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.

Enticed by its rumored wealth, Cid Kagenou happily tags along with his sister, Claire, on a trip to the infamous Lawless City. The region is ruled by three monarchs: Yukime, the Spirit Fox; Juggernaut, the Tyrant; and Elisabeth, a dormant progenitor vampire known as the Blood Queen. Hunting Elisabeth down serves as the perfect opportunity for Claire to prove her true mettle. On the other hand, Cid has different objectives—sneaking away from Claire's sight, collecting as much loot as possible, and making Shadow's glorious entrance at the perfect moment. As Elisabeth's awakening draws near, her subordinate Crimson enacts a treacherous plot, sending the town into a frenzy. Searching for her now-missing brother, Claire finds an unexpected ally in Mary, a vampire hunter, and the pair hurry to the Crimson Tower—the home of the Blood Queen. Meanwhile, Beta and a small team of Shadow Garden recruits also arrive at the Lawless City. As the key players converge on the Crimson Tower, the stage is set for a grand confrontation under the crimson moon.

Yoshino Takigawa, an ordinary teenager, is secretly dating his best friend Mahiro Fuwa's younger sister, Aika. But when Aika mysteriously dies, Mahiro disappears, vowing to find the one responsible and make them pay for murdering his beloved sister. Yoshino continues his life as usual and has not heard from Mahiro in a month—until he is confronted by a strange girl who holds him at gunpoint, and his best friend arrives in the nick of time to save him. Yoshino learns that Mahiro has enlisted the help of a witch named Hakaze Kusaribe to find Aika's killer. However, the witch has been banished to a deserted island due to infighting within her clan. Hakaze's brother, Samon, selfishly desires to make use of the Tree of Exodus' power, in spite of both his sister's opposition and the impending peril to the world. With Hakaze out of the picture, it is now up to Yoshino and Mahiro to help her save the world, all while inching ever closer to the truth behind Aika's death.

The year is 2071. Humanity has been pushed to the brink of extinction following the emergence of man-eating monsters called Aragami that boast an immunity to conventional weaponry. They ravaged the land, consuming almost everything in their path and leaving nothing in their wake. To combat them, an organization named Fenrir was formed as a last-ditch effort to save humanity through the use of God Eaters—special humans infused with Oracle cells, allowing them to wield the God Arc, the only known weapon capable of killing an Aragami. One such God Eater is Lenka Utsugi, a New-Type whose God Arc takes the form of both blade and gun. Now, as one of Fenrir's greatest weapons, Lenka must master his God Arc if he is to fulfill his desire of wiping out the Aragami once and for all. The monsters continue to be born en masse while the remnants of humanity struggle to survive the night. Only God Eaters stand between the Aragami and complete and total annihilation of the human race.