| ShortSummary
| - Guyot is still on the run, with Archanfel following closely. While this is happening, Aptom is able to absorb Gaster and Darzerb, having the power of three Hyper-Zoanoids. ZX-Tole faces Aptom and is able to absorb part of ZX-Tole's body as he was escaping, completing his absorption of the Hyper-Zoanoid Team 5. Guyot is now facing off against Archanfel, using what powers he has. Archanfel is able to deflect his attacks but Guyot has one last trick up his sleeve.
- After the fall of Cronos Japan, Sho has doubts about being himself, as he thinks that he maybe a clone made by Guyver I. Agito, while at home, encounters Guyot, who was thought to be dead. The next day, Tetsuro and Sho encounter a new Hyper-Zoanoid, Panadyne. Sho fights with Panadyne at the cost of his home. Sho is overwhelmed by the new Zoanoid but is aided by a man named Masaki Murakami. After the battle, Mizuki finds out Sho's secret.
- After hearing an explosion from where their friends are, Sho and Mizuki run back to find a large hole that looked like it was from a blast. Among the rubble was Guyot himself. Zoanoids are now sent out to find any remaining survivors. Mizuki and Sho go into hiding in a cave, where Sho questions why he cannot turn into the Guyver. Aptom, disguised as Guyver III, explains to Sho why he is in that condition and what happened in the past Enzyme 2 incident with his father. A traumatized Sho must gather the courage to protect Mizuki and himself.
- Guyver I is killed by Enzyme and Tetsuro is taken captive by Cronos. Guyot explains to Tetsuro in detail about Cronos' plan to dominate the world through the events of X-Day. Meanwhile, as scientists study the Guyver I control metal, Guyver III appears and deals with the scientists and watches Guyver I "regenerate." A regenerated Guyver I causes chaos in the Cronos building, killing everyone and everything in its path.
- The rest of the twelve Zoalords appear on top of Mt. Minakami. Guyot is using his Black Hole attack against Archanfel and is able to get him sucked in. Balcus helps Guyot seal the rift so Archanfel can't escape. With no one to stop him, Guyot obtains the remover and uses it on Agito, almost removing the Guyver unit from him. Murakami then faces Guyot, but Chief Odagiri attempts to save Murakami which gets him killed, enraging Murakami. Guyot and Murakami begin to clash with one another and begin their battle.
- After being helped by Murakami from the fight against the Lost Numbers unit, Sho goes to Mt. Minakami, another Cronos base, with Murakami to rescue his father and the Segawa siblings. Meanwhile, the hostages are taken to Mt. Minakami and are imprisoned until Agito, who reveals himself as Guyver III, frees them. However as they make their escape they encounter the Hyper-Zoanoid Team 5, along with Dr. Balcus and Guyot, who now know Agito's true identity.
- Guyver I, while in Self-Defense Mode, continues to cause chaos in Cronos. Tetsuro encounters Guyver I and awakens Sho, disabling the "SDM" of Guyver I. Meanwhile, Guyver III, being close to achieving his goal in destroying Cronos Japan, encounters Guyver II and the two battle. Meanwhile, Sho and Tetsuro encounter Guyot, who explains to them about the creators of mankind. Guyver II intervenes and faces Sho one last time.
- Guyot introduces the Hyper-Zoanoid called ENZYME, his key to retrieving the Guyver unit. He then reveals his plan to capture Guyver I to Agito. Meanwhile, Sho and Tetsuro are talking about how the monster kidnapped Mizuki and how they made up some stories so she wouldn't become involved. They return to Mt. Narasawa to see if they can learn anything about the Guyver, but are faced by Genzo Makashima. Makashima then transforms into ENZYME and attacks Sho.
- Sho and Agito make their way to Mt. Minakami with little interference. They are able to save Sho's father and escape. The Hyper-Zoanoid members ZX-Tole, Elegen, and Thancrus stop Guyver III from meeting up with Sho and his father. Meanwhile, Dr. Balcus gives a command, transforming Sho's father into a new Hyper-Zoanoid, ENZYME II. Enzyme II catches Sho off-guard and kills Sho. However, Guyver I reactivates itself in Self-Defense Mode.
- After a harsh battle against Aptom, Sho returns to a worried Mizuki, who happens to lecture him about her worrying about him, but is happy that he returned to her. Aptom, trying to recover from the past battle, encounters the Elite Hyper-Zoanoid Five and absorbs Elegan. Sho and Mizuki run off to a town which houses a horde of Zoanoids. Sho tries not to kill any of them because they were all innocent people. They then encounter Guyver III, who wipes the Zoanoids out.
- Murakami continues to explain to the rest of the group about mankind's past. The Creators, or "Advents", created and experimented with new life, especially man, to make bio-weapons. Murakami then explains about the Zoalords and the Guyver's origin and purpose. A shocked Mizuki runs away and Sho chases after her. Sho catches up to Mizuki and comforts her. Meanwhile, Guyot manages to find the rest of the group and attacks them.
- At Agito's home, Guyot reveals new plans to capture Guyver I. Agito then excuses himself and leaves, but comes back as Guyver III and faces Guyot. Meanwhile, Sho and Tetsuro find Mizuki and realize that Sho's secret is exposed. Then, his father is kidnapped by Cronos, forcing Sho to find him. Cronos then abducts Mizuki and Tetsuro as well. While on the chase, Sho encounters the Lost Numbers unit. Sho has a difficult time defeating them but is aided by Masaki Murakami.
- Some time has passed since the Mt. Minakami incident. X-day has already taken place, leaving Cronos the rulers of the world. A year after the events of X-day, life seems normal other than the fact that Zoanoids are among the population. Tetsuro Segawa, Mizuki Segawa, Yohei Onuma, and Shizu Onuma are in hiding in an apartment, unknowing that Aptom is watching over them. They begin to doubt Sho is still alive. Balcus is working on a particular Zoanoid to defeat Aptom.
- Tetsuro and company notice Aptom's fight with Neo ZX-Tole and that Aptom is defending them. Guyver III arrives along with a large cocoon. He explains that Sho is inside the cocoon. Guyver III then faces Neo ZX-Tole, but is powerless against him. The fight goes badly until the cocoon opens up. A gigantic figure emerges from inside. The figure faces and annihilates Neo ZX-tole with ease. After the battle, the figure splits open to reveal Guyver I , whom deactivates his armor and collapses into Mizuki's arms, welcoming Sho back home.
- Sho, Mizuki, and Agito make their way back to Mt. Minakami where their friends are. They head towards the underground lab of a group of ex-Chronos scientists who are planning a mutiny. As the company rejoices in their reunion, Tetsuro explains how they escaped from Guyot's attack. Murakami is healing himself through the "relic" and an unknowing Guyot. The relic begins to vibrate as Murakami heals himself.
- Murakami and Zoalord Guyot go at it. It seems that Murakami was able to inflict a deal of damage on Guyot, but wasn't enough to finish him. Guyot grabs a now powerless Murakami, beating him and then tearing his arm out, killing him. Sho leaves the relic to face Guyot, but is interrupted by the Zoalord council. Archanfel returns and deals with Guyot personally. Both Guyver I and Guyver III attempt to fight against Archanfel with their mega-smashers, but proves no match against Archanfel's power.
- Lisker and Sho face off. Lisker has the upper hand and states that because he is the better fighter, Sho has no chance. However, the damaged control metal on the Guyver II unit malfunctions from damage, allowing Sho and Tetsuro to escape. Commander Richard Guyot shows up and assumes the position of the Head of Cronos Japan. He introduces Hyper-Zoanoid Zerbubuth, While at school, Sho and Tetsuro encounter Zoanoids and Zerbubuth, forcing Sho to face the threat, but with much difficulty.
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