Basically there's this tremendously evil, sentient flower bud thing deep in the woods the Jak World(tm) takes place in, and it needs to bloom, so it in a parasitic sort of way implants "eyes" into the woods' various critters so it can control them and make them see for it, since it itself is immobile. It's looking for...something...to make it bloom, basically.
Sadly Gaia's one of those poor souls. After she sewed everything shut, she lost pretty much all of her memories - and soul - except for a strange fixation on flowers. Of course, this could be reversed, and her mindless slavery can return in an instant if her eyes are re-opened.

lel edgy ecks dee does anybody besides myself even remember gaia