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.

Yukiteru Amano is a shy middle schooler who regularly keeps track of what he does in his daily life by writing down all of his activities on his phone—a digital diary. Despite having no friends at school, Yukiteru is frequently seen talking to his supposedly imaginary friends Deus Ex Machina, the god of time and space; and Deus' servant, Mur Mur. One day, Yukiteru wakes up and discovers that certain events of his day are preemptively displayed on his cellphone. While initially dismissing it as a coincidence, he slowly realizes that the incidents written in his phone actually take place in the near future. After spending the day benefiting from this new asset, Yukiteru learns that his classmate Yuno Gasai possesses a similar diary. As the two team up to defeat an odd pursuer and head back to their respective homes, Deus Ex Machina explains that they—alongside 10 other contestants—have been drawn into a survival game whose victor will become the deity's successor. With no other options, Yukiteru and Yuno must use their cellphones—now called Future Diaries—to survive this unforgiving battle royale.

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.