The story begins with the discovery of a monstrous creature encased in anambermonolith buried inBig Surnational park, which is recovered by the government-fundedEarth Corps,ageological sciencesresearch team. The finding spurs Blackthorne Shore, a corrupt industrialist, to clandestinely uncover a second monster buried elsewhere—a giant vine-like creature calledTendril,who attacks the amber block's public unveiling inSan Franciscoto release the macabre colossus trapped within,D'Compose.They rampage through city streets before fleeing into the watery darkness of the bay.
The Earth Corps member code-named Liquidator returns to Big Sur in search of further clues to the origin of these monsters, whereupon he discovers a race of sentient trees, theRedwoods,who explain that they are members of a subterranean population known asMutores,and that their kind sealed the evilInhumanoidsTendril and D'Compose beneath the Earth ages ago. The malevolent Inhumanoid leader,Metlar,remains imprisoned below the surface, paralyzed by the magnetic field of a Mutore duo namedMagnokor.
A nocturnal assault by Tendril demolishes the Earth Corps base, prompting a chase into the depths of the Earth, but even with the help of another Mutore species, the rock-bodiedGranites,they are forced to retreat back to the surface. When their budget is summarily cut by Senator Masterson, a crooked politician in Blackthorne Shore's shady pocket, they are approached by Sandra Shore, Blackthorne's sister, who has learned of her brother's sinister plot to liberate Metlar. Funded by Sandra, the team constructs new vehicles and embarks back below the Earth's surface, tracking D'Compose and Tendril to the city of the Granites, where an ensuing battle frees Metlar from Magnokor's hold. Having pilfered the Earth Corps's engineering schematics via his ties to Masterson, Blackthorne joins the fray, now equipped with his own battle-suit whose magnetic powers he wields against Metlar, only to be derailed by Tendril's interference while Sandra falls victim to the mutative touch of D'Compose.
Earth Corps manages to escape and forms an alliance with the Granites. Herc accompanies them to D'Compose's domain ofSkellwebwhile Auger and Liquidator venture into Metlar's kingdom ofInfernac,and Bright convinces the Redwoods to help defend the surface world against attempts by the Inhumanoids to acquire sources of power. Herc and the Granites are able to defeat D'Compose's reanimated soldiers and restore Sandra to normal. Blackthorne pursues Auger and Liquidator to Infernac and tries to use his magnetic powers on Metlar once again but is foiled by Magnokor and taken captive by Metlar.
Acting on information forced from Blackthorne, the Inhumanoids raid aSovietair base, stealing a handful of nuclear missiles. A seemingly repentant Blackthorne warns Earth Corps that the missiles are intended to shatter the divide between the Earth's crust andmantle, but upon travelling into the Earth to preclude this catastrophe, the team discovers that Blackthorne has set them up and that the missiles are actually meant to detonate the planet's core. Earth Corps is able to convince D'Compose to allow them access to Infernac — a deal made easier by the fact that the Inhumanoid already fears for his own survival in the face of Metlar's insane plan — and they manage to defuse enough of the missiles to thwart the explosive scheme.
Following a climactic battle, D'Compose is re-sealed in amber casing and Tendril is imprisoned by the Granites. Finally, Magnokor succeeds in neutralizing Metlar even as Blackthorne is arrested by Earth Corps. Senator Masterson provides the Earth Corps team with a new headquarters facility, but atissue samplesecured from Tendril during their first encounter with the monster has mysteriously gone missing.