One year after the Black Rebellion, Lelouch Lamperouge has resumed his normal school life with no apparent memories of the year before. After skipping remedial gym class, he sets off with younger brother Rolo to gamble at Babel Tower. Led by C.C., the Order of the Black Knights launches an attack on the complex to retrieve Lelouch. C.C. reawakens Lelouch's memories, and he resumes his identity as Zero. Suzaku Kururugi declares to the Emperor that he will personally kill Zero.

Lelouch directs the Black Knights in a counterattack against the Britannian forces and recalls how he came to forget his past: after Suzaku arrested him and brought him back to Britannia a year ago, the Emperor used his Geass to implant false memories in Lelouch's mind. The new Knightmare Frame prototype Vincent arrives and wreaks havoc on the Black Knights. They collapse Babel Tower to retreat, simultaneously dropping it on Viceroy Carares and creating a road straight to the Chinese Federation Consulate, where the Black Knights escape to. Zero broadcasts his plan to recreate the United State of Japan. The Britannian military retreats, but the pilot of the Vincent, Rolo, is not so easily swayed. After arriving at the consul grounds, he confronts Li Xingke, revealing that he too possesses the power of Geass.

Lelouch returns to the Ashford Academy during the broadcast, causing Villeta Nu's Special Division to have doubts he was the Zero on television. Needing information on his sister's whereabouts, Lelouch sets a trap to turn Rolo into his pawn. Gilbert G.P. Guilford, Cornelia li Britannia's knight and acting Viceroy of Area 11, presents an ultimatum to Zero: reveal himself or let the incarcerated Black Knights face execution. Elsewhere, Suzaku leads the Britannian frontlines in the Lancelot in the war against the Euro Universe. Lelouch confronts Rolo, but Rolo's unique abilities allow him to gain the upper hand.

Lelouch deduces the nature of Rolo's Geass and convinces Rolo to spare him; in return, he will hand over C.C. Li Xingke confronts the Eunuch Gao Hai and kills him to take command of the consulate. As the deadline approaches, Guilford prepares to execute the captured Black Knights, until Zero appears, challenging him to a duel. Using the same strategy from the Black Rebellion, he collapses the portion of the settlement they are standing on, causing confusion amongst the Britannian military as they are dumped into Chinese territory. While Kallen and the Black Knights rescue the prisoners, Rolo appears in the Vincent to kill Lelouch for his betrayal. However, Lelouch takes a bullet meant for Rolo, giving the youth pause. Lelouch plays on his insecurities about his future and sibling relationship, convincing him to join his cause.

Suzaku returns to Ashford Academy to investigate Lelouch. With the Black Knights reassembled, Lelouch plans to lead the resistance while maintaining his façade as a student. A welcoming party is held for Suzaku at the academy, and C.C.'s love of pizza threatens to reveal Lelouch's secret; Kallen arrives to retrieve her but is seen by Villeta. She tells Lelouch how she came with Kaname Ohgi the previous year, and Lelouch uses this information to blackmail her. Alone, Suzaku reveals to Lelouch his goal of becoming the Knight of One, which would allow him complete governing authority over Area 11. To test Lelouch, he allows him to speak with the new Viceroy of Area 11: Nunnally vi Britannia.

Rolo uses his Geass to buy Lelouch time to say words of caution to Nunnally without revealing his reawakened memories to Suzaku. Unwilling to fight against Nunnally, Lelouch orders the Black Knights to capture her as she is transported to Area 11 by airship. Successfully boarding the vessel, Zero meets with her and tries to convince that Britannia is using her. Nunnally reveals she volunteered for the position, and states she wishes to continue Euphemia's Specially Administrated Zone of Japan, requesting a bewildered Zero to join her. Britannian reinforcements hinder the Black Knights' assault, and as the airship crashes into the sea, Suzaku manages to save Nunnally, taking her away from Lelouch a second time.

Nunnally is sworn in as the new Viceroy of Area 11, and reveals her intention to restore the Specially Administrated Zone of Japan. Knowing he cannot go against his sister's wishes, Lelouch slips into a state of depression. Before he relinquishes himself to Refrain, Kallen steps in, reminding him his duty as Zero to realize the dream he gave to the Japanese. An evesdropping Rolo emerges, attempting to persuade Lelouch to abandon his identity as Zero and return to being a high school student. Meanwhile, the Black Knights are under attack by a Britannian naval fleet, led by Suzaku. A glimmer of hope is revealed to Lelouch after he sees fireworks setting off at Ashford Academy. Rushing to the battlefield, he successfully leads the Black Knights to defeat the entire naval fleet and surprise Suzaku by appearing as Zero, announcing his intention to accept Nunnally's offer to join the Specially Administrated Zone of Japan.