Stock Unsolved Mysteries

The possibility to let your characters witness or even participate in events that actually happened, is probably one of the most appealing aspects of Historical Fiction, Flashbacks, Time Travel stories and the like. But sometimes it can be quite hard to shoehorn your characters in, if you don't want to sacrifice too much of historical accuracy. Especially if your character doesn't quite fit into the historical setting, because he is a Ninja Pirate Zombie Robot.

The solution: Take a famous historical event that is shrouded in mystery, an event of which not many details are publicly known. Then fill the gap of historical records with whatever you want, this way "revealing" what actually happened. This adds the bonus that everyone likes a good mystery (and its eventual solution).

Depending on the tone and genre of your work, your "explanation" can range from mundane, over humorous, to absolutely fantastic.

The Gump likes to cause this events. Of course Historical Domain Characters as well as fictional Public Domain Characters may be involved too. Perhaps they did even use a Public Domain Artifact.

Anyway, in the end you can proudly claim that your story is Very Loosely Based on a True Story.

Closely related to Historical In-Joke. Can also overlap with Beethoven Was an Alien Spy, when the focus lies on specific historical individuals. Often happens at, and tightly involves, a Landmark of Lore. Also, at least one of this events is a must-have for any Conspiracy Kitchen Sink story worth its salt.

Note that sometimes mysteries get solved, or even debunked as not having been that mysterious in the first place. In this case the work either was written in a time before the solution/debunking, or the writer didn't get the memo, or he just didn't care.

Stock Unsolved Mysteries that have its own trope pages

 * The assassination of John F. Kennedy.
 * The extinction of the dinosaurs.
 * The disappearance of Amelia Earhart.
 * The disappearance of Roman legions, especially the Legio IX Hispana.
 * How (and why) the Ancient Egyptians built the pyramids.
 * The murders by Jack the Ripper.
 * The Roswell incident.
 * Ships and airplanes disappearing within the Bermuda Triangle.
 * The Tunguska Event.
 * Fermat's Last Theorem.
 * The Men in Black

Stock Unsolved Mysteries without their own pages, and examples thereof

 * Mysterious murder cases.
 * The gruesome unsolved murder of Elizabeth Short, nicknamed "Black Dahlia", 1947 in Los Angeles.
 * Is a major part of the plot in LA Noire. (It turns out that )
 * Was also the plot of an episode of Hunter.
 * In the '90s adventure game Black Dahlia, it turned out to be part of an ancient magical ritual carried out by Nazis.
 * And then, of course, there's the book Black Dahlia, and the movie adaptation.
 * David Fincher's film Zodiac strongly suggests that a real suspect in the officially unsolved Zodiac Killings was the guilty party.
 * The Grant Morrison/Daniel Vallely comic book Bible John: A Forensic Meditation is a surreal, hallucinogenic speculation on the unidentified Serial Killer's possible motivations.
 * Edgar Allan Poe's story The Mystery of Marie Roget, shows his detective protagonist C. Auguste Dupin solve a real unsolved murder receiving tremendous newspaper coverage at the time. Most students of the case now accept a different solution.
 * Mysterious disappearances.
 * The disappearance of the British peer Lord Lucan in 1974, shortly after his children's nanny was murdered.
 * The disappearance of the American labor union leader Jimmy Hoffa in 1975.
 * The case of Benjamin Bathurst, who disappeared from his hotel one day in 1809. (The actual truth is quite prosaic: Contemporary documents make it clear that he was almost certainly just mugged. Some of his personal belongings were even found during the search for him. It only became a mysterious mystery because of one particular account that made it sound like he'd disappeared into thin air in front of witnesses.)
 * H. Beam Piper, Robert Bloch, Lionel Fanthorpe, and Avram Davidson, among others, have written stories in which Bathurst was transported to the future or to an Alternate Universe.
 * Simon Hawke's Time Wars series has a line in passing attributing his disappearance to somebody changing the past out from underneath him.
 * The mystery of the sailing ship Mary Celeste, whose entire crew did vanish in 1872 somewhere in the Atlantic Ocean. This one has been solved, as stated in the intro, no one cares.
 * In the Doctor Who serial The Chase, the crew were killed by Daleks.
 * The Goon Show (The Mystery of the Marie Celeste (solved))
 * "J. Habakuk Jephson's Statement", a short story by Sir Arthur Conan Doyle.
 * In 1990, the Gibraltarian author Sam Benady published Sherlock Holmes in Gibraltar, a set of two short stories set in the pre-Watson days. In the first one, The Abandoned Brigantine, Sherlock Holmes solves the mystery of the Mary Celeste.
 * The 1945 disappearance of Flight 19, usually linked to the Bermuda Triangle.
 * The disappearance of the Roanoke Colony, an English colony in what is now North Carolina, a generation before the sailing of the Mayflower. An additional point of interest is that among the disappeared colonists was the child Virginia Dare, the first English child born in America.
 * The Roanoke Colony features in Marvel 1602, and Virginia Dare is a significant character.
 * The Doctor Who Missing Adventures novel The Empire of Glass offers an alien-abduction explanation.
 * The Roanoke Colony mystery was a significant part of the Myth Arc of the TV series Freakylinks.
 * One Hundred Bullets has the disappearance of the Roanoke Colony be the work of The Trust, as the colonists refused to cede to the Trust's plans of pulling the strings of the American experiment.
 * The backstory of Werewolf: The Apocalypse has Roanoke wiped out when the Eater of Souls woke up. The word "Croatoan," famously found etched into a tree, was the name of the Native American werewolf tribe that gave their lives to put the thing back down.
 * The short story "Ezekiel" by Desmond Warzel explains where they went, and why.
 * Grant Morrison's Seven Soldiers features the present-day descendants of the colony living in an underground town. The reason for their disappearance: Also, the underground town is inexplicably located close to a New York City Subway tunnel.
 * Andre Linoge, the Big Bad of Stephen King's Storm of the Century, claims to have caused the disappearance and death of the Roanoke Colony by forcing all its citizens to drown themselves in the sea when they would not "give him what he wants", and intends to repeat the tragedy on Little Tall Island. The word "Croatoan" is invoked by a later Driven to Suicide member of the town, but is never fully explained.
 * The disappearance of the so-called "Jewels of Helen" excavated from the ruins of Troy was the subject of the Elizabeth Peters novel Trojan Gold. (The mystery has since been solved, but that was after the novel's publication).
 * The Philadelphia Experiment, allegedly conducted by the US Navy in 1943, involving the destroyer escort USS Eldridge turning invisible and being teleported.
 * The appropriately titled movie The Philadelphia Experiment.
 * Part of the backstory of RASL.
 * The exact cause of Monumental Damage (if not known with certainty), like how the Great Sphinx of Giza did lose its nose or the Venus de Milo her arms.
 * Prince of Egypt shows the Sphinx getting its nose knocked off.
 * So does the comic Asterix and Cleopatra.
 * And the movie Asterix Versus Caesar reveals why the Coliseum in Rome has such a big hole at one side.
 * In The Simpsons, Jebediah Springfield is responsible for the damage on a famous George Washington portrait.
 * In Irregular Webcomic, the Reichstag fire (1933 in Berlin) was neither set by the Communists, nor the Nazis in order to frame said Communists, but instead
 * The exact cause of famous city-devastating fires. (Rome 64, London 1666, Chicago 1871, ect.)
 * A German novel called Der Funke des Chronos deals with Time Travel and the Hamburg fire of 1842.
 * The Great Fire of London is a plot point in The Baroque Cycle by Neal Stephenson. While it isn't exactly presented as something mysterious, one character (the father of Daniel Waterhouse) firmly believes that this is the Apocalypse.
 * Doctor Who has covered both Rome (Nero did it, having been given the idea when the Doctor accidentally set fire to a map of Rome by focusing sunlight through his reading glasses) and London (accidentally started during a showdown with aliens planning to wipe out humanity). The Doctor Who Expanded Universe has also done Chicago (accidentally started during another showdown with a different set of invading aliens).
 * Colony collapse disorder. The sudden vanishing of worker bees from their hives across the world (leaving even their queens behind), first reported in 2006. No conclusive explanation has yet been found.
 * The X-Files used the bees as an integral part of the Government Conspiracy's Evil Plan, about a decade before the CCD was first reported. However, the feral bee population across the world has been rapidly diminishing since 1972... and incidentally, said Government Conspiracy was founded in 1973.
 * The Secret World trailers contain the Arc Words "The Bees Are Returning" (among other things), which is currently believed to have to do with the CCD.
 * Doctor Who used it as a running joke throughout series 4. It ends with the revelation that.
 * Savage Chickens got yet another theory on Venus de Milo. She came from the sea, remember?

Works dealing with more than one example of this trope

 * Ancient Aliens.
 * The Various Star Trek incarnations did a few, be it Jack the Ripper, (TOS), Roswell (DS9) or Amelia Earhart (VOY).
 * In Assassin's Creed, every weird event and person from Adam and Eve to Jesus to King Arthur to Rasputin to Tunguska are explained by the Precursor technology left behind which inspired all the religions in the world.
 * Matthew Reilly's Jack West series of novels do this quite a bit. For example, the plot of the first book revolves around the real life mystery of what happened to the missing capstone on the Great Pyramid of Giza.
 * Doctor Who is intimately familiar with this trope. For example the disappearance of Agatha Christie was given a supernatural explanation in "The Unicorn and the Wasp".
 * The X-Files, being an epic Conspiracy Kitchen Sink and all.
 * The comic book series Planetary has this in almost every issue.
 * xkcd had a strip dedicated to this trope, referencing Amelia Earhart, the Roanoke Colony, Franklin's lost expedition, and Jimmy Hoffa.