The episode begins with Van Flyheight fleeing from a Guysak on his hoverboard. As he runs, he stumbles across some ancient ruins and decides to hide ontop of a derelict Gojulas. The Guysak pilot, wanting to attack Van just because he happened to be the first person he stumbled across after capturing his Zoid, followed Van and proceeded to attack the ruins. In the pilot's hasty attack, the ruins crumbled and his Guysak was buried under a pile of debris. The landslide also damaged Van's hoverboard, stranding him in the ruins. As he heads inside to look for parts, the bandit's comrades converge on the ruins, piloting a pair of Command Wolves.
In their attack, the bandits open a secret passage in the ruins, which leads Van to a still-operating room, containing two mysterious pods. Curious, he opens one of the pods, revealing a silver Organoid. While it acts aggressively toward Van, he laughs it off and befriends the small Zoid, naming it Zeke, after his father's old Zoid. The introductions are interrupted when the Guysak busts into the room. Fighting to defend his new partner, Van uses some cables to electrocute the Guysak, trying to give Zeke an opportunity to escape. Zeke does not run and instead fights to save Van. Initially no match for the much larger Zoid, Zeke picks up Van and uses his boosters, knocking the Guysak out of the way and escaping into the desert.
The Command Wolves outside notice the small Zoid and also decide to capture it, pursuing it to the ruins of a Shield Liger. Zeke sets Van down in the cockpit, before combining with the ruined Zoid, reviving it. Van swiftly turns around and attacks the bandits, knocking out the two Command Wolves' combat systems, forcing them to retreat. However, as he celebrates, Zeke leaves and returns to the ruins. Remembering the second pod, Van quickly assumes there would be a second "newborn" Zoid (as he thinks that Zeke is a baby Zoid, due to his small size). Instead, as it opens, it reveals a a young girl who he names Fiona, who is later revealed to be an Ancient Zoidian.
- In the opening, when Bul chases Van past the old Shield Liger, the orange canopy is seen, however, when Zeke drops Van in its cockpit later, the canopy is missing.
- In the Japanese version, when Fiona is released from the capsule, she is supposed to be wrapped up in tubes and wires. The English version cuts just as she opens her eyes. Also Van is supposed to run up to her, but that is cut as well.
- In the Japanese version, Omoto Motoko is credited as voicing both Zeke and Fiona. This is only for this first episode, before their regular voice actors.