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Elizabeth I was the Queen of England during the 17th century.
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She considered the Doctor her arch-nemesis for reasons the Doctor himself did not know when he first met her (from his point of view) in 1599 (but see below). (DW: The Shakespeare Code)
Elizabeth I's court astrologer John Dee was apparently another identity of Jared Khan, who was still fruitlessly hunting the Doctor at the time. At this point the Queen appeared to be on friendly terms with the Doctor (then in his seventh incarnation. (NA: Birthright)
- The Doctor had met previously met Dee in 1568, and he was not Khan on that occasion. (ST: Mortlake)
Alternative timelines
An alternative version of the Doctor met another version of Elizabeth I: Gloriana of an England with its own star fleet. (DWU: A Storm of Angels)
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The Doctor had previously seen the Queen attempting to influence William Shakespeare's writing via the Time-Space Visualiser around the time the latter had written The Merry Wives of Windsor) (DW: The Chase)