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.

The theft of the Greater Grail from Fuyuki City leads to a splintered timeline in which the Great Holy Grail War is waged on an unprecedented scale.

Bell Cranell is a rookie adventurer and the sole member of his dirt-poor guild founded by the petite goddess Hestia. Adventurers come from far and wide looking to strike it big in the massive labyrinth known as Dungeon, located beneath the city of Orario. Bell is more interested in picking up girls than Dungeon-crawling, but his reality check comes sooner than expected. Saved from a brush with death by the beautiful, renowned adventurer Aiz Wallenstein, Bell falls head-over-heels and sets his sights on winning her heart, but she's not the only woman he's caught the attention of, for better of worse.

Kousei Arima was a genius pianist until his mother's sudden death took away his ability to play. Each day was dull for Kousei. But, then he meets a violinist named Kaori Miyazono who has an eccentric playing style. Can the heartfelt sounds of the girl's violin lead the boy to play the piano again?