguration ceremony of Clovis' memorial art museum is being held, with Euphemia judging the art works. Lelouch agrees to help Kyoshiro Tohdoh's comrades rescue their leader and Shirley finds an old crumpled letter detailing her previous knowledge of Zero's identity. During the rescue mission, Lelouch convinces Tohdoh to join the Black Knights. The Lancelot appears and attempts to stop them, but Lelouch is able to predict its movements and plan a counterattack. When Tohdoh slices open the cockpit, revealing Suzaku within, Lelouch is shocked, having originally planned for Suzaku to become Nunnally's knight. He orders an immediate retreat as reinforcements arrive. Seeing Suzaku's bravery and creed, Euphemia announces to the media that he will be her knight.

As Euphemia knights Suzaku, Lelouch establishes the hierarchy of the Black Knights. Diethard Reid suggests assassinating Suzaku, but Lelouch has other plans for him. He launches a plan to disable and capture Suzaku and the Lancelot at a Britannia military base on Shikinejima. The plan almost succeeds, but Second Prince Schneizel el Britannia appears and orders his floating battleship, the Avalon, to bombard the island.

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.

The Britannian Army fights back against the Kyūshū invaders with the Lancelot. Meanwhile, Nina meets Princess Euphemia and inadvertently gives Euphemia peace of mind about her feelings for Suzaku. As Suzaku becomes cornered when his Lancelot's battery runs out, Euphemia encourages Suzaku to fight on and live. Zero and C.C. fly into the battlefield in the Gawain to recharge the Lancelot, and the two Knightmares end the Kyūshū campaign together.