A year has passed since the events of the "Zero Requiem", a scheme Emperor Lelouch vi Britannia formulated to end conflict with his death, and Nunnally vi Britannia rules Britannia while aided by her bodyguard Suzaku Kururugi, who has taken the identity of Zero. Nunnally and Suzaku are in the middle of a goodwill visit to a desert nation when they are ambushed by a Knightmare squad; Suzaku is easily defeated and they are abducted. The two find themselves in the custody of Shalio and Shamna, the sibling rulers of the Kingdom of Zilkhistan which has suffered from the world peace crippling their primary export: mercenary soldiers. Shamna explains their plan to use Nunnally to access the collective unconsciousness within C's World to restore Zilkhistan's political might.
Suspecting Zilkhistan's involvement, Kallen Stadtfeld, Sayoko Shinozaki, and Lloyd Asplund infiltrate the country and run into C.C. and a physically resurrected but soulless Lelouch. C.C. explains that, after the Zero Requiem, their school friend Shirley Fenette smuggled Lelouch's corpse to her and that she resurrected Lelouch from the dead by reconstructing his corpse, but his memories and personality are trapped in the collective unconsciousness. The group launches an assault on a Zilkhistan prison, where they rescue Suzaku and discover an Aramu Gate, a portal to C's World. C.C. uses the portal to fully resurrect Lelouch. Lelouch once again dons the mantle of Zero and meets up with Britannian forces led by his half-sister Cornelia li Britannia and his former lieutenant Kaname Ohgi.
Lelouch's forces track Nunnally down and find her in a Zilkhistan temple. Lelouch infiltrates the temple and kills Shamna, but she activates her Geass and travels back six hours in the past, allowing her to perfectly predict Lelouch's actions. Lelouch uses his tactical prowess to deduce the mechanics of Shamna's Geass and knocks her out. He frees Nunnally, but learns that her mind has been transported into C's World. C.C. guides him into the collective unconsciousness, and he successfully rescues Nunnally. Suzaku kills Shalio in combat, destroying Shamna permanently. In the aftermath, Lelouch once again bequeaths the title of Zero to Suzaku and departs on a journey with C.C.,[8] taking the alias L.L. as his idea of a marriage proposal.[9]
In a post-credits scene set in an undetermined future, L.L. and C.C. are shown standing over a mass grave in a forest, with L.L. stating he would take away the Geass of those who wield it without resolve. This post-credit scene served as the setup for the movie's picture drama where Lelouch and C.C. confronted a pirate and C.C. took away his Geass.