Byebye world.
I thought it was sort of like a mind meld.
Sara was in there, but her mind was mixed in with the guardian's.
Hence, something that would've seemed abhorent and perhaps even evil to Sara(not necessarily evil, since they WERE violent muderous technophiles) was perfectly rational to GuardianSara, as the Guardian was strongly of the opinion that if we'd made it that far and were still shooting the crap out of each other then we needed to be blasted back to the stone age to try again.
As I see it, the MacZero guardian was a lot like the tower in the NES game Crystalis(a game I strongly recommend playing).
It was an artifact from a civilzation that was destroyed by warfare, and programmed by it's creators to make sure the new society doesn't go down teh same route by brute-forcing any screw-ups out of existence before they can kill everyone, and essentially rebooting the civilization for another chance.
And like the tower, it had a safety mechanism built-in because a human involved in the decision could over-ride the initial activation and shut it down(the activator in MacZero, the artifact's creators in Crystalis).
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That makes sense about the guardian artifact and how it was programmed to mindmeld with the priestress. I suppose that is why the guardian asked Sara if mankind has stopped all wars. This makes much more sense now.