Plot
FF:U follows the story of Ai and Yu Hayakawa, 12-year-old twins who travel into Wonderland, a mysterious parallel dimension, in search of their missing parents. Other main characters include Lisa Pacifist, a 22-year-old woman whom Ai and Yu encounter in the Subway as she becomes their protector while helping them search for their parents in Wonderland. The series is divided into two major sections, defined by the main method of transport the protagonists are utilizing. The first section of the series sees the group using the Ghost Train to reach a part of Wonderland, crossing paths with Kaze as he has no memory of his past save Makenshi, who aids the Lords of Gaudium who attack them. The group also encounter fragments of a destructive being named Omega, which is after the Ghost Train's power source to become whole. Meanwhile, the story from the antagonist's view is periodically revealed with Earl Tyrant's discussion with his lords. Earl is the embodiment of Chaos and is seeking the fragments of Omega to possess a power equal to the Unlimited, beings of immense power like Kaze and Makenshi who could destroy him.
The second section of the series sees the protagonists join up with the rebel faction, the Comodeen, and board the submarine, Jane, which is bound for Telos, the only place in Wonderland that has a natural deposit of the gravity-defying Flying Water. Both parties sought the substance: the Comodeen to power their airship Silvia to reach Earl's flying fortress Gaudium and the Earl's forces using the substance to contain Omega's power. The series climaxes when the Earl himself makes a move on the Comodeen, destroying Jane and capturing the protagonists in his true form: Chaos Tyrant. It was then that the Earl's right-hand man, Oscha, reveals that Ai and Yu were spawned from Chaos in the aftermath of Kaze and Makenshi's sending their adoptive parents to Wonderland. With only Omega's heart, Clear, remaining and fused with his Flying Water suit into a crystal, the Earl intended to absorb the Hayakawa twins as well to increase Chaos's power from their experiences. Luckily, Lou Lupus and Moogle come to their friends' aid as the Earl killed the former. Confronted with Chaos Tyrant, Kaze and Makenshi sacrifice themselves to destroy the Earl, thus ending his reign of terror over Wonderland while Lisa and the Hayakawa family were found by the Comodeen. They are also two mysterious figures that the group encounter, "Black Wind" (黒き風) and Makenshi (魔剣士), beings of incredible power who each lost their world before coming to Wonderland.