Determined to recover the stolen Guyvers, Chronos' headquarters dispatch an agent to confront Sho. But as the young student is about to be abducted, the agent is involuntarily transformed into Guyver II: a fighting unit, specially trained for combat. Sho's only hope is to summon the Guyver, thus thrusting the two mechas into deadly battle for survival.

Commander Gyou arrives from Chronos' headquarters to lead the recovery of the Guyver units. Meanwhile, Chronos Japan creates the Hyper Zoanoid "Zerebus" in a desperate attempt to eliminate the Guyver. To bait the trap, sho's girlfriend is kidnapped and Sho must once again become the Guyver and face challenge of Zerubus and the mysterious shadow, Guyver III.

Finally, Sho is convinced by his friend Tetsuro to publicly expose the existence of the evil Chronos organization. But before they have a chance, Commander Gyou attacks with Chronos' five most powerful Hyper Zoanoids. Escaping only to face a further sudden attack from the deadly cyborg warriors, it is clear that Guyver 1 will not survive the battle alone.

The desperate Commander Gyou commands his men to transform Makishama, the head of Chronos Japan, into a Zoanoid armed with an enzyme capable of disintegrating the Guyver armor. To force a confrontation with Sho, Gyou has both his girlfriend and her brother kidnapped. They are taken to the mountains and forced to watch as Sho and the transmutated Makishama fight in a battle to the death!

Mizuki and Tetsuro are imprisoned under heavy guard at Chronos' headquarters. With Sho believed dead, Tetsuro fears the worst as he begins to comprehend the enormous power of Chronos. Meanwhile, Guyver III's identity is finally revealed as he initiates his plan to destroy Chronos and Commander Gyou. But can Guyver 1 regenerate his control metal in time to save his girlfriend and her brother?