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.
The land has fallen into ruin, and children represent the last hope for humanity. One of them, Hiro, fails to live up to that purpose and decides to walk away from it all.... until he meets a girl with horns.
The parasites struggle to come to terms with Hiro being the one who piloted Strelizia. Even Hiro can't really believe it himself. Things come to a head when he's ordered to participate in a mock battle.
After their failure in the startup trial, things are awkward between Ichigo and Hiro, who decides to ask to ride with Zero Two again.
With the squad still feeling the aftershocks of the previous mission, things come to a head as the leaders run out of patience and decide to summon Strelizia back to the front lines.
It's time for Plantations 13 and 26 to start kissing, and the squad prepares for the huge battle this will cause. They also have to get used to Hiro being Zero Two's partner, and so does he.
Ichigo, Goro, and the rest of Squad 13 engage in a battle far more dangerous than any they've fought before, all while having their mind preyed on by the fact that this will be Hiro's third ride with Zero Two.
Squad 13 is given a much-needed break after defending the kissing plantations in a fierce battle. They head to an unexpected location and find something even more unexpected.
The boys get caught in a compromising situation, causing a rift within Squad 13. Will they be able to bridge this divide? And how will Zero Two react to the most human of spats?
Soon after Goro becomes keenly aware of his feelings, he is put in a perilous situation. How will he and Ichigo respond in this do-or-die scenario?
APE decide to give Squad 13 a reward in order to accelerate their development. The ceremony is held in a place Zorome has always dreamed of living in, and there he meets someone he has always wanted to meet.
Squad 13's growth has been remarkable, but Chlorophytum's score keeps going down. With this in mind, Nana and Hachi propose a partner shuffle, which finds an unexpected taker
Squad 13 heads back to the Garden for testing, with Zero Two's emotional state worsening by the day. They run into Nine Alpha, who offers some insight about her, but the most revealing words come straight from the horse's mouth...
In the deepest, darkest parts of a forest lived a strong and beautiful beast princess. Beckoned by the moonlight, she wandered into a land of humans, and in the moonlit garden of a small castle, she fell in love with a prince.
The information regarding Hiro's condition changes the entire dynamic of Squad 13, much to Zero Two's chagrin. She only wants to speak to Hiro, but people stand in her way one after another.
The fierce battle to take the Grand Crevasse begins, and Hiro is forced to watch from the sidelines. Zero Two may have left, but Squad 13 is still concerned about the way she fights.
The parasites' living situation has changed drastically after the battle for Gran Crevasse. Zero Two's attitude toward them seems to have changed drastically, too.
Having seized Gran Crevasse, emissaries are sent out to demand the surrender of the klaxosaurs' leader. Meanwhile, the Nines visit Squad 13, and there a shocking discovery is made.
Squad 13 is told they will be abandoning Mistilteinn soon, and they decide to go out with a bang by making one last memory of their lives there.
Dr. Franxx confronts the APE brass about what they did to Kokoro and Mitsuru, and their attitude makes him reflect on his past, the choices he and humanity made, and the path they took.
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.