Average 37-year-old Minami Satoru dies and is reincarnated as the most unremarkable creature imaginable-a slime.

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.

Known as a Rogue Hero in the fantasy world Arezard, Akatsuki decided to take upon the request of the defeated Demon King to take his daughter with him. After bringing her back to the world he came from, Akatsuki brought her to join Babel, an academy-like organization that specializes in training those who came from the other world.