Disclaimer: this is a work of fiction.
Part Seventeen: Seasons 36-40 (1999-2003)
Season 36 began with a three-part serial starring Paul McGann, in which the Doctor and Bernice encounter events about which the Doctor knows more than he should, but he is unwilling, or unable, to explain. Events are made somewhat clearer by the next serial in the season, in which Colin Baker’s 6th Doctor encounters the same events after the 8th, events that the 8th Doctor can go on to remember in the first serial.
As the season progressed, more and more plots of this nature were encountered by the Doctor(s) and his Companions, in which events occur in a different order for the viewers than for the Doctor. Eventually it became clear that an unseen opponent was deliberately setting up these encounters for the Doctor, perhaps as some kind of test. In one of the longest story-arcs in Doctor Who’s history, it would be four seasons before the unseen hand was identified.
Season 36 contained four episodes starring McGann, and three each for Davison, McCoy and Colin Baker. Seasons 37 through to 40 continued in a similar vein, though the exact mix of Doctors and their order of appearance was always slightly different. Not every serial contained a complex time-travel-related plot, though intelligent, thought-provoking stories that rewarded viewer loyalty were the standard of this era.
Foreshadowed as far back as season 35, the 40th anniversary special was the high point of the multi-Doctor era, as the multi-Doctors appeared on-screen together for the first and only time, and revealed the unseen, time-manipulating opponent to be Davros and the Daleks, whose return was carefully kept secret and unpublicised (a feat not achieved since the Cybermen returned in 1982’s Earthshock) in favour of promoting the mystery and suspense right up to the moment of revelation.
Season 40’s final story led directly into the storyline that was to dominate season 41 and cast a shadow over Doctor Who for a long time to come:
The Time War.