The story is set in the distant future. The land is ruined, and humanity establishes mobile fort cities called "Plantations". Pilots brought up inside the "Garden" 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 Klaxosaurs, and the children pilot robots called Franxx to face off against them. For the children, riding the Franxx is the reason for 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 with horns known as "Zero Two" appears before him.
Humanity's operation to wipe out the klaxosaurs once and for all begins, and APE sends Strelizia to take control of Star Entity, the enemy's biggest weapon. However, the klaxosaur princess has other ideas.
There appears to be no escape from the impending destruction of Earth. But at the end of the world, Zero Two decides that she will keep her promise, no matter what.
Hiro is left shattered with an unresponsive Zero Two, and the children struggle to come to terms with the aftermath. Left all alone to battle for their survival, what path will they choose to take?
The gang heads off to space to fight in what they believe to be the final battle. Meanwhile, Kokoro and Mitsuru stay behind to fight a battle of their own.