When Caine couldn't defeat Gaia using the missiles that Albert had found in a previous book. So, instead, Caine used his backup plan which was Little Pete inhabiting his body to defeat Gaia.
Gaia later on, finally thinks she won the battle as she doesn't know the backup plan. Only when Caine said 'Hello Darkness', did she understand that Caine was no longer Caine and so she replied 'Nemesis'.
Gaia then raised her hands, in fury and fear on her blood-red face with blistering green light blazed from them. At the same time, Nemesis returned the fire but his light came from every direction at once. It was a white light that shifted into blue and purple and red.
Gaia's light hit Nemesis as she herself absorbed the awesome fire. They both turned bright but they still fired and burned and still fired. Holes then appeared into them and they still fired and only when did they fell into a heap of ash, did the light die.
And this was the end of the Battle of Gaia with the Gaiphage, Peter Ellison and Caine Soren dead.