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- 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 great example 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.
- In Lone Wolf and Cub, the "Grass" are a large network of deep-cover ninja employed by the Big Bad; the recall of the entire remaining network (Itto had sliced through a good deal of them already) to stop the protagonist in the last volume underlines how dire the situation is for Retsudo.
- Appears frequently in Nth Man: The Ultimate Ninja , usually as deep-cover Soviets impersonating American citizens and soldiers.
- Captain America: 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.
- In Judge Dredd, Wally Squad Judges are heroic... well, Mega-City One justice... versions. They're plainclothes judges who live entire lives as ordinary citizens, and are notably the only plainclothes officers on the force. They're called the Wally Squad because being an "ordinary" Mega-City One citizen means being insane, and most of them have become the mask to some extent. Two strips have focussed on Wally Squad members: Low Life and The Simping Detective.
- Marvel's Civil War involved Namor having multiple sleeper cells in the USA. Of course, seeing as this was the B-story, this didn't go anywhere.
- Preacher: The Holy Grail apparently has at least one deep cover agent in every country's government, to make sure they don't get out of line. Hoever, Hoover notes that they've become accustomed to secretly running the world and seeing world leaders squirm, so when the time comes for the final attack mobilizing all the Grail's resources, they don't show up.
- 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, the hero is one, to the point that it appears to the viewer that he's willing to help organize a terror attack killing hundreds just so he can gain a shot at the Big Bad.
- In Salt, the main character is accused of being this. It's true. But then she turns out to be a Double Agent... Sort of.
- 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, Hans Landa demands to be retconned into one when negotiating a change of sides.
- In the 1971 TV Movie "The Death of Me Yet" we're introduced to Doug Mc Clure and Meg Foster as a young couple in a typical American town until he's "called up". It seems he's been drafted but the entire town is a training facility in the Soviet Union for deep cover agents. The story jumps ahead to years later when he's used the crash of a plane he was supposed to be on to escape and create a new identity. Unfortunately it turns out they have caught up with him. He sets a trap for his old commander (Richard Basehart as "Robert Barnes") only to find out that he's his American wife's boss who he's heard of but never met, which means they have her hostage.
- The Cold War-era movie The Experts has John Travolta's character and his friend being hired to manage a club in a quiet suburban town. They are drugged and secretly transported to a town in the USSR designed to perfectly mimic American suburbia (they even found a black guy). Of course, their data is a little off, and the town looks more like it came from the 1950s. The purpose of the town is to train whole families of deep cover agents. Travolta's character's girlfriend turns out to fall in love with him, while his friend's girlfriend betrays them as soon as they reveal that they know the truth. However, the whole town ends up Becoming the Mask and opts to defect to the US when they get the chance.
- Yelena, Asia Argento's character in xXx, is a Russian deep cover agent forgotten and/or abandoned by her agency.
- An extreme example occurs in Face/Off, in which the protagonist and antagonist assume each other's identities and infiltrate each other's lives.
- 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 'Thomas Marik' is himself a deep-cover agent — his son was in fact his son, but 'his' older daughter's DNA doesn't match his at all. It's noted with irony in a later novel that he's also the best leader the Free Worlds League had had in at least a century.
- 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 the U.S. Secret Service.
- 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. And for added awkwardness, falls in love with aq pilot who she'd betrayed in one of her previous infiltrations. Unfortunately, the Wraiths eventually find out about the Awful Truth. She's forced to flee to Zsinj and, since he thinks she was loyal to him all along she's able to infiltrate and sabotage his flagship, ultimately leading to his downfall.
- 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.
- Jacob Kelling from Emma Bull's Falcon, who was planted years ago to bring down a whole planet's government.
- The Romulan Way has Arrhae ir-Mnaeha t'Khellian, outwardly the household manager of a relatively minor Romulan nobleman. Inwardly, she's Lieutenant Commander Terise Haleakala-LoBrutto, a Federation Starfleet officer who underwent Magic Plastic Surgery and was inserted onto Romulus. However rather than having a mission of sabotage, she's an anthropologist tasked to covertly study the secretive Romulans so that the Federation can hopefully have more amicable dealings with them in the future.
- In the Dale Brown novel, Day of the Cheetah, one infiltrates Dreamland to steal a highly secret prototype fighter.
- The titular Charm School of the Nelson DeMille novel of the same name is a school for Soviet recruits to learn to behave like Americans before being sent on deep cover assignments.
- Soviet agent Stirlitz, aka Maxim Issayev aka Vsevolod Vladimirov from Soviet TV show Seventeen Moments of Spring. He infiltrated the Nazis in 1930s and is a high-ranking security official who interacts regularly with top German leaders.
- 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 Lauren Reed from the third season also turn out to be examples of this trope.
- Agents of S.H.I.E.L.D. has Bobbi Morse who happens to be HYDRA's head of security. She has been there for a while prior to the second season. Being a head of security means that double crossing her organization would mean instant doom to any mole within it. Turns out that she was sent there by S.H.I.E.L.D. to watch over Jemma Simmons in case things go south.
- 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.
- In Chuck, the episode "Chuck Versus The Suburbs" shows Chuck and Sarah going undercover in a sunny suburban neighborhood to find a sleeper cell. It turns out that a married couple living on the street are agents of Fulcrum.
- Gets turned Up to Eleven when Chuck discovers that the whole neighborhood is one big front for Fulcrum and its residents are all agents.
- Fringe has the Shapeshifters, who first appear in the second season and are able to assume the physical form of any human being. In the third season episode "Do Shapeshifters Dream of Electric Sheep?", it is shown that some of them have even assumed the lives of the people they've shapeshifted into and grown close to their families and loved ones.
- 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, two of whom are old friends of Steed.
- 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.
- The Elementary episode "Dirty Laundry" has Sherlock Holmes figure out that the murdered hotel manager and her husband are, in fact, Russian spies and a friend of their family is their handler (and the killer). Completely averts the Accent Relapse trope, as none of the agents or their handler drop their American accents (makes sense, considering they have lived in the country for decades). In fact, the husband and the wife didn't love each other but were ordered to conceive a child in order to allow him or her to grow up as a native-born American and a second-generation agent. However, the father refused to let his daughter get mixed up in this. One of the clues that led to Holmes discovering this is that the husband quit his job shortly before the company signed a government contract. The only reason someone would do this is to avoid a deep background check all government contractors must go through, which would quickly reveal the truth.
- Another clue was the father completely stepping out of the house to shake his hand instead of doing it over the threshold, a big no-no in Russian culture.
- An episode of Human Target has Chance being hired by a man who claims his wife wants to kill him. Chance does a bit of investigating and realizes that his wife is a deep-cover Russian spy. He instructs the client to pretend that nothing is wrong and invite him to dinner. At dinner, Chance nonchalantly comments on the meal in Russian, and the client's wife unconsciously answers in the same language before realizing what happened. However, it turns out that she has grown to genuinely love her husband and wants to break ties with her handlers. Unfortunately, it's not as easy as it sounds. In the end, Chance helps her by shooting her in a non-vital area (but looks vital to an onlooker) in front of the handlers and helps the couple start anew somewhere else.
- A flashback in The Event reveals that Sterling's wife was one. His superior found out the truth but wants to let Sterling redeem himself by shooting her. Sterling, however, decides to run away with her. He tells her that he knows and offers to run away. She tries to bolt but is shot by Sterling's superior.
- The FX series The Americans is based around the Jennings, a married couple of deep-cover KGB agents living in suburban America in 1981, at the start of the Ronald Reagan administration, with an FBI agent moving in next door. Series writer Joseph Weisberg, who worked for the CIA in the early 90's, has said that the 2010 FBI bust of a Russian spy ring (see top) was a direct inspiration for him. Both of them seduce Americans for information.
- In Season 2 the KGB decides to recruit the US-born children of S-Directorate agents like the Jennings since these second-generation agents would be able to pass high level security checks that they parents could not. Thus they would be able to infiltrate organizations like the FBI or CIA. The Jennings are divided on the issue with Philip being vehemently opposed to the idea while Elisabeth thinks that it is their patriotic duty to support the plan.
- JAG: Harm's new neighbor, Meghan O'Hara, in "Washington Holiday" turned out to be a trained assasin, whose mission was to kill the Romanian king while in DC.
- One episode of NCIS: Los Angeles has the team uncover a network of eight couples who were inserted into the United States by the Soviet Union to detonate nuclear bombs in the event of a war. However, the agent they speak with tells Callen that while, at first, they would have obeyed the order without question, after a while he and his now-dementia-stricken wife Became the Mask of a normal suburban American couple, and they even have an adult son who doesn't have a clue. Also an In-Universe example of a Stereotype Flip: The couple in question is black (recruited as children in Africa), since a black guy is the last person American counterintelligence would suspect as a Soviet agent.
- Used as a punchline to the Comedy Playhouse episode "Lunch in the Park" (later remade as an episode of Paul Merton in Galton and Simpson's). Two office workers (Stanley Baxter and Daphne Anderson in the original; Merton and Josie Lawrence in The Remake) meet for lunch once every week, and have a rather clipped conversation, mostly small talk, but also with a suggestion they'd like to see each other more often but have to be careful of appearances. It looks like a Brief Encounter sort of situation, until he hands her a microfilm, and Special Branch swoop in on the pair of them...
- In Allegiance, Katya O'Connor, her husband and their eldest daughter Natalie are all secretly Russian spies. The O'Connors' two younger children, one of whom is a CIA analyst, have no idea.
- In an episode of Secret Agent John Drake is assigned to follow an escape route of British Communists being recruited by the USSR. He finds himself in a "British Town" in the Soviet Union where the Britons are used to train infiltration agents. He manages to tape pictures of the agents who will be sent to Britain and then escapes after promising one of the British women that he'll deliver a message to her mother because she regrets her decision and knows they will never let her go. However in one of the many betrayals that leads (I believe) Drake to resign from the service and get abducted to become Number 6 in The Village his superiors refuse to do anything to help the woman because "She doesn't exist".
- On Orphan Black, Beth's boyfriend Paul, as Sarah finds out soon after taking over her life, is secretly a monitor for the DYAD Institute which created the clones. He turns out to be a Double Reverse Quadruple Agent for the military. In season 3, the Prolethian Mark is revealed to also be an agent for the Project CASTOR military conspiracy.
- '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.
- Possibly the most iconic in gaming is the Metal Gear series' Revolver Ocelot, AKA Major Ocelot, AKA Shalashaska, AKA Adamska, AKA Liquid Ocelot. He's so good at convincing people that he's on a given group's side that it doesn't become entirely clear who he really is working for (if anyone) until after his death.
- 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.
- Hobbes, 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.
- It doesn't work.
- 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, Omen Deng was raised from birth to be a double agent for Taiwan.
- The Imperial Agent class storyline in Star Wars: The Old Republic features several such examples, but the most memorable of all might be "Bas-Ton", an imperial human agent who has been surgically altered to impersonate a Voss alien for several years. The original's wife, brother and two children don't seem to suspect a thing. To top it off, when talking to the agent, Bas-Ton is openly xenophobic against the aliens he lives with. Now that's some dedication to your cover story.
- In The Silent Age there's Frank, who's been sent to the US in his early twenties and doesn't even have any accent, but who in fact is a Russian spy.
- Susan in Plague and Treachery on the Oregon Trail.
- 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. She justified her actions because she thought she was helping Earth, but defected when she learned that Earth would be destroyed in the process.
- 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.
- In Phineas and Ferb, Perry the Platypus, aka Agent P, has an impenetrable cover identity as the boys' harmless pet, and everyone knows a platypus doesn't do much. Even his evil nemesis Dr. Doofenshmirtz doesn't recognize him if he's not wearing his Fedora of Asskicking, though that could be at least partly due to Doofenshmirtz being a Ditzy Genius.