Mother

At the very end of the game, Tommy finally comes across the being that is in direct control of the Sphere, who is a human woman who was abducted from Earth long ago. She says that, originally, she was just like Tommy; fighting tooth and nail every step of the way to what has become the Mother's den. At the time, the creature in the Sphere's Core was old and tired of being in control, so it made a deal with her: stop fighting and take its place, so that it would be allowed to die, and she and her people will live. Seeing as it was either this or a swift death, she chose to become the Mother. Now she makes the same offer to Tommy.