Fourteen years after the Third Impact, the Earth is a post-apocalyptic wasteland, human civilization is in ruins, and the people Shinji Ikari knows are almost unrecognizable. Trapped inside Evangelion Unit-01, he is recovered from space by Asuka Langley Shikinami and Mari Illustrious Makinami, only to find himself a prisoner of WILLE, a military faction led by his former guardian Misato Katsuragi. Cold and bitter, his former allies view him with suspicion and refuse to support him as he comes to terms with the consequences of his actions. A hurt and confused Shinji is rescued from WILLE by Rei Ayanami and returned to NERV headquarters. There, he meets and quickly befriends the enigmatic Kaworu Nagisa, who offers him warmth and insight into the state of NERV's war with the Angels. But Shinji and Kaworu's brief respite lies on the eve of a new battle, one in which Shinji finds that his enemies are no longer Angels but former comrades. In this bitter confrontation to determine the future of the world, Shinji will learn first-hand that the past truly cannot be undone.

In the Japan of the future, employing androids for various purposes is nothing out of the ordinary. However, treating androids on the same level as humans is frowned upon, and there is constant paranoia surrounding the possibility of robots defying humans, their masters. Those who appear too trustworthy of their androids are chided and labeled dori-kei, or android-holics. High school student Rikuo Sakisaka notices when his house droid, Sammy, starts behaving curiously—she has been leaving the house without his instruction. When he inspects the movement logs in her database, a cryptic line grabs his attention: Are you enjoying the time of EVE? Accompanied by his friend Masakazu Masaki, Rikuo tracks the whereabouts of his houseroid to a cafe called Time of Eve, where it is forbidden for customers to display prejudice against one another. The cafe, Rikuo realizes, is frequented by both man and machine, with no evidence to tell either apart. Each customer—from the cheerful Akiko, to a robot dangerously close to breaking down—has their own story and challenges to overcome. While Rikuo tries to reveal Sammy's intentions, he begins to question the legitimacy of the fear that drives humans to regard androids as nothing more than mere tools.

In the backwater town of Bellforest lives a 14-year-old boy named Renton Thurston. He desires to leave his home behind and join the mercenary group known as Gekkostate, hoping to find some adventure to brighten up his mundane life. However, stuck between his grandfather's insistence to become a mechanic like him and the pressure of his deceased father's legacy, the only excitement Renton finds is in his pastime of riding the Trapar wave particles that are dispersed throughout the air, an activity akin to surfing. Everything changes when an unknown object crashes through Renton's garage, discovered to be a Light Finding Operation—a robot capable of riding the Trapar waves—specifically known as the Nirvash typeZERO. Its pilot is a young girl named Eureka, a member of the Gekkostate, who requests a tune-up for the Nirvash. Their meeting sparks the beginning of Renton's involvement with the Gekkostate as he takes off alongside Eureka as the co-pilot of the Nirvash.

In a post-apocalyptic world, the last remaining human settlement in Japan is the heavily fortified city of Tokyo-3. Fourteen-year-old Shinji Ikari is brought to the headquarters of NERV, an underground organization lead by his estranged father, Gendou. He requests that Shinji become a pilot of an Evangelion, a colossal android built to fight against monstrous and destructive alien creatures known as Angels that wreak havoc on the planet and threaten the survival of the remaining human race. Although initially reluctant, Shinji is swayed by the idea of reconciling with his father, and agrees to aid in mankind's perilous endeavor against its alien threat, as the pilot of Evangelion Unit-01. Thrust into the midst of a dangerous battlefield, Shinji must find the necessary courage and resolve to face against the Angels' incursions before it is too late.