We know, because official sources state that zero's consciousness was temporally taken out so his body could be studied in the first place.
That statement doesn't exist anywhere. They say he was researched and that his heart was moved to a new body, never in relation to each other. These are the sources talking of Zero's admittance into the research institute:
Underground Laboratory (Forgotten Laboratory)
The facility built to house Zero, who was discovered to be the source of the Sigma Virus outbreak. For half a century, Zero was used in many Sigma Virus-related experiments. This laboratory is also where Ciel's ancestors studied Cyber-elves, and where Weil created Omega. But because all records of its existence were wiped from history by Neo Arcadia, only a select few still know where it is.
Unfortunately, by tirelessly fulfilling his destiny as a Maverick Hunter, Zero inadvertently spread the virus throughout the world. Eventually, as the host of the virus, Zero was taken to a research facility for study.
The Forgotten Laboratory
The laboratory that Zero was taken to was equipped with the latest technology available at the time, and the researchers there were doing a great deal of research on Reploids and DNA. In the laboratory, two scientists worked tirelessly to bring an end to the Maverick Wars. One of the scientists was Dr. Weil, who believed that the best way to end the fighting was to eliminate all of the humans and Reploids that were, in his eyes, silly enough to fight over matters he found to be trivial - and to then build a utopia for the survivors of the wars on their corpses. The other scientist was a distant female ancestor of Ciel's. By using properties and samples of the Sigma Virus, she created Mother Elf, who had the ability to restore a Maverick to normalcy - indeed, she was able to reverse the effects of the very virus that was used to create her. Unfortunately, Mother Elf was overwhelmed by the effects of the Sigma Virus used to make her, which caused her to become Dark Elf and set Elf Wars into motion.
What kind of savior kills off over have the population of humans? You're using a mere taunt as plot evidence.
Vile's savior would kill everyone, that's because Vile is Vile. TELOS and MMOCW both speak of Omega as the messiah of Vile's new world and MMZOCW mentions Omega being created to end the war only to end up dealing a devastating blow to humanity.
Suzuki (Character Designer): Up till now, we've been answering the questions, but now we have one for the sound team. What you tell us about the speech of Omega's third form?
Yamada (Sound Director): It's "Ware wa messhia nari!" ["I am the messiah!"] It certainly sounds like that "I am God" kind of speech, something a terrorist or anarchist or someone like that would say, doesn't it? I think that's the kind of impression we we're trying to give. It's not the speech by itself alone that holds significance, however, if you could express Omega's brutality and ferocity and everything into one line, that's what it would be, right! By the way, what's the creation story behind the personality of Omega form three?
Yabe (Background Designer): Omega form 3's personality program (cyber-elf), was programmed by Vile to be his messiah.
Though, as to Omega form 3's...Original Zero's personality being completely Vile-made, I couldn't say that.
Ito (Series Director): I can't deny the possibility that the original personality that "a certain doctor who tried to take over the world innumerable times" created for Zero was remaining in the body, and that side of the personality having won over.
Yabe: I guess we're entrusting everyone to use their imagination (he laughs).
Dr. Weil had always had his eyes on Zero's body, which had a natural immunity to the Sigma Virus. He knew that a Reploid with no risk of going Maverick would make the perfect weapon to bring an end to the war. To that end, he designed Omega and created him from Zero's body. As Weil expected, the damage wreaked by Omega was enormous - but it only added to the costs of the war, instead of bringing and end to it.
Fortunately, he was eventually defeated by X, the hero of the Maverick Wars, and the Reploid now housing Zero's soul. Omega was subsequently exiled to space. Dr. Weil, who was deemed the one responsible for starting the Elf Wars, was sentenced to eternal regeneration, a punishment worse than death.
Dr. Vile was the one who had his eye on the inmate Zero's body at the research facility. Vile would use the body of the one who had no worry of infection, Zero to create a weapon of destruction to end the wars, and intended for him to fight on the front lines in the Irregular Wars
However, Omega would deliver a devastating blow to humans and Repliroid
s, and as a result of that Omega would be destroyed and exiled to space by Zero, whose heart was moved to a different body, and the hero of the Irregular Wars, X.
And then, Vile who was also held responsible for the damage in the war, was given a punishment far heavier than the