The story is set in the far future. The land is ruined, and people build the mobile fort city Plantation. Pilots made inside Plantation live in Mistilteinn, which is also known as the "birdcage." Children live there and don't know anything about the outside world or the freedom of the sky. Their lives consist of fighting to complete missions. Their enemies are mysterious giant beings called Kyouryuu, and the kids use robots called Franxx to fight them. For the kids, riding the Franxx proves they exist. A boy named Hiro is called Code:016, and he was once known as a child prodigy. But he has fallen behind, and his existence seems pointless. Not piloting a Franxx is the same as stopping to exist. One day, a mysterious girl named "Zero Two" appears before him. Two horns come out of her head.