My interpretation - which may be wrong - was that the being from the opening movie of Divine Divinity wasn't a Goddess. (It couldn't be a Goddess, all the Seven Gods had to leave the mortal plane), but the Divine Being, an artificial angel created by the Gods to sleep until the appointed time for the next Divine One to be created.
The Black Ring, knowing this and not being stupid, sent some of their members to kill her before she could awaken, but it got away anyway because the spell used to hold her only worked on one entity, and they didn't know she could split herself into three.
When she escaped, she sought our three potential candidates, Lucien, Joris, and Wouter, and partially merged with them, changing them somewhat (rendering them immune to the Black Ring's mind-control spells, perhaps) going back to sleep.
In the Lands of the Dead, when the Gods performed the Divine Ritual, they awoke the Divine Being fully, which completely merged with the Divine One. She vanished completely as a separate being, but that's fine, as her purpose was fulfilled.
