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.

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.

Cid prepares his river vessel, Catharine, to take Lisa, Ai, and Yu back to the subway. Mireth provides them with some instant food, but Pochepoke eats half of it in one gulp, prompting Ai to muffle it. Then they take off, but are interrupted by Fungus, back to full size again, riding a giant serpent named Viking. Now, he starts chasing the group. They manage to get rid of him with the help of several secret James Bond-type gadgets and the chocobo’s super kick... but not for long! A surprise attack damages Catherine. Cid goes insane, breaks out a bunch of weird machines, and hammers Fungus until he's flat. Lisa, Ai, and Yu run for the subway, leaving a heartbroken Cid behind. However, Fungus shows up again, only to be killed again by Kaze's Ixion summon. Cid is forced to leave Catherine behind in the explosion. The group catches the subway and escapes.

The gang arrives in a desert that spits out fire. Lisa then uses Chobi's thirst as a way to find an oasis in the desert. However, Herba soon attacks with these bulb type monsters. Kaze shows up, but is eaten by one of them. Lisa then must use her Kigen Arts to help save the kids. She's captured, however, and Ai and Yu try to use Poshipocket to help, but he only spits out random junk. Lisa remembers training with her mother when she was younger and uses her Kigen Arts to an extreme to save them. She accidentally reads the water spirit wrong (the alenium in it reacts) and she lights it on fire. Ai ends up drowning. Kaze uses the Magun from inside the monster and summons Bismark to destroy them all. Lisa uses her Kigen Arts to revive Ai.

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.

Pist, a Lord of Gaudium, enters the picture now. He explains that he has a plan to stop the Magun. Makenshi participates for demonstration. During his Mist attack, Pist captures the bottle in his watergun. However, as Pist turns around, his watergun is broken due to Makenshi's attack. The group arrives in a desert area once again. Lu declares her love for Kaze after saving her life and clings to him. Pist makes an appearance to get rid of them. He uses a water gun that captures weapons. Kaze tries to use the Magun, but Pist uses sandgum in the soil around them to steal it for himself. Lu helps the group escape underground through her sonic beams. Pist catches them and counters all of their attacks. Lu blames Gaudium for sending Omega out. Pist says they had nothing to do with it. Kaze dares Pist to use the Magun to destroy them and Pist does. The gun backfires however and returns to Kaze. Kaze replies that the Magun is his heart and cannot be fired by anyone else.

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.

Lisa, the children, and Chobi come to a town completely made of stone statues, even the buildings. Yu thinks he spots his parents and runs after them in a mansion. They find a room full of giant chili peppers called dead peppers. Chobi eats them and turns red and begins moving rapidly. The group separates. Yu follows the two people and is soon captured by a vine plant. Ai falls down a shaft. Lisa finds a small blue boy named Sagi. He asks why Lisa left him alone. Lisa doesn't understand, but takes him with her. They are captured however as well. Herba brings them together and shows them her Walnut that is a dimensional portal throughout Wonderland to find pieces of Omega. She plans to feed the gang to her Hug Hugs. However, Kaze comes through the Walnut and summons Atomos to suck up the entire mansion. The gang desperately hangs on and Ai has Poshipocket pull out a dead pepper to feed Chobi to save them. Sagi is nowhere to be found and the kids say they never say the boy.

The group is attacked by the same mushroom monster from "Wonderland" but is saved by a herd of chocobos. Chocoimo, Chocobaba's younger sister, is their herder. She explains about the Ciel Chocobo who was the fastest racer and could fly. Chobi finds a pink chocobo he's interested in and decides, with Yu's persuasion, to stay with the herd. Lisa and the kids leave on the subway, but are attacked by Omega's hair. Chobi sees the statue dedicated to the Ciel and sticks his foot in it, giving him armor and the ability to fly. He flies in and saves Yu from certain death. Kaze comes along and summons Titan to revert the hair to crystal form.

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.

Pist gives his plans to the Earl to put the submarine in his Ocean Floor Puzzle which will help give more energy to Chaos. Everyone boards the submarine and explores it. They find Kaze floating in the water and quickly save him. A monster attack the ship, but they use their "blow missles" to destroy it easily. Pist makes and appearance sucks them all into his Ocean Floor Puzzle.

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.

The Frog Hermit appears in front of Cid and turns him into a frog. He then begins sinking the sub into mud where is will eventually end up in Chaos. Frog cannot talk in frog form and cannot control the ship. He must find a way to change from frog to human again. He finds Fungo and believes his instincts will notice he's Cid, but instead he tries to eat him. Cid then is found by Yu and Chobi and is kept as a pet. Ai discovers him and flushes him down the toilet and out into the mud. Cid is sucked into another dimension with Chocobaba and Chocoimo who think he'll turn to a prince if they kiss him. It fails, but the idea may prosper. He heads back to the ship and tries to find Lisa to kiss him. However, she attacks him with her Kigen Arts. They then believe that Cid is an enemy sent by the Earl and search for him. Miles ends up finding Cid and takes him in.

Shiroi Kumo's elder brother Akai Kiri (Madoushi) is reserected by Oscha. The main party lands in the clouds only to be attacked/paralyzed by Madoushi. Kumo appears and we learn Kiri was killed protecting his homeworld from Chaos and he wants to challenge his little brother for the title of the strongest between them. Kumo reluctantly battles his brother, smashing Kiri's sword (thanks to Kaze's help), which contains his very soul. Kiri then tells his brother to finish what he started then he disapears. Kaze and the others are set free and Kumo and Kaze are about to battle when Pist decides it would destroy the ocean puzzle and he transfers the main party and the comodeen to a new area, leaving Kumo standing looking out on the remains of his homeworld

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.

Jane arrives in a desert area. Ai accidentally pulls a Cactuar out of Poshipocket and they try to capture it. It proves too fast and dangerous with its needles for capture however. They chase it into the desert and find a whole mess of Cactuar. Fungo translates that their world was destroyed by an immense force and that they are stuck here. Soon, a giant tidal wave comes to destroy them all. Cid tries his machines to stop it, but it fails. Lisa uses her Kigen Summon to stop it, but it fails. Even, Kaze summons Bismark, but he cannot stop it. Eventually, the Cactuars join together to create a vortex that disperses the tidal wave. They appear unharmed and Jane heads out once again.

Jane now arrives in a very peaceful looking town. Soon, the adults of the group, excluding Kaze, begin to revert back to their childhoods and are overcome by their memories, making them useless. Ai and Yu explore a mansion and find Moogle who is dressed just like Kaze. It turns out that Moogle and Kaze were partners in their other world called Windaria. Moogles pom pom on his head keeps him from going back to his memories and it can also fix the Magun a little bit. They find out that a giant tower that houses the soul of an evil black mage is giving off the memory waves. They plan to destroy it to move on. As the reach it, Kaze chooses to fire the Magun, but it fails to move when Ai and Yu revert back to their memories. Kaze then begins to be affected by the waves, but Moogle snaps him out of it and uses his pom pom to fix Kaze's Magun. Kaze then summons a powered up form of Ixion called Ixion Zero that destroys the tower and everyone goes back to normal. Moogle joins the group.

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.