The 3 Guyver units are stolen from the enigmatic Chronos corporation in Japan. A high school student named Sho Fukamachi accidentally discovers Guyver 1 and triggers the control metal. He becomes the Guyver and battles biomorphic Zoanoids controlled by Chronos.

Lisker, an agent of Chronos headquarters, unwittingly joins with Guyver 2. He abducts Sho and his friend Tetsuro in an attempt to locate the other missing units. Sho summons the Guyver and the two are thrust into a deadly battle for survival!

Commander Guou arrives from Chronos headquarters to lead the recovery of the Guyver Units. Meanwhile, Chronos Japan creates the Zoanoid "Zerububuse" in a final desperate attempt to eliminate the Guyver. To bait the trap for Sho, Mizuky is kidnapped and Sho once again must become the Guyver and face the challenge of Zeruububuse as well as the mysterious shadow, Guyver III.

Commander Guou takes full control of Chronos Japan and deploys his Hyper-Zoanoids against Sho. Together with Tetsuro, Sho tries to expose Chronos but the media won't believe their story. In order to force out the Guyver, the Hyper-Zoanoids attack Sho's school.

Chronos Japan transforms Makishima into Enzyme, a powerful Zoanoid created to eliminate the Guyver. To force a confrontation with Sho, Commander Guou again kidnaps Mizuky and Tetsuro. They are taken to the mou ntains and forced to watch as Sho and Enzyme battle in a fight to the death!

Tetsuro and Mizuky are held hostage at Chronos headquarters. Meanwhile, Guyver III's identity is revealed as he initiates his plan to destroy Chronos. Will Guyver regenerate in time to save Tetsuro and Mizuky?!