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Having destroyed the evil Commander Gyou and his branch of the Chronos organization, the Guyver's battle to defeat them has only just begun. Chronos' leading scientist, Dr. Balcus, takes command and devises a plan to destroy the Guyver, using Sho's father, Tetsuro and Mizuki as the focus of his attack. Fearing for their lives, Sho fights dangerously along side his mysterious new ally, Murakami, in a desperate attempt to protect his friends from death.

Sho's horrifying nightmare continues as he heads for Chronos headquarters at Mount Minakami, where death threatens Mizuki and his father. Spying on Sho's every move, Dr. Balcus decides to test out his research and orders the "Lost Units" - Enzymes with unlimited powers - to challenge and destroy the Guyver. Will the Guyver have the strength to defeat them?

The Guyver's mission to save his father and Mizuki appears accomplished as they all attempt to escape from Mount Minakami. Dr. Balcus is unalarmed by this because he has programmed Sho's father to transform into a terrifying deadly Zoanoid, and using his psychic powers, he commands him to kill the Guyver. Faced with this moral dilemma, will the Guyver fight back and kill his father to save his own life?

Sho and his friends, desperate to escape Mount Minikami, work out an escape route. Guyver III returns to Chronos to intercept Dr. Baclus' evil plans to destroy the Guyver, but is in serious danger when the secret of his identity is revealed. Meanwhile, Sho and the others have fallen into Dr. Balcus' trap having arrived at a village full of Zoanoids controlled by Balcus. Traumatized by his father's death, Sho is unable to transform into the Guyver. Will he fail to save himself and his friends from the evil that surrounds them?

Hiding from the evil clutches of Dr. Balcus, Sho and his friends are in constant danger of attack from Zoanoids in the surrounding area. Agito is desperate to know the dark, deep secrets of the Chronos organization and persuades Murakami to reveal all he knows, beginning with who created the Guyver and Zoanoids, right up until the horror of the present day. Finally the terrifying truth is disclosed.

Sho and Mizuki are saved from Balcus' Zoanoids by a mysterious being disguised as Guyver III. They soon realized that it was Aptom - the only remaining survivor of the Lost Units. Seeking vengeance for the death of his friends, he draws on his superhuman powers to torture and destroy the Guyver. Will Sho find the power to transform into the Guyver and defeat him? Can he save Mizuki and his friends from the danger they face in this last gripping episode?