The series follows the story of Van Flyheight, a teenage boy who discovers a mysterious girl named Fine, and an Organoid named Zeke. Van discovers that Zeke has the ability to merge with a Zoid, increasing its fighting power, and with that skill, Van and Fine set off to discover the secrets of Fine's past. During their travel, they meet up with a transporter named Moonbay, and a mercenary named Irvine, who initially thwarts their progress, but eventually begins traveling with them. As they travel across the Helic Republic, a new war breaks out, with the group of travelers being caught in the middle of it.
