Okay so back when Nemesis returned he did so in a cloned body of Monguse. (sort of a add insult to injury kinda thing) And when he was beaten the body remained. For some unknown reason the body gained consciousness of it's own. A body with no soul, but a mind. It was taken by the same rouge faction that took over The City at the Edge of Time before. Trained with a military mind Deus has all of Monguse's powers an a few he doesn't have. Monguse's unpredictability and his ability to think out of the box allowed him to beat his more focused and logical doppelganger. Left with no place to go Deus wanders around trying to find his purpose and his reason for existing.
MT

Deus (c) Miguel Tigre