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.

When the threat of the Angel menace escalates, mankind's defense force is pushed to its limits, with NERV at the forefront of the struggle. Shinji Ikari and his partner Rei Ayanami are assisted by two new pilots: the fiery Asuka Langley Shikinami and the mysterious Mari Illustrious Makinami. With the aid of their mechanized Evangelion units, equipped with weapons perfect for engaging their monstrous opponents, the four young souls fight desperately to protect their loved ones and prevent an impending apocalypse. But when startling secrets are brought to light, will the heroes' greatest challenge prove to be the monsters...or humanity itself?

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.

Following NERV's failed attempt to retrieve the Spears of Longinus and carry out the Human Instrumentality Project, the destruction caused by the Fourth Impact has been largely averted. In a state of disarray, Shinji Ikari, Asuka Langley Shikinami, and Rei Ayanami travel to Village 3—a survivor settlement free from Earth's ruination. There, Shinji slowly comes to terms with his past, developing an entirely different life from his days as an Evangelion pilot. Meanwhile, NERV makes preparations to continue the Instrumentality Project by means of a new Impact. When WILLE's main aerial battleship arrives at the village, Shinji decides to board, believing that he can help by piloting an Evangelion. As new secrets are uncovered and a battle between WILLE and NERV approaches, the future of Earth hangs in the balance. Can Shinji save humanity and the rest of the world one last time?