The second version of Enzyme was developed at Cronos' Mount Minikami base by the organisation's co-founder, Dr. Hamilcar Barcas. With the original Enzyme data lost along with Cronos Japan, this new model had to be developed from scratch. The original test subject for Enzyme II was Fumio Fukamachi, Sho Fukamachi's father.
Enzyme II, like its predecessor, had a large body and possessed superior physical strength. It was also more agile than the original, its dexterity enhanced with the addition of four multi-jointed limbs extending from its back, offering it increased attack range and the ability to cling to different surfaces. The enzyme in its blood could be passed through its claws and its scythe-like feelers, and since it had been enhanced to the point where it no longer oxydized upon air contact, it could also be expelled from the creature's mouth in thick streams.
When Cronos abducted Fumio Fukamachi - the father of Guyver I - they used him as the first Enzyme II test subject. When Sho later rescued his father from Mt. Minikami, Dr. Barcas used his Zoalord telepathy to command Fumio to attack his son. Fumio transformed and father and son fought, but Sho was hesitant to use the Guyver's weapons and could not protect himself against Enzyme II's assault. Enzyme II managed to rip out a portion of Sho's brain, causing him to lose consciousness and activating the Guyver's self-defence mode. Without its host guiding it, the Guyver mercilessly attacked the transformed Fumio and obliterated him with the Mega-Smasher. For a time after regenerating from his wounds, Sho was unable to bio-boost again due to the trauma of killing his own father. He would later be able to reactivate the Guyver, but Cronos would also continue producing Enzyme units.