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.

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.