The overarching plot of Zoids: Chaotic Century is a journey of discovery that reveals the planet's hidden, apocalyptic past. Fiona is an Ancient Zoidian, placed in suspended animation thousands of years ago. Her people were nearly wiped out by their own creation, the Death Saurer, a Zoid designed to end all war by destroying everything. Zoid Eve, the object of her search, is the life-giving source for all Zoids, which the Zoidians sealed away in the city of Evopolis to prevent the Death Saurer from ever accessing it again.
The first major twist is that the war between the Helic Republic and Guylos Empire is entirely orchestrated by Imperial Regent Gunther Prozen. He seeks to overthrow the legitimate heir, the young Prince Rudolph, and use the chaos of war to locate the resting place of the Death Saurer to seize ultimate power. Van and his friends end up protecting Rudolph and helping him reclaim his throne, ending the war. Prozen's defeat comes when he activates an imperfect clone of the Death Saurer, which Van manages to destroy with his Blade Liger.
The second half of the series, 'Guardian Force', reveals even darker secrets. The new antagonists, Hiltz and Reese, are also surviving Ancient Zoidians with a twisted goal. Hiltz believes the current human inhabitants of Zi are a mistake and seeks to wipe the planet clean using the power of Zoid Eve and the Death Saurer. He merges the cores of two ancient guardian Zoids to create the Death Stinger, a prelude to his true goal. The series culminates in a shocking turn where Prozen, presumed dead, is revealed to have merged his consciousness with the original Death Saurer's core. Hiltz then forces this core to absorb himself and the Death Stinger, resurrecting the true Death Saurer. In the final battle, Van's rival Raven, having completed his redemption arc, fights alongside him. To defeat the nearly invincible monster, Van pilots the Blade Liger directly into the Death Saurer's core, overloading it with Zeke's energy in a massive explosion that finally destroys the ancient threat for good.