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.

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.