Natsuki Subaru, an ordinary high school student, is on his way home from the convenience store when he finds himself transported to another world. As he's lost and confused in a new world where he doesn't even know left from right, the only person to reach out to him was a beautiful girl with silver hair. Determined to repay her somehow for saving him from his own despair, Subaru agrees to help the girl find something she's looking for.

In a war-torn world of elemental magic, a young boy reawakens to undertake a dangerous mystic quest to fulfill his destiny as the Avatar, and bring peace to the world.

Japan has been invaded and conquered by the Britannian Empire. Japan is now known as Area 11 and its citizens known as Elevens. The Britannian Empire takes away Japan's autonomous power and imposes its rule through the use of Knightmares. The Empire's rule has never faltered, but cracks have begun to show...

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.