In a far-off future, humanity has been pushed to the edge of extinction by enormous creatures called Klaxosaurs, forcing the survivors to dwell inside massive fortified cities known as Plantations. Children raised in these cities are trained to pilot giant mechas called FranXX—the only weapons capable of fighting the Klaxosaurs—in male-female pairs. Created solely for the purpose of operating these machines, these children have no knowledge of the outside world and can only justify their existence by protecting their species.
Hiro, a would-be FranXX pilot, has lost his drive and self-assurance after failing an aptitude test. Skipping his class's graduation ceremony, he goes to a forest lake, where he meets a mysterious girl with two horns protruding from her head. She introduces herself by her codename Zero Two, known to belong to a notorious FranXX pilot called the "Partner Killer." Before Hiro can process the meeting, the Plantation is suddenly attacked by a Klaxosaur. Zero Two engages the creature in her FranXX, but the mecha sustains heavy damage and crashes near Hiro. Finding her partner dead, Zero Two asks Hiro to pilot the mecha with her, and together they easily defeat the Klaxosaur. With a new partner at his side, Hiro has been given a chance to redeem his past failures—but at what price?