Lethbridge-Stewart's universe (The Forgotten Son)

One universe, with divergences focused on the life of Alistair Gordon Lethbridge-Stewart, the wider Lethbridge-Stewart family, and Counter-Measures, was created when the Great Intelligence went back in time and interfered with its own history; despite not being the "original timeline", (PROSE: The Forgotten Son, Night of the Intelligence) the Accord would describe this reality as the essential timeline or timeline zero from which the entire multiverse stemmed. (PROSE: The Shadowman, Home Fires Burn)

Relation to other realities
This universe was connected to the positive-time universe via Sunyata, which spanned all realities. Touching Sunyata, Owain Vine witnessed a history alternate to his own in which (PROSE: Night of the Intelligence) Counter-Measures fought the Great Intelligence in 1974. (AUDIO: Time of the Intelligence, PROSE: Night of the Intelligence) Additionally, the Great Old Ones encountered by the Fifth Doctor, Erimem, and Peri Brown (AUDIO: The Roof of the World) were a parallel Sunyata-impression to the Great Intelligence of Owain's universe. (PROSE: Legacies)

Owain saw other universes in which Sunyata's impression took the form of a being from before the Big Bang, (PROSE: Night of the Intelligence) Yog-Sothoth. (PROSE: Legacies) The universe in which Yog-Sothoth (PROSE: Legacies) faced the Sixth Doctor (PROSE: Millennial Rites) was a parallel reality to Lethbridge-Stewart's universe. (PROSE: Legacies)

The Great Intelligence's invasion using New World University (HOMEVID: Downtime) occurred in, by one account, another universe parallel to this one. (PROSE: Legacies)