Hardcore Doctor Who fans have noticed that the 11th season of the show has so far not featured any recycled characters from the past, staying true to showrunner Chris Chibnall's promise to keep the newest series feeling fresh. But, in the very opening moments of “The Witchfinders,” Jodie Whittaker’s 13th Doctor says something that indicates she nearly crossed paths with one of her past selves, and probably still has a crush on a very big historical figure.
Though the primary plot of the “The Witchfinders” takes place in Lanchester in 1612-ish, the Doctor initially says she wants to go watch the coronation of Queen Elizabeth, the First, which happened in 1559. Now, although the TARDIS doesn't land there, and King James ends up being the British historical monarch de jour in this episode, the mere mention of Queen Elizabeth I recalls a long and tumultuous history between the Doctor and Elizabeth, one that culminated when the 10th Doctor married her.
Queen Elizabeth's most important Doctor Who appearances took place in 2007 and 2013 episodes, but the monarch has graced the series before. Her first appearance was in the 1st Doctor (William Hartnell) adventure “The Chase,” although the Doctor only observed Elizabeth chatting with Shakespeare. In “Thicker Than Water,” a 2005 audio adventure with the 6th Doctor (Colin Baker), the Doctor mentioned visiting the court of Queen Elizabeth I, which seems like an advanced continuity error, simply because the people producing the Big Finish audio plays in 2005 couldn’t have known that Queen Elizabeth I would actually appear in new episodes of Doctor Who in both 2007 and 2013.
This happens again in another 2005 audio adventure called “Terror Firma,” in which the 8th Doctor (Paul McGann) also (briefly) visited Queen Elizabeth I. Because the Doctor regenerates, these appearances could still be canon, because Queen Elizabeth I only knows the Doctor in this 10th incarnation, meaning she wouldn't recognize him in a different form.
So, had Team TARDIS ended up in 1559 at the coronation of Elizabeth I, the Doctor would have been in the clear in terms of being recognized by the Queen for two reasons: First, she looks nothing like Colin Baker, Paul McGann, or David Tennant these days, and 1559 is three years before the 10th Doctor briefly married the Queen in 1562. But does the 13th Doctor still have a crush on Elizabeth I? It depends on how you interpret “The Day of the Doctor,” “The End of Time,” and “The Shakespeare Code.”
In terms of canonical TV appearances in Doctor Who after the 1965 appearance in “The Chase,” Elizabeth I first shows up in the 2007 10th Doctor episode “The Shakespeare Code,” in which she straight-up wants to kill the Doctor. Now, this episode is set in 1599, which means she’s been the Queen for like 40 years at this point. At the time this episode aired, we had no idea why Elizabeth wanted to kill the Doctor, but in the final regular David Tennant two-parter, “The End of Time,” he makes an off-hand comment about marrying her and probably conjugating their union. At this point, the idea that he then skipped-out on her was the implied reason why Elizabeth wanted to kill him many years later.
And, the idea that the Doctor actually had sex with “the virgin queen” is corroborated in the 2013 crossover episode “The Day of the Doctor.” When the War Doctor (John Hurt), the 10th Doctor (David Tennant), and the 11th Doctor (Matt Smith) all meet in 1562 — the same year the Doctor married Queen Elizabeth I. In this one, we discover that the reason the Doctor got “busy” was because he was trying to figure out which version of the Queen was a shapeshifting alien Zygon.
“What you get up to in the privacy of your own regeneration is your own business,” the 11th Doctor said to the 10th. Plus, in "The Beast Below," the 29th-century monarch named Liz X — queen of Starship UK —mocks the Doctor about his relationship with her predecessor, too, proving, that the notion that the Doctor messed around with Elizabeth I becomes future historical fact. Does the 13th Doctor have thoughts and feelings about this?
If the 13th Doctor wanted to visit the coronation of Elizabeth I three years before she briefly married the Queen, it feels significant. Is the Doctor nostalgic about her old adventures? Does she feel like seeing Elizabeth before their relationship got screwed up? Is this just the curiosity of visiting an old crush? Sadly, because the TARDIS missed the Doctor's intended destination and the episode took Team TARDIS to the early 1600s instead of 1559, we’ll never know.
Still, even though the Doctor didn’t get to see Elizabeth I in “The Witchfinders,” there was one other connection to the Queen’s appearances in “The Day of the Doctor” and “The Shakespeare Code”: witches! In “The Shakespeare Code,” the primary monsters looked and acted like witches, but were really aliens called the Carrionites. So, that episode had witches and ended with the now-infamous Queen Elizabeth cameo. “The Witchfinders” teased a big Queen Elizabeth cameo at the beginning, and then had witches throughout. But witches were mentioned in the other Queen Elizabeth Doctor Who episode, too.
When the three Doctors are surrounded by Elizabeth’s troops in “The Day of the Doctor,” the 11th Doctor convinces them that the voice of Clara Oswald is, in fact, the work of “witchy witchcraft.” In that episode, the Doctor was sort of joking about the concept of witches in 1562, tossing the comments aside like it was no big deal. But now, the 13th Doctor seems to care a little bit more about this kind of thing, and instead of joking about accused witches, swims the opening scenes to save an accused “witch” who is about to be drowned. Meaning, even if the Doctor is still nostalgic about her past lives — and her previous dalliances with Queen Elizabeth I — she’s certainly not someone who makes jokes about witches anymore.