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 (Sho), whom deactivates his armor and collapses into Mizuki's arms, welcoming Sho back home.
Cronos scientists are seen with a large cocoon-shaped object in their lab but are soon interrupted by Guyver III. He is leading a group called the Zeus Thunderbolt against the Cronos corporation. Guyver III recollects his memories of the aftermath of the battle against Archanfel, which led to their apparent deaths. Sho sacrificed himself and manages to save everyone. In the present, a recovered and renewed ZX-Tole attacks Aptom and the two face off. Aptom's attack are useless against Neo ZX-Tole.
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.
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.
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.
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.
Chief Odagiri, one of the ex-Cronos scientists, explains how Cronos obtained the Guyver units. Sho and Agito make their way into the relic and find where the units were stored. Sho connects to the relic, where he learns more about the Advents and the very first Guyver (Guyver 0). He also learns that he can control the relic through his own will. Archanfel still questions Guyot about the "remover" but Guyot denies him and runs away.
After their reunion, Mizuki starts to think that she maybe a burden to the group. The twelve Zoaloards meet and talk about Richard Guyot. Archanfel goes to deal with the problem. Murakami then is fully recovered, but explains that he only has one transformation left before he meets his fate. Mizuki starts to worry about Sho's fate. The group discuss plans on reviving the "relic". Archanfel faces Guyot about the "Remover". Sho and Agito prepare to enter the "relic".
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" (an Advent ship) and an unknowing Guyot. The relic begins to vibrate as Murakami heals himself.
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.
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.
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.
Sho is found unconscious and his group must leave the hideout because it has been discovered by Cronos. Tetsuro explains the events that happened from when they Guyver allowed Sho's brain to regenerate to the present situation the group is in now. As the group make an escape, three ENZYME II Zoanoids get in their way. Guyver III attempts to fight against them but is overpowered. Guyver I also attempts to fight but his armor deactivates. Murakami is the only one left to fight. Murakami then reveals his past.
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 (as Guyver I) off-guard and kills Sho. However, Guyver I reactivates itself in Self-Defense Mode.