In the 21st century, the existence of animal-humans came to light after being hidden in the darkness of history. Michiru lived life as a normal human, until one day she suddenly turns into a tanuki-human. She runs away and takes refuge in a special city area called "Anima City" that was set up 10 years ago for animal-humans to be able to live as themselves. There Michiru meets Shirou, a wolf-human who hates humans. Through Shirou, Michiru starts to learn about the worries, lifestyle, and joys of the animal-humans. As Michiru and Shirou try to learn why Michiru suddenly turned into an animal-human, they unexpectedly get wrapped up in a large incident.
The distant future: Humanity established the mobile fort city, Plantation, upon the ruined wasteland. Within the city were pilot quarters, Mistilteinn, otherwise known as the “Birdcage.” That is where the children live... Their only mission in life was the fight. Their enemies are the mysterious giant organisms known as Kyoryu. The children operate robots known as FRANXX in order to face these still unseen enemies. Among them was a boy who was once called a child prodigy: Code number 016, Hiro. One day, a mysterious girl called Zero Two appears in front of Hiro. “I’ve found you, my Darling.”