The story is set in the distant future. The land is ruined, and humanity establishes the mobile fort city Plantation. Pilots produced inside Plantation live in Mistilteinn, also know as the "birdcage." Children live there knowing nothing of the outside world or the freedom of the sky. Their lives consist of battling to carry out missions. Their enemies are mysterious giant lifeforms known as Kyouryuu, and the children pilot robots called Franxx to face off against them. For the children, riding the Franxx proves their existence. A boy named Hiro is called Code:016, and he was once known as a prodigy. However, he has fallen behind, and his existence seems unnecessary. Not piloting a Franxx is the same as ceasing to exist. One day, a mysterious girl known as "Zero Two" appears before him. Two horns grow out of her head.

Hachimitsu Academy, once an all-girls school, has become co-ed, and teen Kiyoshi is one of five boys to enroll. When he is caught peeping, Kiyoshi is sent to the schools prison, where his punishment is carried out.

Ichigo Kurosaki's school is attacked by strange spirits called Unforgiven (Togabito), revealed to have escaped from Hell, and Rukia Kuchiki and Renji Abarai are sent to investigate. Ichigo's family is targeted by the Unforgiven, who are led by Shuren, and Ichigo's younger sister Yuzu Kurosaki is abducted. An Unforgiven named Kokut? saves Karin Kurosaki from being abducted as well, and convinces Ichigo to accompany him and the Soul Reapers to Hell to save her. When they are attacked by monsters called Kushan?da, the guardians of Hell, on the journey, Ichigo's Hollow mask begins to spontaneously manifest. Kokut? warns him to avoid using his mask lest he lose control and hollowfy entirely, and tells him that the Kushan?da torture Unforgiven for their sins by killing them, as Unforgiven continuously revive, and that spirits killed in Hell become Unforgiven themselves.

To prevent a ninja from reviving a powerful demon that could destroy the world, Naruto teams up with a young priestess, despite her vision of his death.