Deep-Cover Agent

She seems to be the all-American woman. She's married to a nice man, she helps out at the PTA, bakes cookies for charity and drives a car with the US flag on it. She speaks like she's lived in the US all her life, and every Memorial Day lays flowers on her war-hero parent's graves.

Deep down, however, she's got a dark secret. She's from Commie Land or somewhere like that. She's been sent on a long-term secret spying mission and got herself a senior government or Cloak and Dagger figure, who she can get information from in their intimate moments (Reds in the bed!). Add a sprinkle of Neuro Vault and you get the Manchurian Agent.

Since the actress playing said agent is usually non-Russian, you get the interesting situation of a Recursive Crossdresser-esque Fake American Fake Russian. They're sometimes in danger of Becoming the Mask.

This is Truth in Television, even in a post-Cold War world.

Anime and Manga

 * In Death Note, Light Yagami joins the task force looking for Kira to throw off suspicion as he himself is Kira. At one point, he erases his own memory, and becomes such a Deep-Cover Agent that even he doesn't know he's undercover! He's practically a Manchurian Agent, except that he isn't being manipulated by anyone other than himself. Everything goes exactly as planned.
 * Mitsuko's mother in Kikaider, who was hired to spy on Dr. Komiyoji, and only gave birth to her as a means to appear like a normal happy family.

Comic Books

 * Appears frequently in Nth Man the Ultimate Ninja, usually as deep-cover Soviets impersonating American citizens and soldiers.
 * Bucky Barnes, during his time as the The Winter Soldier often served this role during the Cold War, given that he was an American brainwashed into serving as a Soviet assassin.

Film

 * Ur-example -- the Evil Matriarch from The Manchurian Candidate.
 * The Long Kiss Goodnight had a case of this, but Charlie's Deep Cover situation (which fractured at inopportune moments) was more a case of amnesia (which resulted in sweet, cute housewife displaying mad skills) based on a sudden betrayal.
 * In Traitor,.
 * In Salt, the main character is accused of being this.
 * The Debt: The main characters are undercover as Germans who recently moved to Berlin from Argentina. Two are Undercover As Lovers.
 * In No Way Out, a Pentagon Witch Hunt for a supposed Soviet mole is used as a cover story to frame someone for a murder committed by the Secretary of Defense. Of course, it turns out that there really is a mole, who was inserted into the country as a child and managed to work himself up through the military until he was in a position of absolute trust.
 * In Inglourious Basterds, demands to be retconned into one when negotiating a change of sides.

Literature

 * The Bourne Ultimatum novel features another such facility, where Carlos the Jackal was trained (until he got thrown out). There's also a character who's trained to be an American. His mother (another Deep-Cover Agent) has been captured by the Americans and he wants her freedom.
 * Protagonist Trystin Desoll of L.E. Modesitt, Jr.'s The Parafaith War, though his infiltration didn't actually last that long. Because he looks a lot like the vaguely-Aryan "revs," he gets put through heavy training to learn how to infiltrate their home planet. His training would've allowed him to stay indefinitely, but he carried out his assassination mission in about a week.
 * In the BattleTech novel Bred for War, it's a DNA test performed by a (mostly unwitting) deep cover agent that leads to the discovery that the son of Thomas Marik, Captain-General of the Free Worlds League, has died of his leukemia and been replaced by a double while undergoing treatment in the Federated Commonwealth. This does not go over well (it starts a war, in fact), but in the end also clues the Commonwealth's ruler in to the fact that.
 * The movie and book Telefon have this as the primary plot driver. Communists wanted to cause havoc in America immediately prior to an invasion, so they took a few dozen people, hypnotized them extensively so they actually became average American citizens, living perfectly normal lives, until they heard the code phrase which activated them to go destroy some defense facility. The only problem was that they had been forgotten about for a while, so all of the defense facilities were obsolete and/or not being used, which confused the heck out of the American agencies who were wondering why perfectly normal Americans attacked things of absolutely no strategic or military value.
 * Jos Musey from the Warchild Series goes into deep cover aboard the starship Macedon. He learns a new accent and slang for the part, and acts the part of a soldier perfectly, even fighting against his own people.
 * In Tom Clancy's novel Executive Orders, the Iranian religious leader placed deep cover agents in several countries with orders to become part of their respective leaders' security details. The first use of one of these agents is to assassinate the president of Iraq, starting the book's major conflict. Naturally, there's another agent, in.
 * In the X Wing Series Gara Petothel, after being disgusted by her superior's willingness to sacrifice the crew of a Star Destroyer, arranges for his death to come a little sooner and sends out the evacuation order that he had been unwilling to make. Then she implements her backup plan, taking an identity as her superior's drugged-up unwilling mistress, and gets into an escape capsule. The New Republic gets her over an addiction to various drugs and sets her up with a modest job and apartment on Coruscant, where she secretly sends a message to Warlord Zsinj, her boss's boss, saying that she's in position and will keep doing what she's been ordered to do. She's a professional mole and has joined, served for long periods, and betrayed the New Republic before. This time, Wraith Squadron recruits her in a complicated scheme, and although she joins the squadron with the intent to betray it and bring down the Rebel hero Wedge Antilles, she gets sucked in by The Power of Trust and how Good Feels Good, and becomes the mask. Unfortunately, the Wraiths eventually find out about the Awful Truth.
 * Honor Harrington takes this to extremes; the Mesan Alignment has deep-cover families that have been in place for generations, waiting patiently for the time to be right for Mesa to call on one of them.
 * from Emma Bull's Falcon, who was planted years ago to bring down a whole planet's government.

Live Action TV

 * Irina Derevko/Laura Bristow from Alias, a KGB agent tasked to marry an American CIA agent. The show also features a training facility in Russia where people are trained to blend in in American Suburbia.
 * A minor character in the second season and from the third season also turn out to be examples of this trope.
 * In the Lois and Clark episode "Super Mann", a star quarterback, country singer, and model are revealed to be deep cover agents from Nazi Germany.
 * Ingrid Bannister in the MacGyver episode "The Enemy Within". She hypnotises her husband into telling her secrets on a frequent basis. Played by Lynn Holly Johnson, in case you're interested.
 * Rather common on Mission Impossible when they faced foreign agents. A first season episode even showed the training facility.
 * The 1991 BBC series Sleepers was about two KGB agents who had been in Deep Cover for 25 years - when they're finally activated, they don't wanna do it. When it was aired on Masterpiece Theater it was advertised as "the first Masterpiece Theater Comedy."
 * NCIS has had at least two of these, both of whom had married sailors. One was a Korean agent who did a Heel Face Turn after falling in love with her husband and having a baby. The other was a terrorist who murdered her husband.
 * The New Avengers episode "House of Cards" features a rogue Russian agent activating an old cold war project of deep, deep cover agents,.
 * In Kamen Rider Dragon Knight, the reporter Michelle Walsh turns out to have been working for the No Men all along, helping them squash the rumours that other reporters were stirring up.
 * In one episode of Castle the bad guy turned out to be a Soviet Deep-Cover Agent in the CIA who had gone rogue after the fall of the Soviet Union.

Poetry

 * 'My Neighbour Mr Normanton' in the poem by Charles Causley. Outwardly as British as can be ('He keeps a British bulldog, and British Summer Time'), he is observed by the narrator hiding microfilm and meeting with foreign gentlemen.

Video Games

 * Metal Gear Solid, Revolver Ocelot/Major Ocelot/Shalashaska/Adamska/Liquid Ocelot.
 * The manual to Metal Gear 2 reveals that Snake used to be one of these in the CIA. Nothing is revealed about what he actually did (leading a lot of fangirls to jump to the sexiest possible conclusion), but at one point Campbell threatens to blackmail him with records of the things he did, so it was probably extremely dubious.
 * Need for Speed Undercover features the player, as a cop, going into deep cover as quickly as possible. This means, basically, that he becomes a reckless criminal, doing crazy stuff like street racing, car thefts and high speed police pursuits just to get in good with the criminals.
 * , in Wing Commander III, specifically of the Manchurian Agent variety.
 * Modern Warfare 2 has the infamous airport level where the player has to take part in a massacre to maintain their cover.
 * In Splinter Cell: Double Agent, Sam is sent to infiltrate a terrorist group named John Brown's Army, and actually has to help them get materials for a nuclear weapon.
 * In Alpha Protocol, was raised from birth to be a double agent for.
 * In Alpha Protocol, was raised from birth to be a double agent for.

Web Original

 * in Chewbots Let's Play of The Oregon Trail, Plague and Treachery On The Oregon Trail.

Western Animation

 * Hawkgirl in the Justice League animated series, who in the "Starcrossed" story arc at the end of the second season was revealed to have been a spy for the planet Thanagar, in preparation of its invasion of Earth.
 * Shockwave, of Transformers Animated, who, as Longarm, was the head of Autobot intelligence. He even has two robot modes and two vehicle modes, to further disguise himself.