Conveniently Unverifiable Cover Story

"Baltar: ...So, uh, tell me, are you from Aerilon? Slight trace of an accent there...

Boomer: What? Uh, no - Troy.

Baltar: Troy... tell me, why is that familiar?

Boomer: The mining settlement? The accident.

Baltar: The explosion, right. That was tragic. Your family, uh...

Boomer: They died with the rest."

- Battlestar Galactica Reimagined, "Flesh and Bone"

Designing a good cover story is one of the most difficult and crucial parts of going undercover for The Mole. Lack of research into the details and customs of the identity they're assuming can be a dead giveaway in casual dealings, and even the best falsified documents backed up with hacked databases and bribed records keepers can eventually be cracked with enough research and cross referencing. What a lot of moles end up doing is sacrificing authenticity for security by creating a conveniently unverifiable cover story. This cover story creates or assumes an identity whose background can't be verified or disproved, by claiming to come from a place or period with no personal records or witnesses. Commonly, it's a burned down orphanage, though being the "lone survivor" of an accident, or coming from a place that suffered a natural disaster or been in a civil war are also common. Potentially non-tragic unverifiable cover stories are coming from communities that shun modern things like hospitals and birth certificates, or where the hall of records has been destroyed.

The catch of course is that they also can't positively prove they are who they say they are, and a Genre Savvy character will instantly suspect them. Usually the mole will play patriotic and use the benefit of the doubt, or "innocent until proven guilty" to get their mission accomplished. One especially evil twist is for the mole to claim to come from a village his Big Bad boss personally razed explicitly to create this cover, and uses it to earn the sympathy and acceptance of the heroes by claiming to want revenge. It helps if the heroes are Genre Blind characters or horrible judges of character.

A determined investigator will usually try to find someone who can prove if the mole is who they say they are. Like a family member, another survivor, records, or the corpse of the person they're impersonating. The odds of finding these records vary, but usually come just too late. This trope may be paired with Laser-Guided Amnesia, Fake Memories, and an implanted Split Personality to create a persona wholesale to sell the role, though these tactics have a high risk of agent meltdown and conversion.

Anime

 * Averted in Tenchi in Tokyo.
 * Durarara: Kazutano, an illegal immigrant living in Japan, once claimed his birth certificate was burned during the World War II firebombings. He's too young for that story to be at all credible, though.
 * In The World God Only Knows, Elsie uses her supposed status as illegitimate daughter of Keima's father to convince his mother to let her live with them. Since his father is pretty much never home, there was no way to really confirm the story, though the fact that he couldn't prove it false outright does raise some interesting questions.

Fan Fiction

 * Subverted in the Symphony of the Sword subseries of Undocumented Features: Utena Tenjou and those of her friends from Cephiro who make it to Midgard are given elaborately detailed and otherwise genuine identities by Gryphon and MegaZone, who are for all practical purposes the legitimate government of Zeta Cygni.
 * Inverted in the Mass Effect self-insert Mass Vexations. Author Avatar Art arrives in the ME universe, and knows that nobody will believe him if he tells them he literally teleported into the Citadel from an alternate dimension where everything that Art now sees around him was part of a video game. Thus, he makes up a cover story about having taken a ton of stims before smuggling himself onto a ship headed to the Citadel to avoid suspicion. He's not actually a mole for anyone, fortunately.
 * Not to mention, it doesn't entirely work- he ends up making both Kaidan and Jacob suspicious of him. Neither works it out, but they don't stop suspecting him, either.

Film

 * Total Recall has a double-example of this. Arnold's character initially infiltrated the Martian resistance, convincing them to trust him and believe that he was betraying the Big Bad. The Big Bad then captured him and erased his memory to stop him from revealing all of his secrets to the resistance. It later turns out that this was just an elaborate ruse to help him infiltrate deeper into the resistance, since they are then convinced he really had a major secret to reveal.
 * Reservoir Dogs has this with . The made-up cover incident in question is referred to as "the commode story".
 * In Salt, a Russian operative claims that Evelyn Salt was a deep cover agent who was planted in America at the age of 12. They faked a car crash to kill an American family living in Russia and replaced the daughter's corpse with their agent. Because her supposed family is dead (and her other relatives haven't seen her in years) there's no one to dispute her identity.

Literature

 * Done in Robert A. Heinlein's Friday by the protagonist and many other "artificial persons" who need cover stories. Her "birthplace" is Seattle (destroyed in an earthquake) and Friday cynically comments that the recent destruction of Acapulco in a corporate war means that a lot of artificial persons will end up being "born" there as well.
 * In Lois McMaster Bujold's Brothers in Arms, Elli Quinn spots the bad guy partly because his cover identity is from a planet wrecked by a tectonic disaster. Indeed, it's implied that only amateurs use that planet for a cover identity any longer, as every professional intelligence agency in the Nexus considers 'survivor of Frost IV' an automatic red flag requiring double-checking.
 * In SS-GB by Len Deighton the hero finds a fake ID on a member of La Résistance. The town listed as his birthplace had its records office destroyed in the war. The hero notes that lots of fake IDs use that town.
 * in Ursula Vernon's Black Dogs purportedly escaped from an evil magic user . In the time this character was in captivity, he/she claimed to have his/her innocence destroyed by all the cruelly calculated murder and remains inconsolably guilty for things that were not really his/her fault. This character pretty much becomes The Woobie to some of the other characters for these reasons. However, it is later revealed that this person's persona is just a  part of his/her personality, later on it's revealed that  this character's True Self is somewhere between these two extremes.
 * Lensman. When Kinnison infiltrates the Boskone hierarchy, the Arisians (unknown to him) adapt his cover even to the extent of correctly aging the ink on all the documents, knowing that he'll actually be up against their own evil counterparts, the Eddorians.
 * In the Expanded Universe of Star Trek: Voyager, it's explained that Tuvok is able to infiltrate the Maquis by making a false cover story of how his family was killed by Cardassians on a border planet. He further endears himself to them by giving up a Starfleet Intelligence operative and putting a big hole in the Hood (but not killing anyone) when all was said and done.
 * And in The Original Series novel Time Trap, the Klingons do this repeatedly to surgically-altered agents, giving them false memories to match. Spock figures out the plot when he notices a suspicious number of people in critical positions who are from disaster areas.
 * One Captain Future novel featured the Captain trying to pass off as a pirate from a ship which was destroyed. There is a minor problem when he meets with a guy who really served on that ship, but he manages to convince those around him that it's because the real pirate was a gunner - and he was a mechanic, so they had no interaction.
 * In the Merchant Princes series by Charles Stross, Miriam Beckstein manages to become the Widow Fletcher, returning from the New British Empire with her "deceased husband's fortune." The corrupt lawyer who affirms her identity lists her hometown as Shreveport, which was completely destroyed in the last World War. She lampshades just how weak her identity is, and how basic SEC due diligence checks would completely shred it, but nobody in New Britain bats an eye at it.
 * In James Bond novel Moonraker, Hugo Drax is really a Nazi officer who adopted the identity of one of the countless British servicemen missing in action in the aftermath a large battle in World War Two.

Live Action TV

 * Battlestar Galactica Reimagined had Sharon "Boomer" Valerii, whose "family" perished in a notorious mining accident on Troy. She believed it, and even kept pictures of it post tomato for a while.
 * If you haven't seen the season three finale yet, don't highlight:
 * Dark Angel: When Alec poses as Simon Lehane, he claims to have been tragically orphaned.
 * In Kyle XY, Kyle is given a plausible backstory for his lack of memories, intelligence and absence of a navel. His female counterpart, Jessi, however, is given false memories because an agent for a Corrupt Corporate Executive finds her first.
 * In the short-lived series Runaway, the mother of a fugitive family manages to pass off their lack of legal documents as having been lost in Hurricane Katrina. Cynical, but effective.
 * Wiseguy. Averted, as the main character uses his own identity, including an 18-month prison sentence to establish his credentials as a criminal. Unfortunately this alienates him from his own mother, who doesn't know he's a federal agent.
 * The Meeting Place Cannot Be Changed has one of its heroes, Sharapov, infiltrating the gang that he and the rest of the police are trying to bring down. To win over the gang's highly suspicious leader, one story is not enough, and Sharapov is soon spinning lies that span into an entire (fictional) biography, complete with fictional girlfriend, fictional criminal father, fictional jobs, etc.
 * In the "Vicki's Adoption" episode of Small Wonder, Ted and Joan had Vicki write two letters, in different styles of handwriting, claiming that Vicki was born in the Seychelles (hence her being named Victoria), her birth parents had died while traveling (see Stereo Fibbing), and she was raised in a convent before being brought to the United States.
 * In the "Vicki's Adoption" episode of Small Wonder, Ted and Joan had Vicki write two letters, in different styles of handwriting, claiming that Vicki was born in the Seychelles (hence her being named Victoria), her birth parents had died while traveling (see Stereo Fibbing), and she was raised in a convent before being brought to the United States.

Video Games

 * This is ending in Twisted Metal 2.
 * Interesting variation in Tales of Phantasia. Early in the game, the party meets a girl named Ria, who wants them to help her get revenge on a guy named Demitel for killing her family. When the party finally meets Demitel, he reveals that he killed the entire family, including Ria. After you beat Demitel, the whole truth comes out - Ria was
 * Deus Ex has the Denton brothers, whose parents were killed in some sort of vague accident or terrorist attack. Turns out.
 * In Ace Attorney Melissa Foster claims that she has no identity papers because she recently fled an unnamed country that had exploded into civil war.

Western Animation

 * W.I.T.C.H. - the sob story that Miranda gives Elyon.
 * In Justice League, the backstory that Hawkgirl originally gave was that she was a Thanagarian police detective, and that she had been accidentally teleported to Earth by a stray Zeta Beam. And that Thanagar was too remote for her to find her way back (it's so remote that they hadn't even heard of the Green Lantern Corps)--and too remote for her teammates to check her story and find out why she's really on Earth.
 * In the episode "Twilight of the Gods" has a subtle hint of Foreshadowing on this; when the League infiltrates Brainiac's base, Jon Stewart suggests that Brainiac's database may have information on Thanagar, including its location. In retrospect, you realise how desperate Shayera was to direct Jon away from that line of thinking.

Real Life

 * The non-fiction book KGB: The Hidden Hand mentions how a KGB agent in the United States was ordered to get details on an orphanage that had just burnt down (thus destroying all records), presumably so it could be used to create fake 'legends' for later spies.
 * During World War II, the Red Army had units claiming to be Polish so as to avoid the fact that they really wanted to take over Poland. The Russians pretending to be Polish would claim to be from Polish villages that had been wiped out by the Germans.
 * While not exactly following the example at least in jokes Kokossovsky was not considered Polish. Like "during nomination on Polish Minister of National Defence foreign journalist asks "How is it possible that person taking such office speaks Polish so badly?" "I'm surprised he speaks Polish"".
 * The San Francisco Earthquake of 1906 was used by numerous Chinese immigrants to get into the USA despite the Chinese Exclusion Act.
 * Today, many U.S. government agencies that require documentation will make allowances for anyone from New Orleans or Haiti. So, y'know, if you needed a fake background...