While reading 8 Historical Mysteries That Would Make Great 'Doctor Who' Episodes, I came across the following:

Doctor Who has co-opted a number of historical figures and events, putting the Time Lord in position to explain some of the world’s biggest mysteries. We’ve had Agatha Christie’s disappearance, Shakespeare’s missing play, and the Mary Celeste’s missing crew.

I was a little confused as I had no idea those were real life mysteries. It got me thinking, which Doctor Who episodes "explain" real life mysteries?

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    You mean aside from the three you've mentioned? – Valorum Aug 25 '16 at 22:14
  • @Valorum you can include those too (if you want), since I have no idea what they're talking about. – RedCaio Aug 25 '16 at 22:15
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    @RedCaio Agatha Christie's disappearance: The Unicorn and the Wasp (S4E7, one of the better historical DW episodes). Shakespeare's missing play: The Shakespeare Code (S3E2, silly and forgettable). The Mary Celeste's missing crew: I hadn't heard of this one, but apparently it's a First Doctor serial. – Rand al'Thor Aug 25 '16 at 22:24
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    Aside from real historical mysteries like the ones mentioned, they've also given explanations for various claims of cryptozoological creatures and supernatural mysteries, like the Loch Ness Monster (Terror of the Zygons), the Yeti (The Abominable Snowmen), vampires (State of Decay), devils (The Daemons), etc. – Hypnosifl Aug 25 '16 at 22:34
  • @Hypnosifl And let's not forget the "three possible versions of Atlantis"! – Rand al'Thor Aug 25 '16 at 22:36

This is a Community Wiki answer - please add examples/details as needed.

Real-life mysteries:

Alternative explanations of events not generally considered mysterious

Bonus round: Cryptozoological creatures and supernatural mysteries:

  • A useful Wikipedia resource for this answer. – Rand al'Thor Aug 26 '16 at 1:13
  • I wasn't aware that Haemophilia in the British Royal Family was a real thing :O – tilley31 Aug 26 '16 at 17:57
  • Note that the second section ("Alternative explanations") could potentially get very long, and doesn't strictly answer the question. I considered deleting it, but decided I should ask for opinions before doing so. – Blackwood Aug 27 '16 at 19:30
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    @tilley31 That's where the expression "blue blood" originates. – TRiG Oct 9 '16 at 2:44
  • @Randal'Thor I'm not sure that Nefertiti is currently considered to have disappeared. The sources cited in her Wikipedia article suggest that despite earlier theories to the contrary, she remained influential through the end of Akhenaten's reign and into the early years of Tutankhamun's. Perhaps the item about her belongs in the "Alternative explanations" section. – Blackwood Oct 9 '16 at 2:48

I think the episode "Horror of Fang Rock" from 1977 is supposed to be an explanation for the Flannan Isles Lighthouse mystery of 1900. (https://en.wikipedia.org/wiki/Horror_of_Fang_Rock#The_Ballad_of_Flannan_Isle)

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    As the first answer is marked "Community Wiki", feel free to edit this item into that answer. – Blackwood Aug 28 '16 at 20:18
  • Although now I have read the Wikipedia article you linked to, it seems that the episode was inspired by the Flannan Isles Lighthouse Mystery, but it doesn't attempt to explain it. – Blackwood Aug 28 '16 at 21:16
  • @ElliottFrisch In that episode, the Rutans are responsible for the deaths on Fang Rock (off the south coast of England). However. the story is not the same as that of the Flannan Isles Lighthouse mystery, so I don't think it can be considered an explanation of the mystery. – Blackwood Sep 1 '16 at 3:48
  • @Blackwood Ah yes, I see your point. The deserted light house mystery was explained, but the island was fictionalized. – Elliott Frisch Sep 1 '16 at 4:14

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