By the Doctor's time those who knew about the universe before it was logical assumed that it was the universe that came before N-Space, although it was actually N-Space before history was created. (PROSE: All-Consuming Fire, Millennial Rites,Christmas on a Rational Planet)
When the universe was rationalised, many powerful species fled into other realities, many found their way back into N-Space and some (such as the Ancient Lights, Great Old Ones and the Beast) still followed the rules of the pre-time lord universe giving them god-like powers. Thus, some of the most powerful beings in existence came from before Rassilon created a structure for time, making them older even than time itself. (PROSE: All-Consuming Fire, Millennial Rites, Christmas on a Rational Planet, TV: The Impossible Planet)
The physics of this pre-Rassilon universe were different from the post-Rassilon universe. Magic was a powerful force here, and science did not exist. Before the Web of Time the universe was never rationalised, and thus, science never worked, and magic always did. (PROSE: Christmas on a Rational Planet)
The Doctor described the pre-universe to Anne Travers.
Before this universe was created, there was another one. A totally different universe, with alien physical laws. The heavens were green, and the stars looked like... giant doughnuts, to be brutally frank. Very, very different. And, as in this universe, there were people who discovered the deeper mysteries of time and space.
Because of new laws like the speed of light or the charge of the electron, the Great Old Ones found they had great power and became terrible gods. (PROSE: All-Consuming Fire) The Shepherd and Shepherdess escaped the "extinction of their universe" (presumably the destruction of the everything illogical that occurred when time was mapped by Rassilon) and arrived in N-space where their appearance became transparent. They moved without touching the ground and their hair and nails grew longer because they were dying in the new reality. (AUDIO: Persuasion)
Amongst the races that claimed to be older than the universe itself were the Great Old Ones such as Azathoth, Yog-Sothoth and Shub-Niggurath. (PROSE: All-Consuming Fire, Millennial Rites) On many planets, these beings became part of the legends and religions. The Great Old Ones were worshipped by the first intelligent species to evolve on Earth - the Silurians. (PROSE: All-Consuming Fire) It is unclear whether the Great Old Ones were a single species, or merely a term to describe any unimaginably powerful being that had escaped the Pre-Universe into ours.
The Beast claimed to have originated before the universe and to have been imprisoned by the Disciples of the Light, likely placing both in the Pre-Universe. The Beast was also said to have been the inspiration for all Satan-like figures in the mythology of countless races, including the Demons of human mythology, the ancient Kaled God of War and the Draconian God of Evil. (TV: The Impossible Planet / The Satan Pit)
Knowledge of this universe was a closely guarded secret.[source needed] The Sixth Doctor only knew about it as a result of his connection to the Matrix during his time as Lord President. (PROSE: Millennial Rites, TV: The Invasion of Time) During an encounter with the Carnival Queen the Seventh Doctor learned that the Time Lords had misinterpreted their knowledge of the pre-universe. (PROSE: Christmas on a Rational Planet) When the Beast claimed to have existed before the universe, the Tenth Doctor had trouble accepting the claim, as he knew the pre-universe was not a different universe. (TV: The Satan Pit)