Plot
Prior to the series there was war between the Guylos Empire and the Helic Republic which ended in a ceasefire. The series starts with Van being chased by a group of bandit Zoid pilots and discovering the organoid Zeke in ruins near his village. Zeke revives an abandoned Shield Liger, which Van uses to fight off the bandits. Returning to the same ruins, he discovers Fiona, a mysterious girl with no memories. When Van returns to his village, the gang of bandits return and try to take Zeke from Van. To keep his village safe, he leaves with Fiona. Van hears Fiona speak of something called Zoid Eve and decides to help her find it in hopes that it will help her memories return. Shortly afterwards, they meet Irvine. Initially, Van and Irvine are enemies because of Irvine's attempts to steal Zeke, but they end up traveling together when they meet Moonbay. Van has to travel with Moonbay because she blew up her cargo to help him.
Later, the four arrive at one of the Republic's army bases and help to stop an invasion by the Empire orchestrated by Prozen. Afterward, Van, Fiona, Irvine, and Moonbay try to stay out of the war. However, Van is drawn back in when he meets the Guylos ace pilot Raven, quickly developing a grudge after witnessing Raven's brutal nature. They fight, but Van proves to be no match for Raven. Van later challenges Raven again, losing a second time, and Zeke suffers near-fatal damage, but Van manages to save him. During this time the Imperial army is marching farther and farther into Republican territory but are eventually stopped by the Republic's new weapon, the Gojulas. Van and the others eventually reach the Republic's capital in hopes of finding information about Zoid Eve, but are caught up in the Empire's surprise assault on the city. During the battle Van is finally able to defeat Raven, the latter destroying his own Zoid as he attempts to pierce the Liger's energy shield.
The war is stopped when the Empire's crown prince Rudolph orders a ceasefire, but Prozen refuses to give up on conquering the Republic and attempts to assassinate the prince. His attempt is foiled by the bandits Rosso and Viola, who kidnap the prince for ransom. However, Prozen announces that the prince is dead, seizing control of the Empire for himself. Prozen finds the remnants of legends about an apocalyptically powerful Zoid, the Death Saurer, and attempts to clone it. As a byproduct of the cloning research, the Geno Saurer is created and given to Raven. Raven uses the Geno Saurer to destroy Van's Shield Liger, but Zeke and Fiona later revive the Shield Liger as the Blade Liger.
It is revealed that Fiona is actually an ancient Zoidian that existed before humans came to the planet Zi. Rudolph joins Van and his friends, who try to take him to the Empire's capital Guygalos to stop Prozen from taking over the Empire and restarting the war. When Rudolph resurfaces, Prozen claims that he is an imposter, manipulating the imperial forces into fighting against the prince and his friends. Eventually, Van faces Raven again, and after an extremely difficult battle destroys the Geno Saurer. Raven survives thanks to his organoid Shadow.
Van and his friends succeed in returning Rudolph to the capital, but Prozen unleashes his cloned Death Saurer. The Death Saurer goes on a rampage and almost destroys the capital, with the joint forces of the Empire and Republic powerless to stop it. Van is able to destroy the Death Saurer using what he learned fighting against the Geno Saurer. Prozen, riding the Death Saurer, appears to be killed in the process. Rudolph is then crowned the emperor and peace finally begins between the Empire and Republic, but Van and Fiona don't take part in the celebration and instead leave to find Zoid Eve.
Guardian Force
Two years after the Death Saurer's defeat, Van is shown to have joined the Helic army. On a trip home he meets up with Fiona, now a researcher for the military, and the two decide to try to find the Zoid Eve again. Van and Fiona are assigned to a joint task force, the Guardian Force, formed by the Empire and Republic. They work with Thomas Schubaltz of the Empire to fight against those who threaten the peace between the nations. The Guardian Force faces a number of antagonists. Most notably, they have multiple encounters with two mysterious individuals who have organoids, Reese and Hiltz. Raven also resurfaces, piloting various Zoids until he obtains a new Geno Saurer that later evolves into the Geno Breaker. The Guardian Force's members clash with Reese, Raven, Hiltz, and other criminals a number of times.
Eventually it is revealed that Reese and Hiltz are working to awaken a mysterious Zoid known as the Death Stinger, a very large and extremely powerful Zoid capable of destroying cities with its charged particle beam. Hiltz uses the Death Stinger to destroy the Republic's capital, despite a massive mobilization of Imperial and Republican military forces. The remaining forces gather and awaken the Ultrasaurus, a giant mobile fortress Zoid meant to be used as a last resort. The Ultrasaurus is fitted with the gravity cannon, an immense weapon nearly as large as the Ultrasaurus itself.
Hiltz continues his campaign of destruction across the continent. The Ultrasaurus pursues, and Van, Irvine, and Thomas close in to pin down the Death Stinger for the gravity cannon. They successfully hit the Death Stinger with the gravity cannon's third and final shot, crushing it. Its Zoid core shuts down and the Zoid begins to turn into stone. However, Hiltz's organoid Ambient appears and fuses with the Death Stinger, resurrecting it. Van and friends make headway against the still-weakened Death Stinger, but Hiltz, the Death Stinger, and Fiona all suddenly dissolve into light.
Fiona materializes before the Dark Kaiser, revealed to be Prozen merged with the Death Saurer's Zoid core.