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Yes. The Shalka Doctor, the Doctor from "The Curse of Fatal Death", and Christopher Eccleston's Ninth Doctor are all version of the Ninth Doctor from other universes. Additionally, the unspecified incarnation of the Doctor in "The Infinity Doctors" (BBC Past Doctor Adventures novel #17) is also hinted to be a parallel Doctor. "Timewyrm: Revelation" (Virgin New Adventures novel #4) reveals the dictator from "Inferno" to be another 'sideways' Doctor.

Additionally, some sources claim that the TV series, the Virgin Novels, the BBC Novels, and the audios to all exist in separate universes, but some stories contradict this, for example the Faction Paradox, as well as appearing in their own series of novels and audios, appearing in both the Virgin New Adventures AND the EDAs, Bernice Summerfield returning in "Big Bang Generation" (BBC New Series Adventures novel), and various mediums references/having characters from/doing sequels to each other. The TV Series also attempts to canonise all mediums, with a picture of Abslom Daak in "Time Heist", the Chelonians returning in "The Pandorica Opens", and the Eighth Doctor mentioning his Big Finish companions just before regenerating.

The universe seen in "Rise of the Cybermen", "The Age of Steel", "Doomsday", and "Journey's End" has no Doctor, which becomes an important plot point.

Finally, in "Turn Left" we see a universe where the Doctor drowned during the events of "The Runaway Bride".