In the year 2010, the Holy Empire of Britannia is establishing itself as a dominant military nation, starting with the conquest of Japan. Renamed to Area 11 after its swift defeat, Japan has seen significant resistance against these tyrants in an attempt to regain independence. Lelouch Lamperouge, a Britannian student, unfortunately finds himself caught in a crossfire between the Britannian and the Area 11 rebel armed forces. He is able to escape, however, thanks to the timely appearance of a mysterious girl named C.C., who bestows upon him Geass, the Power of Kings. Realizing the vast potential of his newfound power of absolute obedience, Lelouch embarks upon a perilous journey as the masked vigilante known as Zero, leading a merciless onslaught against Britannia in order to get revenge once and for all.

One year has passed since the Black Rebellion, a failed uprising against the Holy Britannian Empire led by the masked vigilante Zero, who is now missing. At a loss without their revolutionary leader, Area 11's resistance group—the Black Knights—find themselves too powerless to combat the brutality inflicted upon the Elevens by Britannia, which has increased significantly in order to crush any hope of a future revolt. Lelouch Lamperouge, having lost all memory of his double life, is living peacefully alongside his friends as a high school student at Ashford Academy. His former partner C.C., unable to accept this turn of events, takes it upon herself to remind him of his past purpose, hoping that the mastermind Zero will rise once again to finish what he started, in this thrilling conclusion to the series.

Fifteen years after a cataclysmic event known as the Second Impact, the world faces a new threat: monstrous celestial beings called Angels invade Tokyo-3 one by one. Mankind is unable to defend themselves against the Angels despite utilizing their most advanced munitions and military tactics. The only hope for human salvation rests in the hands of NERV, a mysterious organization led by the cold Gendou Ikari. NERV operates giant humanoid robots dubbed Evangelions to combat the Angels with state-of-the-art advanced weaponry and protective barriers known as Absolute Terror Fields. Years after being abandoned by his father, Shinji Ikari, Gendou's 14-year-old son, returns to Tokyo-3. Shinji undergoes a perpetual internal battle against the deeply buried trauma caused by the loss of his mother and the emotional neglect he suffered at the hands of his father. Terrified to open himself up to another, Shinji's life is forever changed upon meeting 29-year-old Misato Katsuragi, a high-ranking NERV officer who shows him a free-spirited maternal kindness he has never experienced. A devastating Angel attack forces Shinji into action as Gendou reveals his true motive for inviting his son back to Tokyo-3: Shinji is the only child capable of efficiently piloting Evangelion Unit-01, a new robot that synchronizes with his biometrics. Despite the brutal psychological trauma brought about by piloting an Evangelion, Shinji defends Tokyo-3 against the angelic threat, oblivious to his father's dark machinations.

In the distant future, humanity has been driven to near-extinction by giant beasts known as Klaxosaurs, forcing the surviving humans to take refuge in massive fortress cities called Plantations. Children raised here are trained to pilot giant mechas known as FranXX—the only weapons known to be effective against the Klaxosaurs—in boy-girl pairs. Bred for the sole purpose of piloting these machines, these children know nothing of the outside world and are only able to prove their existence by defending their race. Hiro, an aspiring FranXX pilot, has lost his motivation and self-confidence after failing an aptitude test. Skipping out on his class' graduation ceremony, Hiro retreats to a forest lake, where he encounters a mysterious girl with two horns growing out of her head. She introduces herself by her codename Zero Two, which is known to belong to an infamous FranXX pilot known as the Partner Killer. Before Hiro can digest the encounter, the Plantation is rocked by a sudden Klaxosaur attack. Zero Two engages the creature in her FranXX, but it is heavily damaged in the skirmish and crashes near Hiro. Finding her partner dead, Zero Two invites Hiro to pilot the mecha with her, and the duo easily defeats the Klaxosaur in the ensuing fight. With a new partner by his side, Hiro has been given a chance at redemption for his past failures, but at what cost?