Erupting without warning to shatter the tranquility of the Japanese nightlife, an ominous pillar of darkness descends from the heavens. Two fearsome creatures proceed to annihilate the warships and attack aircraft that come to greet their arrival. Watching the transpiring events in amazement are Mary and Joe Hayakawa, two research scientists who would later make the first trip to the world beyond the pillar. A second trip to Wonderland would lead to their mysterious disappearance. Twins Ai and Yu seek out the hidden subway that leads to the mystifying world that lies beyond the dark column, in hopes of finding the whereabouts of their missing parents. Joining them on their journey is a woman named Lisa.

Rescuing the twins and their companion from danger, the man in the black cloak continues his search. The children name the mysterious traveler Kaze, in homage to the winds that accompany him on his path. Kaze’s exploits do not escape the watchful gaze of the tyrannical overlord who rules these lands. The tempestuous Earl Tyrant orders the removal of these intruders from the Outside World, dispatching the lumbering Fungus, one of the Four Lords of Gaudium, to attend to this troublesome matter.

Meanwhile, the twins are elsewhere, busy getting to know their new companion Lisa. However, they’re interrupted by the appearance of the strange Chocobo they’ve dubbed Mr. Birdy. Mr. Birdy leads the travelers into a bizarre forest, where they are greeted by Chocobaba, who informs them that Mr. Birdy’s real name is Chobi. Unfortunately their pleasantries are cut short with the arrival of Fungus and his minions, but Kaze and his Magun arrive in the knick of time to fend off these fiends.

Riding the mysterious ghost train to its next destination, Lisa and the twins find themselves in a strange new town full of lifeless, apathetic people. Noting that everything seems to be made of fruit, Ai sits down for a bite of the nearest wall, but soon finds herself hot on the trail of a thief who makes off with her backpack. The chase continues throughout the town, but the crafty thief escapes his pursuer, and the townspeople are unsympathetic to her plight. Despairing over the situation, Ai ends up meeting Fabula, who gives her the strange Poshepocket as a bit of a consolation gift.

Earl Tyrant, meanwhile, is not pleased by the results of Fungus’ previous fight with the Magun-wielding Kaze, and orders another of his henchmen, Herba, to go and play with the man of the black wind. Arriving with her minions, she uses her henchman to torment the town, and brings Yu, Chobi, and Lisa into a laughing fit with her spores. However, with Kaze’s formidable arsenal and Ai’s new Poshepocket on the scene, playtime for Herba turns out to be a little more than she can handle.

Racing desperately to catch the ghost train before it departs to the next destination, Lisa and the twins wind up watching helplessly as their mode of transportation leaves them behind. Stranded, fate seems to intervene when the thief from earlier appears and leads the stranded travelers to the secret base of the Comodeen - an armed resistance organization training to liberate Wonderland from Earl Tyrant’s rule. It is here that the group is introduced to Knave, the leader of the Comodeen, along with Miles, and the talented inventor Cid.

The gang gets on the subway with Kaze this time. They find a mysterious girl named Lu onboard. Her world was destroyed by a monster named Omega. They explore the train and find its core. Suddenly, Omega's claw attacks. Omega was broken into pieces and scattered all through Wonderland. Lu gets a mirror from Poshipocket and transforms into a werewolf that can fire super sonic beams. She fights Omega but is thrown from the train. Kaze summons Ifrit to destroy the claw and return it to crystal form. Lu is returned by Kaze and they all continue.

Now, the group comes to a factory place where all the workers work constantly. They build up parts and then take them down again, making their work eternal. Oscha attacks by making the workers build the machine completely which is a giant gold robot that looks like Oscha. The group fights, but cannot destroy it. Kaze summons Odin to pierce through its armor and it is destroyed. Oscha escapes. Kaze leaves the group on their own and Lu decides to leave as well with a tearful goodbye to the children.

Fungus is disappointed because all the other Lords, including Makenshi, have found a piece of Omega. Oscha tells Fungus that he can find a piece of his old world and become strong again. The group happens to arrive in this world and Fungus uses its powers to make him large and powerful. Lisa's Kigen Arts are no match. Kaze comes and uses his Magun to summon Phoenix and Ixion, but they are no match for Fungus' regeneration powers. In the end, Kaze is defeated

The twins and Chobi are captured by Fungus and sent on his ship. He plans to sacrifice them to the Earl. Makenshi comes along to warn Fungus about his certain destruction. Kaze and Makenshi spot each other and fight. Kaze cannot fire the Magun. Makenshi gloats that Kaze cannot fire the Magun at will anymore. Fungus grows once again and ties Chobi and the twins to his giant club. Crux comes along and uses a black mold on the world, killing the fungus. Fungus' powers become useless. Kaze uses the Magun to summon Meteor Master to destroy Fungus for good. Fungus respects Kaze in the end and dies with honor.

Lisa, the twins, and Chobi get on the subway yet again. This time, Omega's tail comes to attack them, and without Kaze, the train is destroyed as Omega extracts the core of the train for itself. Fabula decides to intervene and saves the group from death. They then find the Comodeen again and learn that they are searching for flying water to power Cid's new airship, Cynthia. They plan to use his submarine, Jane to get on the other side of the world to find it in Teros.

Jane arrives on top of land, unmovable. A giant Japanese mermaid named Samosan gives them a challenge. Three of them shall try to answer her riddles. Each one they get wrong, they will be sent closer to Chaos. If they cannot solve a riddle, they shall be consumed by Chaos. The Commander, Miles, and Lisa go up in that order. She asks riddles that seem easy, but turn out to be only knowledeable to those that live in Wonderland. The Commander and Miles lose and are turned to water. Lisa tries, but misses the first two. She tries to stall by laughing and smiling to Samosan for the last answer, but Kaze tells her that it's all a lie. Lisa then challenges Samosan's quesitons saying that there are no answers. Samosan, knowing she lost, tries to destroy the cube they inhabit. With their doom inevitable, Lisa uses her life energy to summon a Kigen Dragon that saves the sub. However, she survives, but was knocked unconscious. Ai and Yu call her attack a Kigen Summon.

Ai and Yu get into an argument and Ai is accidentally thrown from the sub. She meets up with a boy named Clear that wears flying water. He claims he cannot be touched or he could break them. Kaze comes along to protect them from monsters sent by Earl to capture Clear. Kaze says that Clear is dangerous, but Ai doesn't care. The monsters return and Kaze can't beat them because his Magun won't move. Clear tries to save Ai and she accidentally pulls his glove off. He destroys the entire cube as Kaze saves Ai and the ship barely escapes.

Jane lands up in Gaudium on top of one of their protective satellites. Chobi turns into his Ciel form and flies to the castle with Yu on top of him. Chobi runs off and Yu goes to find him. He meets up with the Earl who seems to befriend him. Yu discovers that his parents are actually working for the Earl and that they are the ones cooking his food and working on Chaos. Makenshi comes along. Kaze tries to use the Magun, but it won't move. Makenshi uses his mist dragon to release Jane from the grip of the satellites as Chobi saves Yu from the castle and flies them onboard Jane. Yu, however, is far from okay.

Pist finally has perfected his ultimate weapon that will counter Kaze's Magun called Blue Elenium. Jane reaches Teros and the group meets Bumbol who weaves the clothes that Clear was wearing out of Flying Water. They also reunite with Lu who has a cape of Flying Water allowing her to fly. Cid sends out teams to retrieve the Flying Water when Pist attacks and begins to destroy them. Kaze uses his Magun to summon Phoenix, and with the help of Moogle, it becomes Giga Phoenix. However, Pist uses his Blue Elenium to take control of Giga Phoenix and has him destroy the field of Flying Water and attack the gang. However, Makenshi shows up and uses two Mist Dragons to destroy Giga Phoenix and sends Pist running. Everyone except Kaze and Moogle run for the sub to escape. Kaze intends of facing Makenshi to a final showdown.

As expected, Kaze's Magun fails once again and Makenshi summons two Mist Dragons to run Kaze through. However, Makenshi actually returns Kaze to the sub with everyone else and reveals that he's really a spy working against the Earl. He also reveals that Kaze has been helping the Earl without his knowing because every shot from the Magun actually feeds Chaos. Makenshi takes his leave, refusing the offer to join the Comodeen. Pist returns to his lair, licking his wounds. Makenshi finds him and plans to silence him for good. He turns Pist into Mist and uses him to destroy his Ocean Floor Puzzle, setting Jane free from its clutches. As things begin looking up, the Earl begins to take matters into his own hands as he confronts Jane himself. He turns into a giant red monster, Chaos, and destroys Jane. The fate of everyone becomes unknown.

The Earl now has everything that he needs to finally revive Omega, and things take a turn for the worst. It appears as though everyone has followed right along with his diabolical plan, it perhaps there is no way to stop him. However, self-sacrifice may be the key to finally ending his scheme for good.