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!
Part of Fiona's memory comes back and realises she is an Ancient Zoidian but cannot tell Van yet. On their way to the capital Van and his friends are attacked by bounty hunters in Hel Digunners who are after Zeke.
Upon entering a town Van and his friends find out Prozen has given orders to arrest Rudolph, telling everyone he is an imposter. Van, Irvine and Rudolph are captured but a familiar Imperial guard helps them escape.
Van and his friends stop at a deserted town and are mistaken for bandits who are stealing medicine from sick children. Irvine mobilises the Command Wolf with Van and the Blade Liger to steal back the medicine.
Van and his friends come upon an Imperial Base which houses the Eisanback Black Redler unit. Believing that the Rudolph that is with Van is an imposter, they attack despite Major Schuboltz recognising him as the real Prince. Outnumbered they are saved by two mysterious Storm Sworders.
Van and his friends are saved from the Imperial Army by McMann, Moonbay's former lover. It appears Moonbay still has feelings for him too so Van, Irvine, Fiona and Zeke try to sneak away and leave her there, but she finds out.
Van and his friends arrive at Guygalos and are taken to Prime Minister Homalap, one of Rudolph's allies against Prozen who has been doing research on Zoid cores. Van and Fiona investigate and the Death Saurer awakens as if it senses Fiona's presence.
Van and his friends arrive at Guygalos and are taken to Prime Minister Homalap, one of Rudolph's allies against Prozen who has been doing research on Zoid cores. Van and Fiona investigate and the Death Saurer awakens as if it senses Fiona's presence.[
Prozen unleashes the Death Saurer, which quickly begins to destroy everything in it's path including the combined force of the Imperial and Republican army. It is up to Van to destroy the Death Saurer and save the world.
While travelling Van comes across a Republic bomb disposal squad disguised as bandits. Van tracks them down with the help of Investigator Dorset, a master pilot of the Gun Sniper, but Dorset isn't as he seems...
Van and Fiona investigate newly discovered ruins only to find everyone in the town gone. The townsfolk are being held captive by Rease and her organoid Spekula in their Double Sworder
While investigating a mysterious Zoids, Van and Fiona meet Lieutenant Thomas Schobaltz in his Dibison who immediately takes command of the operation but causes more trouble than good.
Thomas and Van investigate a group of bandits who are actually excavating ruins for a man called Hillz and his red organoid Ambient. While trying to stop them Van and Thomas are attacked by Stealth Kat's.
Sleeper Zoids are being stolen and stripped of their Zoids cores aboard a Whale King. While on the Whale King, Van meets Irvine who quickly swaps sides to help Van capture the thieves.
News arrives that Republic and Imperial bases have been destroyed by Raven and Shadow whom were thought dead. Van confronts Raven as he is about to attack their base and a fierce battle erupts.
Rudolph and his fiancé, Mary-Anne, take a short break from their duties to visit Van, Fiona and Thomas but their holiday is interrupted by Stinger who is trying to kidnap Rudolph.
Two experimental Storm Sworders are stolen but thieves must return to the base to collect the combat data. Van and his friends are no match for the enemy until Rosso and Leola arrive to help out.
Raven is moved away from the Geno Saurer cocoon but it hatches and the Geno Breaker is born! Irvine attacks Raven and his new Geno Breaker but the Command Wolf is critically damaged
Van, Irvine and Thomas begin training for this next battle with Raven using a new formation. Before Raven can get to Van he is challenged by Rease in her Geno Saurer.
Raven attacks the base where Van and his friends are, together they try their new formation out but are quickly beaten. Van must face Raven alone but is pushed off a cliff during the battle.
Van's becomes frustrated with Blade Liger's poor performance but realises that it's his skills have improved. To improve the Blade Liger, Van makes some modifictations.
Moonbay enters the Guylos Grand Prix using a modified Sinker. Meanwhile Van and Thomas are hunting The Phantom - an assassin who has been hired to kill Rudolph!
A meeting is held by the Guardian Force to discuss how to defeat Rease, Hillz and Raven once and for all.
Irvine is arrested and his Lightning Saix confiscated under suspicion of weapons smuggling. To get his Lightning Saix back and clear his name Irvine must battle the Storm Sworder!
Van and Thomas investigate the destruction of numerous Zoids after they are challenged to a battle by a mysterious group. Thomas is attacked and defeated and Van must battle a giant three headed Atack kat!
Fiona begins to notice a feeling she hasn't had since the Death Saurer was awoke, Hillz, overseen by the mysterious Dark Kaiser, have created a new Zoids - The Death Saurer
With the Death Stinger awakened, Hillz loads it aboard the Hummer Kaiser - a huge hammerhead, and flies high above the Earth. Irvine and Thomas are sent to destroy it in specially modified Storm Sworders!
While Van battles Rease, the Death Stinger surfaces in New Helic City and quickly destroys it. The Guardian Force retreat to a lake which holds the largest Zoids ever created - Ultrasaurus!
Hillz begins to attack the Ultrasaurus before it is able to be awakened so Van, Irvine, Thomas, Karl and Rob are forced to hold off the Death Stinger.
With the Ultrasaurus operationalit must now be equipped with a specially created Gravity Cannon on a secret island base. Hillz sends every Zoids he has to stop it.
The Gravity Cannon needs one test shot to confirm that it works, but that would reveal it's position. Using a Hammerhead and Ptera Strikers, Van and friends must defend their position.
The Death Stinger continues to destroy everything in ti's path, it is up to Van, Irvine and Thomas to stop it long enough for the gravity cannon to launch it's attack. The Death Stinger destroys the first shot but the second is a direct hit!
The Death Stinger, crushed by the massive force of the gravity cannon comes back to life and escapes underground but with most of it's weapons destroyed. Van and Irvine chase the Death Stinger and have it trapped when it mysteriously disappears.
Fiona reappears in front of the Dark Kaiser who is actually Prozen fused with the Zoids core of the Death Saurer! Prozen takes Fiona to Zoids Eve to reawaken her and begin the end of the world! The Death Stinger confronts the Blade Liger.
The Death Stinger is resurrected by Zoids Eve then fuses with the Zoids core that is part of Prozen. With both cores fused, creating the most powerful Zoids core ever, it is implanted into the Death Saurer.
The Ultimate Death Saurer has been resurrected and the combined armies of the Republic, Empire and Guardian Force fail to even slow it down. Van and Raven try and combined attack but fail instantly.
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