A warrior from a post-apocalyptic future travels to 1997 to protect an AI scientist being hunted by an unfeeling — and indestructible — cyborg.

Yukihira Souma's dream is to become a full-time chef in his father's restaurant and surpass his father's culinary skill. But just as Yukihira graduates from middle schools his father, Yukihira Jouichirou, closes down the restaurant to cook in Europe. Although downtrodden, Souma's fighting spirit is rekindled by a challenge from Jouichirou which is to survive in an elite culinary school where only 10% of the students graduate. Can Souma survive?

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.