Not much is known about Gaia's origin besides her having spent thousands of years chained to the Universal Amalgamator at the end of Time, a device that would be used to merge all sentient consciousnesses into one being. Gaia was apparently the safeguard that was supposed to prevent the Amalgamator from being activated by malicious people. She even claimed that her entire galaxy was wiped out at one point for her refusing to activate the Amalgamator.
However, when M-Plate, the synthesis of Emplate and M, tried to have Synch use his power to tap into Gaia's and activate the Amalgamator, Everett refused. The Citadel of the Universal Amalgamator began to crumble around them and Generation X wanted to leave, but Synch went back, along with Penance, to save Gaia. Banshee thought him lost but Gaia knew of a secret portal that was hidden underneath the altar that she had been chained to and--coincidentally--led back near the Academy. With the Amalagamator destroyed, Gaia was freed from her responsibility and ran off to live a life that was now her own.
When she was seen next, she had gotten into an accident with a sporty car and pink hair, probably courtesy of her reality-shaping powers. The policeman who came to the wreck knew of the Academy, and suggested that she be put into their hands. She lost some of her abilities to the Shadow King's telepathic shockwave, and stayed with Gen X, hoping to sort out that difficulty with their help.
She appeared to have some feelings for Synch, and flirted with him a lot. Gaia formally enrolled in the Xavier's School for Gifted Youngsters, but left after a short time, saying that she wanted to experience Earth, not just learn about it. This announcement came after a particularly difficult experience with her nascent empathy, and a conversation with Nate Grey, also a transplant to Earth.
It is unknown if Gaia was one of the 90-95% of mutants who lost their mutant powers on M-Day due to the Scarlet Witch's tamperings. Since she is from another dimension she may possibly be immune from her reality warping powers.