Omega was trapped in and ruled over the anti-matter universe. It was situated in a black hole, leaving it a pocket universe. Omega shaped this universe as he saw fit, creating his own paradise in which to dwell.
Over the centuries, however, he grew despondent due to his isolation. The landscape slowly became unstable because of this. Omega planned to escape the anti-matter universe and return to N-Space. However, living inside the universe had a corrosive effect, causing Omega's physical body to wear away. This made it impossible to leave the universe, because only his will allowed him to live, and keep it from collapsing. (TV: The Three Doctors, Arc of Infinity)