While being chased by desert bandits, a young boy seeks refuge in some old ruins where he finds an Organoid which he names Zeke, and a mysterious girl named Fiona. While trying to escape the ruins, Zeke revives an abandoned Shield Liger and helps Van and Fiona get away.

After escaping the desert bandits, Van returns to his village with Zeke and Fiona. Unfortunately the bandits follow, attacking the village and kidnapping Van's sister. Fiona and Zeke help Van face the bandits, and Fiona displays a mysteriously power.

Separated from Zeke and the Shield Liger, Van and Fiona are rescued by Irvine, a Command Wolf pilot who offers shelter but secretly aims to capture Zeke. Van and Fiona discover an ancient tablet that triggers Fiona’s memory of something called “Zoid Eve”, prompting them to search for its meaning.

Van and Fiona encounter Irvine again, but this time he has been hired to protect a village from bandits. When the bandits turn out to be the Desert Alcabaleno Gang, the same group who gave Van trouble earlier, the group decides to lend their aid.

Van and Fiona meet Moonbay who drives a Gustav carrying cargo across the desert. The group is forced to flee when they are attacked by sleeper Zoids and must reluctantly join forces with Irvine to defeat them.

Van and his friends are mistaken for Imperial soldiers by a Helic Republic patrol and captured, their Zoids impounded. Irvine secretly breaks himself and Van out, and they rush to reclaim their Zoids.

Fiona and Moonbay are recruited by the Republic army to haul explosive cargo intended for detonation at Fire Bridge. Meanwhile, a standoff occurs at Red River between the Republic and the Empire, which only Van and Irvine can help resolve.

Captain Herman gives Van and friends a lead on the search for Zoid Eve and they head toward the Republic capital. Meanwhile, the Desert Alcabaleno Gang plans to capture Zeke to regain the favor of the Imperial army.

Van and his friends wanter into a mysterious valley where all of their Zoids including Zeke begin to act weirdly. The Zoids have been affected by a rarehertz, a strange pulse that has made Zeke insane!

Van finds an old man in a hut frozen in ice while looking for the legendary Dr.D. It turns out the man in the ice is Dr.D and he knows about the "Zoids Eve" but will only tell Van if he helps him build a snow machine.

To get to the capital Van and his friends must cross the misty mountains of Iselina. While staying at a village they are attacked by the Desert Alcobolino Gang led by Leola, who used to live in the same village they are attacking.

Van and Zeke are wanted by the Republican Army after an entire battalion owas destroyed by a young boy called Raven and another organoid called Shadow. Van meets Raven and tries to stop him from destroying more Zoids.

The Imperial Force attacks Fort Cronos but they are trapped by the Republican Army. The Fort, along with half the Imperial Force, is blown up. During the attack Van challenges Raven to another battle.

Van and Moonbay travel into a volcano crater in search of Zoids Magnite to help heal Zeke after Van's loss to Raven. Irvine re-equips his Command Wolf and challenges Raven to a battle.

Major Schobaltz attacks the Republican base, Mountossa, only to be forced back by Captain Herman in the unstoppable Gojulas

Van and his friends arrive in New Helic City, capital of the Republic. During a victory parade Van helps an Imperial soldier escape a mob, only to haev the soldier attack the city in an experimental Command Wolf.

Captain Herman goes missing while inspecting a suspicious iceberg - which is actually a disguised Imperial force attacking from the Sea instead of on land. During the attack Raven appears and challenges Van to a battle.

Just as New Helic City is about the be overrun by the Imperial army, the Emperor dies and his nephew Rudolph demands a cease fire. Meanwhile Raven and Van continue the fight to the death!

Prozen plans to kidnap the new Emperor Rudolph and replace him on the throne but Rosso kindaps him first and escapes. Meanwhile Van and his friends continue to look for "Zoids Eve".

Arriving at the Gurill ruins, Van and his friends are attacked by sleeper Rev Raptors placed there by Prozen, who has already removed the secrets from inside the buildings.

Rudolph meets Van and his friends when he wanders away from Rosso and Leola to find food. Unfortunately Prozen has sent Raven and his Geno Saurer to kidnap Rudolph. Rosso and Leola, in their Iron Kong, attack Raven so Rudolph can escape with the others.

Rudolph asks Van to take him to the capital and on the way train him to be a warrior. Raven attacks Van and, during the fierce battle, the Geno Saurer critically hits the Shield Liger with it's charged particle gun.

With the Shield Liger seemingly destroyed, Van and Irvine must fight together to rescue Rudolph after he was taken by Raven and handed over to Mettlenich.

Fiona units with Zeke and they enter the Shield Liger causing a cocoon of light to surround the fallen beast. An evil bounty hunter looking for Rudolph appears and drugs Irvine, Moonbay and Rudolph while Van is away.

Using his paralysis drug, Stinger has captured Moonbay, Irvine and Rudolph and is planning to kill them. Van arrives with a Red Guysack that he captured but is defeated by Stinger is his Zaber Fang. Just then the cocoon around the Shield Liger breaks and the Blade Liger is born!