well if you remember, she was on earth during the firing of the halo arrays, and if she survived(which she probably did) I'm sure some humans could've survived with her. And gaeas are given to someone, and it passes down to their descendants, so Johns ancestor probably got the Gaea at first. And the monitor in priordinium wasnt 343GS, it was Chakas. If you read the book again, the ONI Science team isn't even sure whether or not it's spark. I believe the monitors of the halo arrays are each a fragment of Chakas , which is supported by the fact that he says something like "I believe one of me has caused you trouble."