In a post-apocalyptic future, humanity retreats into mobile fortress cities called Plantations to escape the relentless onslaught of giant, biomechanical monsters known as Klaxosaurs. Society is stripped of natural reproduction and culture, with children raised solely to pilot giant mechs called Franxx in male-female pairs. These children, known as Parasites, view piloting as their only purpose and hold Supreme Commander Nana and the mysterious adult rulers, APE, in near-religious reverence.Hiro, a gifted child nicknamed Code:016, suffers a psychological block that prevents him from synchronizing with a partner, branding him a failure destined to be washed away. During a ritualistic renaming ceremony, he encounters Zero Two, an infamous elite pilot with horns and part-Klaxosaur blood, rumored to kill all her partners after three rides. Desperate for meaning, Hiro willingly rides with her, surviving the fatal threshold and earning the moniker "Darling." Their burgeoning bond grants them immense combat power, though Zero Two's erratic behavior and human-like desires increasingly alienate the other Parasites.Assigned to Squad 13—a rebellious experimental unit including Ichigo, Goro, Mitsuru, and Kokoro—Hiro and Zero Two fight fiercely on the frontline. As the squad forms deep emotional ties, defying APE's cold pragmatism by experiencing love, puberty, and marriage, dark truths begin to surface. Hiro discovers that he and Zero Two actually met as abused children in a laboratory, where he promised to make her human. Meanwhile, the squad learns that Parasites are rapidly aged and discarded, and that APE's true leaders are actually the Virm, an ancient alien race bent on assimilating all organic life in the universe.The conflict escalates when the Klaxosaur Princess—the ancient ruler of the monsters—captures Hiro, revealing that the Klaxosaurs are Earth's original inhabitants fighting a desperate war against the Virm invaders. Realizing the Virm are the true enemy, humanity's remnants and the Klaxosaurs form an
uneasy alliance. Zero Two merges with the massive Strelizia True Apus mechs to fight the Virm fleet in low Earth orbit, while Hiro pilots her consciousness to the edge of the galaxy in a
suicide mission to destroy the Virm home planet.Victorious at the cost of their physical lives, Hiro and Zero Two's souls promise to return. Years later, their reincarnated spirits are born anew on a healing Earth, finally reuniting beneath the cherry blossoms as children of a truly free world.