A year after the Black Rebellion, Lelouch is once again a student at Ashford Academy. Following their attempt to kill one another at the end of the first season, Suzaku captured Lelouch and turned him over to the Emperor. The Emperor used his Geass to rewrite Lelouch's memories, removing any knowledge of Zero, Nunnally, or his royal heritage. The student body's memories were also rewritten by the Emperor to maintain the lie, with Rolo Lamperouge assigned as Lelouch's younger brother. Lelouch's memories are restored by C.C., and he resumes leadership of the Black Knights.
When Nunnally is appointed as Governor of Area 11 and announces her plans to reestablish the Special Administrative Zone of Japan, Lelouch falls into depression since he would be impeding her wishes by continuing his rebellion. He nearly takes Refrain before Kallen stops him. With the help of Kallen and his friends at Ashford Academy, Lelouch realizes that his mission no longer revolves solely around Nunnally but concerns everyone. To solve both concerns, Lelouch engineers the legal exile of the Black Knights by getting the Britannians to agree to exile Zero in exchange for bringing one million participants for Nunnally's new Japan. By having all the participants (within include the Black Knights) dress as Zero, he forces Suzaku to exile them all rather than order a massacre.
The Black Knights escape to the Chinese Federation, where Lelouch begins forging an alliance with the other world powers to create a force that rivals Britannia. He starts by destabilizing the Chinese Federation, returning control to Empress Tianzi from the High Eunuchs. Kallen is captured during the battle, and Lelouch works to free her from their custody when he returns to Area 11 while having the Black Knights subdue any resistance.
During his time in Area 11, Lelouch is targeted by Jeremiah Gottwald, now an assassin for the Geass Order. Jeremiah unintentionally restores Shirley's memories in his search for Lelouch. After Lelouch discovers that Jeremiah's loyalty is to his mother Marianne and not to Britannia, he reveals to him his true identity as Marianne's son and gains his allegiance. Lelouch later finds Shirley, who has been shot by Rolo. Unable to directly retaliate against Rolo, a grief-filled Lelouch changes his plan to destroy the Geass Order instead: Jeremiah having provided him with the complex's location. During the assault, V.V.'s immortality is passed to the Emperor, and Lelouch learns the true nature of his contract with C.C., which is to take on her immortality as the Emperor has with V.V. However, C.C. has decided to spare him this fate by giving her immortality to the Emperor. Lelouch refuses to let her die unhappy and convinces her to live on, but the ordeal results in C.C. losing her memories of her life after gaining Geass.
Once Lelouch's new alliance, the United Federation of Nations, is formed, their first act is to liberate Japan. After learning that his father is still alive, Lelouch arranges a meeting with Suzaku in an attempt to convince him to help ensure Nunnally's safety. However, Schneizel's troops interrupt the meeting to arrest Lelouch, convincing him that Suzaku sold him out. Lelouch escapes with the help of Guilford, whom he used his Geass on earlier, and starts his attack on Tokyo while Rolo and Sayoko are sent in to retrieve Nunnally and Kallen. When Suzaku arrives in defense of the city, he attempts to warn Lelouch of the F.L.E.I.J.A. bomb, but Lelouch refuses to believe him. Suzaku is forced to fire it while under the influence of the command Lelouch placed on him, destroying a large portion of the Tokyo Settlement. When Nunnally is believed to be dead, Lelouch is heartbroken and jealous at Rolo. This is only made worse when Schneizel convinces the Black Knights to betray him using recorded evidence from his meeting with Suzaku that makes it appear he deliberately caused the massacre that started the Black Rebellion, with Lelouch lying about the Black Knights being his tools to get himself killed by them. After Rolo evacuates Lelouch at the cost of his own life, Lelouch admits that his previous outbursts were lies, since because everything he's done has been based on lies, that too must have been. Despite his sibling connection with Rolo being a lie, and having viewed him as nothing more than trash, Lelouch, in the end, values Rolo in the same regard as Nunnally and Shirley and buries him properly, placing upon his grave the locket that Rolo had always cherished.
Lelouch then decides to go to Kamine Island and defeat his father, using his Geass to cause an uprising among the Britannian military as cover, and uses a bomb to destroy the Thought Elevator while being trapped with the Emperor within the Sword of Akasha. Facing his father, Lelouch learns of the Emperor's full plan to destroy "God", C's World, the collective unconsciousness of all humanity, and remake the world without lies, thereby creating peace. He also learns the truth behind his mother's assassination, and that her soul lived on through the Geass power C.C. gave to her prior, as she inhabited Anya's body. Furthermore, every action Charles took since obtaining Geass was planned out to find C.C. and complete the Ragnarök Connection. Though conflicted at first, Lelouch realizes that their intentions are selfish as they put their plans first before the people, and the dead will be reunited with the living. Lelouch denounces his parents' new world as nothing but a retreat into a deluded past and concludes that what he wants for himself and the world is "tomorrow". Fully awakening his Geass, Lelouch's request causes C's World to sever the Ragnarök Connection and then absorb his parents, dissolving them into oblivion for their selfishness, in spite of Charles' final words to Lelouch that forsaking the world he envisioned would only make Schneizel's a reality. One month later, he installs himself as the 99th Emperor of Britannia and appoints Suzaku as his "Knight of Zero" to set the stage for their plan, Zero Requiem.
As Emperor, Lelouch establishes himself as an ally of justice, dismantling the Britannian class system and freeing every colony (thereby abolishing the concept of "Numbers") while resorting to repression against those who may oppose him. However, the seemingly benevolent acts are a smokescreen for his intention to take over the world, as part of the Zero Requiem. After disposing of the last Britannian resistance, and knowing he has to act before Schneizel makes his move, Lelouch announces that Britannia intends to join the U.F.N. As she escorts him to the meeting, Kallen tries to confront him about what she means to him along the way, but Lelouch remains silent on the matter, even when she kisses him, not wanting to involve her. She bids him farewell when it becomes clear he will not respond, and Lelouch does the same once she walks away. At the meeting, Lelouch takes the council members hostage after it is revealed that Britannia's large population would give him a majority voting block. This brings him into conflict with Schneizel and the Black Knights, the former bringing his F.L.E.I.J.A.-equipped floating fortress Damocles into the battle. The biggest surprise comes when Nunnally is revealed to be alive and declares herself to be his enemy. Though initially reluctant, Lelouch is convinced that he must fight her for the sake of his plan. After successfully deploying a countermeasure to the F.L.E.I.J.A with Suzaku's help, he is able to board the Damocles and outwit Schneizel in his escape shuttle, placing him under a Geass command to serve Zero.
When Lelouch comes to retrieve the F.L.E.I.J.A. control key from Nunnally, she reveals that she somehow managed to overcome her blindness, caused by the effects of their father's Geass, through her own willpower, as well as her plan to turn Damocles into a symbol of hatred that would unite the world. After hearing this, Lelouch uses his Geass to force her to relinquish the key, thus putting Damocles under his control. With no one left capable of opposing him, Lelouch becomes the ruler of the world. Two months later, Lelouch arranges for the public execution of the Black Knight leaders and the U.F.N. representatives. Suzaku, disguised as Zero, interrupts and stabs Lelouch through the stomach, this being the culmination of the Zero Requiem as they had planned. Lelouch gives his life to create a more peaceful world as the only hated one left was Lelouch himself. Lelouch gives Suzaku a final order: to discard his old identity and play the role of Zero for the rest of his life. Lelouch declares in his final breath that he has destroyed the world and created it anew.
The aftermath is narrated by Kallen, who states that Lelouch's actions did improve the world after he became the main focus of the people's hatred, even though certain problems may still remain during the reconstruction. C.C. makes one last remark during the final scene of the series addressed to Lelouch.

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