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.

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 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.