After discovering the Creator relic at Mount Minakami, it was decided by the Zoalord Council to be in humanity's best interest to continue and eventually complete the research left behind by the Ouranos. Many bio-weapon samples were contained within the ancient ship, among them the three Guyver Units. The units were shipped to Cronos's Japanese branch - which was concealed by a cover company called Max Pharmaceuticals - where they were to be studied. However, the units would later be stolen by a traitor within the company who planned to trade the alien devices in exchange for having his Zoanoid mutation cured. The escaped Zoanoid fled into the Nanisawa mountain range but was pursued by Cronos troops. With no hope of escape, the incomplete Zoanoid commited suicide by blowing himself up with a grenade. The explosion scattered the Guyver units all over the area and the Cronos troops were only able to recover one of them which had been damaged in the blast. The other two would be discovered and activated by high-school student Sho Fukamachi (Guyver-I) and traitorous Cronos officer Agito Makishima (Guyver-3). The recovered unit would later be activated by Cronos agent Oswald A. Lisker (Guyver-II).
After the activation of one of the Guyver units, Cronos Japan made Sho Fukamachi their primary target and made various attempts to capture or kill him. They succeeded eventually after deploying the prototype anti-Guyver Zoanoid Enzyme against Sho, which brutally murdered him and pulled the Guyver's control medal from his head. Unfortunately for them, Cronos were not aware that the control medal was capable of reviving its deceased host so long as any trace of the host's DNA remained connected to it. To make matters worse for them, Guyver-III had appeared within the Japan branch and had begun tearing it apart. When Guyver-I had finished regenerating, it too went on a rampage within the Max Pharmaceuticals building, slaying every Zoanoid in sight. Sho had not yet regained consciousness and so the Guyver was acting on its own until its host came to, which he did after encountering Guyver-III attempting to rescue Sho's captured friend Tetsuro Segawa. Despite the attempts of the Hyper-Zoanoid Zerbebuth and Lisker/Guyver-II, the two Guyvers succeeded in destroying Cronos Japan. But despite this setback, Cronos remained a powerful and deadly force and the loss of one branch only encouraged them to re-double their efforts to destroy the Guyvers.
Cronos would later lure Sho Fukamachi toward Relic's Point, their primary research facility in Japan where the Creator bio-ship had originally been discovered. Sho's father Fumio and girlfriend Mizuki (Tetsuro's sister) were abducted in order to lure Sho into a trap. They would dispatch their Lost Number Commandoes and the Hyper-Zoanoid Team Five to battle against Sho and also Agito, who had been discovered to be the third Guyver. When Sho and Agito managed to infiltrate Mount Minakami to rescue Mizuki and Fumio, they realized to their horror that Dr. Hamilcar Barcas - the Cronos executive overseeing Relic's Point - had already turned Sho's father into a Zoanoid: Enzyme II. Barcas used his telepathy to control Enzyme II and forced father and son to fight. Sho was rendered unconscious when Enzyme II ripped out a portion of his brain, forcing the Guyver's self-defence mode to activate and ruthlessly attack the Zoanoid. The Guyver destroyed Enzyme II with its Mega-Smasher and then regenerated its injuries, but when Sho regained consciousness he discovered what he had done. Traumatized by the revelation that he had killed his own father, Sho lost the ability to bio-boost and for a time could not transform; he also repressed the memory of killing his father, but would later be reminded of his actions by the Lost Number Aptom, and regain his ability to become the Guyver.
Cronos would later have to contend with a traitor amongst their leading council: Richard Guyot. Guyot was secretly plotting a rebellion against the organisation and had managed to procure a device from the alien ship that could seperate an active Guyver unit from its host. As well as this, Cronos also faced other internal threats: Aptom had begun attacking and slaughtering Cronos personnel and the Guyvers had infiltrated Relic's Point and were being concealed by the facility's basement staff who were also working toward destroying Cronos from within. While the Guyvers delved inside the Creators' ship in order to reactivate it, Aptom fought against the Hyper-Zoanoid Team Five and Guyot was forced to contend with Archanfel. Between all the fighting and the take-off of the alien ship, Relic's Point was all but destroyed. In spite of everything, Cronos would emerge triumphant: Guyot was killed by Archanfel and his Unit Remover destroyed, the rebel scientists' movement was crushed and both Agito and Sho were supposedly killed. Mere days following the destruction of the Creator vessel and Mount Minakami, Cronos initiated its X-Day plan by triggering the many Zoanoid sleeper agents around the globe. The world's military powers were unable to withstand the might of the Zoanoids and the governments of the Earth's nations soon fell. Cronos had conquered the world.
One year following Cronos' rise to power, society had undergone significant changes. While everyday life appeared to be unchanged on the surface, conflicts between races and nations had all but ceased completely, medical technology had advanced by leaps and bounds and crime, hunger and disease were virtually eliminated in many parts of the world. Much to the public's surprise, Cronos did not force Zoanoid optimization on the populous and provided it as a public service, which they strongly encouraged through PR studies, advertisement and propaganda. Relatively few people volunteered to become Zoanoids, though some would undergo processing as an employment necessity and many young people would choose optimization as the latest fad. What Cronos continued to keep secret however, was that anyone who became a Zoanoid would become susceptible to the psychic commands of the Zoalords.
With the whole of Earth under their control, Cronos continue their Zoanoid research unchallenged until the emergence of Zeus' Thunderbolts, a terrorist group led by Agito Makishima, who survived the destruction of Relic's Point. At the same time, Cronos officers are disappearing in Tokyo, which are later revealed to be the work of Aptom. Believing Sho Fukamachi to still be alive, Aptom is secretly protecting Sho's friends who have been in hiding since Relic's Point. However, Aptom is merely waiting for the chance to have his rematch with the Guyver.
Cronos' plans are jeopardized by the return of Guyver-I, who had been regenerating inside a chrysalis-like object since his apparent death at Mount Minakami. Cronos had discovered the chrysalis and begun analyzing it without results, but as it turned out the chrysalis was restoring and enhancing Guyver-I, which had undergone a new transformation into a "Gigantic" Guyver. Alarmed by the Guyver's return, Cronos begin producing new Hyper-Zoanoids to combat the threat, and even the Zoalords themselves are spurred into direct battle against the Guyver.