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Anime and Manga
- In Code Geass: Tales of an Alternate Shogunate, Lelouch is Zero, head of the Black Knights rebelling against Britannia, and also head of the Shinsegumi, which are tasked with capturing Zero.
- In Dangan Ronpa 3, Yukizome is the leader of one of the branches of the Future Foundation. Only bad thing is that she is Brainwashed and Crazy, and is part of the organization's only real enemy.
- In Death Note, Light is suspected of being the mass murderer Kira, but manages to throw off suspicions enough that he's allowed to join the task force hunting Kira, partly so he can fully clear his name, partly so L can keep a close eye on him. Being The Chessmaster, he figures out a way to kill the people in charge and assume control of the task force without letting anyone else in the organization realize his involvement.
- King Bradley from Fullmetal Alchemist is the Führer and General of the Army of Amestris. Secretly, he's the homunculus Wrath (Pride in the 2003 anime) and he's working for Father (Dante in the 2003 anime). In the manga, Father's agents have controlled the highest offices of the country for its entire 400 year history because he founded it himself.
- One Piece:
- Vergo, a member of the Donquixote Pirates, infiltrates the marines and ends up becoming a Vice Admiral, the third highest rank in the organization, with a military base and hundreds of men under his direct control.
- Stussy is the leader of a very popular red-light district and a major figure in the global underworld. She is also a high-ranking government agent who uses her power and influence in the underworld to make contact with other highly influential criminals and arrest them. Or assassinate them, depending on the circumstances.
- Tokyo Ghoul has several examples, as major twists.
- Kishou Arima is the most famous Ghoul Investigator, in charge of handling the most dangerous targets and guarding the vital Main Office for the organization. His duties also include pursuing the One-Eyed Owl, and the legendary One-Eyed King. It's eventually revealed that he is the One-Eyed King, and has been the Owl's partner for more than a decade in a long-running plan to bring down the Government Conspiracy.
- After the Washuu Clan are massacred, the late chairman's bastard son is named as the next leader of the CCG. Nimura Furuta is an insignificant investigator, but quickly proves himself as a natural-born leader and takes charge during a surge of brutal attacks by the Clowns. Of course, it helps that Furuta himself led the massacre, and the Clowns are carrying out the attacks on his orders. His experience as a Double Reverse Quadruple Agent makes him an excellent actor, playing the role of a talented rookie with no confidence in order to propel himself into leadership.
- This seems to happen to S.H.I.E.L.D. depressingly often in Nick Fury stories. As well after Carol Danvers is forced to step down Post Ultimatum. Her replacement is someone who in the 616 is known as Mentallo.
- The premise of the Marvel Comics storyline Dark Reign and especially the Dark Avengers series.
- One Avengers story had the Red Skull become the U.S. Secretary of Defense.
- This caused more than a bit of Fan Dumb as it was during the Bush presidency and the name the Red Skull was using at the time had the initials D.R. OK, admittedly that's a funny coincidence, but "Dell Rusk" is an anagram of "Red Skull", so what else should the writers have called him?
- Furthermore, if "Dell Rusk" were a reference to a real life Cabinet member, it would probably be to Dean Rusk, who was Kennedy and Johnson's Secretary of State.
- This caused more than a bit of Fan Dumb as it was during the Bush presidency and the name the Red Skull was using at the time had the initials D.R. OK, admittedly that's a funny coincidence, but "Dell Rusk" is an anagram of "Red Skull", so what else should the writers have called him?
- Runaways: Alex Wilder becomes the undisputed team leader, only for it to be revealed that he was working with the Pride the entire time.
- Daredevil once found himself ostensibly running the evil ninja assassins called the Hand. They corrupted him to the point that a demon actually possessed him briefly.
- This is the entire premise of Agents of Atlas.
- In Superman & Batman: Generations, Batman ultimately ends up accepting Ra's Al Ghul's offer to become his heir, and turns his terrorist organization into a world-spanning anti-crime unit.
- In Superman: World of New Krypton, General Zod is severely injured before he can unleash his plan to invade Earth. While he recovers, the supreme commander of New Krypton's military forces is ... Commander Kal-El. Kryptonian foreign policy suddenly becomes a lot more diplomatic; unfortunately, it's temporary.
- For a long time, this was a running sub-plot of the Kree/Skrull war in the Silver Surfer comics; a Skrull (locked in the form of a Kree woman) had somehow risen to the very top of the hierarchy of the Kree Empire.
- Block 109: Zytek was first recruited by the anti-Nazi Admiral Wilhelm Canaris before the war to infiltrate the Nazi Party. Zytek's decision to assassinate Hitler ended up creating an even worse war than he feared, but he was eventually able to ascend to leadership of the Third Reich so he could dismantle it from within.
- In Paperinik New Adventures this turns out to be a typical Evronian tactic to deal with planets that may actually pose a threat to an invasion force: infiltrate Shape Shifter Super Soldiers into the appropriate position of power, and then attack the moment the mole has lowered the defenses. They applied this tactic against Xerba (the mole had replaced a government member and cast the decisive vote that led to the Xerbians signing the commercial treaty with Evron that led to them temporarily deactivating their orbital defenses, allowing the Evronians to destroy them and overrun the planet with a sudden attack) and Earth (they infiltrated Grrodon in the place of a Dept. 51 officer planning to have him rise the ranks, only for him to be outed as a spy and imprisoned. They never found out he was an Evronian). The reboot also had them apply the tactic against Earth, neutralizing all nuclear arsenals and throwing the militaries into chaos right before their invasion.
- In The Swarm of War, a lot of senior human military commanders (the most successful ones) are actually the Swarm's spies. Then, Alena, the disguised Queen of Blades, makes herself the human queen.
- Out of the Corner of the Eye has Director Joseph White. Nominally Captain Black's superior, administrative leader of Section 13 and head of its psychological division, he's also a servant of the Outer Gods (in fact, he's implied to be a member of the Whateley family).
Film — Animated
- In Frozen, Anna names Prince Hans regent while she goes off to look for Elsa. At this point, his status as a villain hasn't been revealed yet.
Film — Live-Action
- Cambridge Spies and all other retellings of the story of Kim Philby and his colleagues, Communist agents who rose to the top ranks of MI-5.
- In Captain America: The Winter Soldier, this turns out to be the case with S.H.I.E.L.D In the present day. Alexander Pierce, Fury's direct superior, is HYDRA.
- The Departed: Frank Costello is an FBI informant. Though that was after he had built up his empire as a self-defense measure. A better example is Colin Sullivan, Frank's mole in the State Police, and the head of a special Task Force in charge of finding the mole in the State police.
- Nikolai pulls this off by the end of Eastern Promises.
- G.I. Joe: The Rise of Cobra ends with COBRA agent Zartan having replaced and imprisoned the real U.S. President, and it continues on into its sequel, G.I. Joe: Retaliation.
- This is the villain's objective in Headhunters. Clas needs to land the job at Pathfinder to secure their technology and sell it to an American company.
- In Kingsman: The Secret Service, Arthur, the oldest and most senior of the Kingsmen, is secretly one of Valentine's willing converts.
- In The League of Extraordinary Gentlemen, M brings the titular league together on the premise that he needs their help to bring down The Fantom, a renowned criminal mastermind. In reality, M is one of The Fantom's alter-egos, and his real reason for recruiting the league was to steal from the members who had superpowers (Mina Harker's vampire blood, a skin sample from the Invisible Man, and Jekyll's Super Serum), duplicate their effects to add to his arsenal, then kill off the entire league in one swift blow.
- In My Favorite Martian, the man in charge of the organization hunting aliens is himself an alien stranded on Earth, apparently looking for a spaceship that can finally take him home.
- Now You See Me: It turns out at the end that the mysterious "Fifth Horsemen" giving the main character their orders, was Dylan Rhodes, a.k.a. Dylan Shrike, the FBI agent who had been trying to capture them the entire movie.
- RoboCop (2014): Crime boss Antoine Vallon has both the lead DPD detectives investigating him, as well as the Detroit Chief of Police on his payroll.
- In Salt, the ending strongly suggests that the President dies from his wounds, and the Vice President who ascends to succeed him is another Russian sleeper agent. There's also the fact that the CIA agent in charge of hunting down the sleepers is actually a sleeper himself.
- In Smokin' Aces it's revealed that the leader of the mob is really an FBI agent who was burned by his handlers and had to become a criminal for real to survive, eventually rising up the ranks to the top position.
- Star Wars: In the prequel trilogy, Senator Palpatine becomes Chancellor of the Republic and Darth Sidious is the mastermind behind the invasion of Naboo and the Separatist Crisis, which turns into the Clone Wars. They're the same person, whose ultimate goal is the downfall of the Republic and destruction of the Jedi Order, to be replaced with his own Empire. This succeeds. It then evolves into the conflict of the Galactic Civil War in the original trilogy (Episodes IV-VI).
- John le Carré's The Quest for Karla: Tinker, Tailor, Soldier, Spy]] does this, more or less. The Mole is nominally the number 2 member of the organization, but actually in control of it. It was inspired by the unearthing of the Cambridge Five, who included Kim Philby (see below).
- The Spy Who Came In from the Cold does the same thing, in reverse. Although he technically isn't the top man in the Stasi, Mundt is the highest-ranking East German intelligence officer who appears in the story and it turns out that he'd been turned years prior to the events of the book.
- In The Illuminatus! Trilogy, Hagbard Celine, leader of the Legion of Dynamic Discord, is also a Primus Illuminatus, as well as a high-ranking member of A.'.A.'.. Given his stated beliefs, the conflict of interest makes perfect sense.
- Of course, he took the place in The Illuminati purely to screw them up after he realized that he couldn't guide them to a more constructive path. His true loyalties, if such thing exists, lie with the A.'.A.'.
- In the Arsène Lupin novel 813, the Head of the French Police, the best detective ever seen, the only man everyone trusts to be able to catch Gentleman Thief Lupin... turns out to be Lupin himself in disguise.
- In The Man Who Was Thursday the protagonist discovers that the Council of Days, supposedly the supreme council of the British anarchist underground, is made up entirely of undercover police officers like himself.
- In Robert A. Heinlein's novel The Moon Is a Harsh Mistress, Adam Selene, figurehead of the Rebellion against the Lunar Authority, is in actuality a virtual construct of the Authority's main computer, who has quietly attained both sentience and a sense of humor.
- David Weber is very fond of this trope. The third book in Empire from the Ashes has it. The taking over of Safehold by the staff of the colony ships. Wind Riders Oath in the Bahzell series has several of them. Much of the backstory and the conclusion of Prince Roger. The Honor Harrington books managed to avoid them for quite some time, but then the Mesans, with an entire multi-generational network of moles, appeared. The entire Legislaturists class were Alpha lines.
- Older Than Radio: Konrad Wallenrod by Adam Mickiewicz is a classic of Polish Romanticism, in which he postulated using deceit (as opposed to direct action) against the occupiers. The plot involves a Lithuanian who rises in ranks of The Teutonic Knights, and after many years leads their army to a total defeat.
- An odd variant occurs in Jack London's The Assassination Bureau, Ltd. when Winter Hall, having paid the Bureau to kill its own leader, is placed in charge of handling the Bureau's correspondence and finances — the things the leader would normally do — while said leader is on the run from his team. The members of the Bureau know Hall is out to destroy them, because he told them ... but they all have an overpowering sense of ethics, and so they respect his honesty and consider him a friend. And he considers them friends, and now wants to find a way to destroy the organization without harming the members.
- The Wingman pulp series by Mack Maloney begins when the United States Vice President, a Soviet mole, arranges for the assassination of the President and lowers the Star Wars missile shield, allowing the remnants of the USSR to nuke the United States in revenge for destroying them in World War III.
- In Vernor Vinge's Rainbows End, when Grünberk Braun discovers the existence of the Mind Control virus, he turns for help to Albert Vaz, the man who has secretly created it as part of his plan to save the world from itself.
- The Mediochre Q Seth Series. Dean Kiwi Mashuga of St Merlin's University is secretly the head of the Sapphire Smuggling Syndicate. When an SSS member is asked - while attached to a lie detector - whether anyone in the university works for the SSS, she is able to truthfully answer 'no', because technically, the SSS works for Kiwi.
- At the end of the President's Vampire novel Red, White and Blood, Vice President Lester Wyman, who has been the Mole for the Shadow Company throughout the series, gives himself a Klingon Promotion.
- In The Leonard Regime, the mole also happens to be the second in command of the entire rebellion.
- In finalle of Faded Steel Heat the head of xenophobic pro-human organisation is shown to be a shapeshifter. Hasn't been there for long, though.
- In The Lensmen Chronicles Second Stage Lensman, Lensman Kinnison goes undercover into the enemy military and works his way up to become a military dictator, Tyrant of Thrale, to find out who The Man Behind the Man is an inter and to sabotage an upcoming battle.
- In the X-Wing Series novel Mercy Kill, the A-plot follows a team of Wraiths assembled under Face Loran at the behest of his boss, General Maddeus, head of Galactic Alliance Intelligence. Their job is to look into the head of the army, General Stavin Thaal, and see if he has any connection to the "Lecersen Conspiracy", a plot by hard-line loyalists to return power to the Empire. It transpires that not only is Thaal part of the conspiracy, but so is Maddeus. He was worried that evidence might link them to the other known conspirators, so he sent Face to find it and report back to him, allowing him to tip off Staal before the Wraiths could catch him. Then, he would eliminate both Face and the leaks he had revealed. Face outmaneuvers him by arranging for two teams of Wraiths while reporting on the actions of a third, fictitious, team; when Maddeus tries to warn Thaal about the fake Wraiths, his cover is blown.
- The Hunger Games: Plutarch Heavensbee is the Head Gamemaker for the 75th Hunger Games. And a key member of La Résistance.
- As told in Horrible Histories, the story of Fernando Buschman, a Brazilian-German violinist who was executed during World War I in the Tower of London for spying. He, as well as a group of spies, were all sent to their deaths by their spymaster, a British mole serving in Germany's intelligence wing. The Germans' entire "infiltration" method was a signal for the British Intelligence to quickly identify them and get them captured.
- Similarly, 24 has given us versions of President Evil who are really The Mole for hostile foreign powers.
- In the Agents of S.H.I.E.L.D. episode "Fractured House", Julian Beckers, Belgium's Foreign Minister is revealed to be a HYDRA agent.
- This happens on Alias at least once every thirty seconds. Between the "real" nature of SD-6, the loyalties of Derevko, the actions of Sark and the constant flip-flopping of characters between the CIA and other organizations... heck, there are even situations where a mole infiltrates an organization, rises to the top, then stages the infiltration of the organization they were moling for in the first place!
- While most of the fifth season of Angel is a case of Good Running Evil, towards the end Angel pretends to have been corrupted by the experience, becoming more of a Mole in Charge.
- Babylon 5: Sheridan is this twice over — hired by the Clark government to spite the Minbari because of their perception of him as a war criminal, but actually a highly placed member of La Résistance, sent to determine the B5 crew's loyalty or lack thereof to the increasingly fascist Earth Gov.
- In Caprica, Gara Singh is chief agent in the Caprica Global Defense Department and leader of the Soldiers of the One monotheistic terrorists on Caprica.
- In Cases of the 1st Department, technician Strompf is kicked off the department when Maj. Kozak finds out that he's the bastard selling tips to TV. However, Strompf blackmailed Maj. Korejs (head of the department) who gives him great references, so the mole gets hired by Internal Affairs. He later tries to destroy some of his former colleagues out of spite and is put in charge to investigate Maj. Kozak who is suspected of getting around a warrant search.
- In the Castle episodes "Pandora" and "Linchpin" the villain is the second-in-command agent of a CIA operation. Strike that it was really the number one in command and she framed him. It further turns out she was a KGB agent who infiltrated the CIA just as the USSR went under and was thus a double mole.
- Lena Smith in Covert Affairs.
- On Criminal Minds the BAU team have been called in by the CIA to find a mole in their ranks, the mole was the Deputy Director.
- In addition, in the episode "Amplification," the BAU is looking for someone who unleashed an anthrax attack onto a group of people in a park. The person who did it turns out to be a high-ranking researcher for a government anti-terrorism agency. He unleashed the attack because he wanted the American populace to take terrorism more seriously and to demonstrate vulnerabilities in his agency's methods.
- Scorpius from Farscape is in charge of the Peacekeeper's wormhole weaponization project while being a double agent for the Scarens. Except, it turns out Scorpius isn't really working for the Scarrens. He just lets them think that he is for as long as he can, so that he can develop wormhole weapons with which to destroy them.
- Played for laughs on Get Smart when all four members of a KAOS cell turn out to be moles from different agencies: the CIA, the FBI, Naval Intelligence and Scotland Yard. The only real KAOS agent had died years ago without being replaced.
- Played with on Grimm. Nick's boss, Captain Renard, is initially portrayed as The Mole and quite possibly the Big Bad. However, we later discover that his loyalties are way more complex. He is the illegitimate son of the head of the Royal Families but is also one of the leaders of the Resistance, a group of Wesen who oppose the Royals.
- In Highlander, the Watchers have a research division that's dedicated to finding Methos, the legendary first Immortal. The lead researcher is Methos, and guarantees that they never find him.
- In The Hour , the rumoured Soviet mole in The BBC ultimately turns out to be Clarence.
- On Intelligence (2006), a seasons-spanning storyline involved the discovery of a CIA mole in the highest echelons of the Canadian Security Intelligence Service and its fallout.
- The series finale of Intelligence (2014) revealed that Weatherly, the Director of Central Intelligence was a deep-cover Iranian mole.
- MacGyver (2016) has Patricia Thorton, who was trying to stop Mac from finding out about Nikki being a deep cover agent trying to expose Patricia.
- Madam Secretary: It turns out in "The Ninth Circle" that CIA Director Munsey is part of a Renegade Splinter Faction trying for regime change in Iran to stop them from getting the bomb, rather than let Liz and President Dalton's peace talks run their course.
- One NCIS: Los Angeles episode has the team trying to prevent a highly placed US mole inside the Iranian military from having his cover blown. At the end of the episode, they've managed to reinforce the cover of the general in question so well that he's been promoted to head of counterintelligence.
- Subverted in The Prisoner episode "Free For All". Number 6 is elected to the position of Number 2, technically putting him in charge of the Village, but it turns out to be a cruel trick to break his mind.
- Happens twice in The Sandbaggers, complete with references to Philby. Burnside makes sure they are both killed.
- The Star Trek: Deep Space Nine episode "Inter Arma Enim Silent Leges" has this as a major twist that changes your perception of the events of the episode: Koval, the chairman of the Tal Shiar (the Romulan intelligence organization) and staunch opponent of the Federation-Romulan alliance against the Dominion turns out to have been a Federation agent all along. The entire thing was a plot to remove a less reliable Senator from power and lend additional force to Koval's turn to supporting the alliance.
- In Supergirl, the leader of the Department of Extranormal Operations, a US government Men In Black group, turns out to be an alien in disguise who killed and replaced the real guy. In fact, he's the DC TV universe version of the Martian Manhunter. Subverted, since it's revealed that the original leader was a fanatical and malevolent xenophobe, while the infiltrator wants to change the agency to genuinely protect the Earth from evil aliens while acting as a benevolent immigration service for more moral ones.
- One episode of Yes, Prime Minister revolved around the revelation that a former head of MI-5 had, during his time in office, been a Russian agent.
- After the formation of the nWo, The Giant (later The Big Show) quickly became the leader of WCW's makeshift resistance. That is, until he had a Face–Heel Turn and became a member of the nWo. Later, WCW's Executive Vice President, Eric Bischoff also joined the nWo, and revealed that he'd been working for them the entire time.
- When the Aces and Eights invaded TNA, Bully Ray went out of his way to get the trust of Hulk Hogan and, seemingly inadvertently, the love of his daughter Brooke Hogan, which resulted in the Hogan family essentially anointing him as The Hero for TNA against the Aces and Eights and giving him a fast track to a World Heavyweight Championship match. The thing with that, as they painfully found out the night of said title match, is Bully Ray is the President of the Aces & Eights.
- A bit of Planescape lore tells how an Anarchist infiltrated the Harmonium so deeply and for so long that he ended up the head of the latter faction. The Anarchist then ordered the Harmonium to disband... which promptly lead to his being arrested and tried for treason, and revealed as The Mole. Depending on your perspective, either a tremendously Chaotic Stupid move by a mole in a position of power making life more difficult for any moles who come after him, or a brilliant Paranoia Gambit to make the Harmonium forever wonder what damage he had done on the way up and hindering their ability to trust one another ever after.
- Technically the case in Paranoia, which notes that there is a secret organization where every single member is a mole for some other secret organization. Which must, logically, include the guy at the top.
- Sam & Max give us a literal example, since the mole inside the toy mafia takes over the mafia... and is actually a mole.
- In Bioshock 2, Sofia Lamb put Stanley Poole in control of Dionysus Park, her sanctum. He was Andrew Ryan's spy all along.
- You can do this in the game Seven Kingdoms 2: The Frythan Wars (And possibly the first one, but I have not played it so cannot say for sure) using your spy units. The spy looks like any ordinary unit to everyone but the owner and the enemy treats it like an ordinary unit, including for being promoted to general status and running a fort. And even for promotion to king if their king is killed and the spy is a general. Having a spy as a general allows you to take control of a fort and make it switch colors as well as some of the units in it, depending on loyalty or simply screw with enemy operations by conflicting orders. If the spy becomes king then you automatically defeat that enemy. Be warned though, the AI is good at using spies against you too.
- Ace Attorney has a major one. The head of the Yatagarasu case is the Yatagarasu, or at least one member of the group. Hell, the original Yatagarasu was made up of the prosecutor, detective, and the defense attorney on the case. Considering there's no jury in the Ace Attorney world and the Judge is an idiot, you can't get much more in charge than that.
- One of the key plot points of Dawn of War II: Chaos Rising. Towards the end of the game the Blood Ravens learn that their Chapter Leader is actually a follower of Chaos. The game ends with the Blood Ravens under the player's command going rogue and setting off to expose the traitor.
- In Soldier of Fortune 2, the Obviously Evil second-in-command of the anti-terrorist organization is also the leader of the main terrorist organization. It turns out he actually founded the terrorist organization to drum up business when the end of the Cold War caused a drop in demand for anti-terrorist services.
- In the 2005 remake of NARC, the chief of the N.A.R.C. anti-drug task force is also the leader of K.R.A.K., the main drug cartel. It turns out she founded N.A.R.C. specifically to eliminate all the other competing drug cartels.
- Happens in Fallout: New Vegas: There's a spy planted by Caesar in the NCR at Camp McCarran who's radioing out information, and they're trying to root out who it is. It happens to be the officer in charge of the investigation.
- In Fallout 4, it's eventually revealed that Mayor McDonough of Diamond City is actually a Synth infiltrator, with the real one having been killed and replaced long ago.
- Big Boss, in the original Metal Gear.
- In Strife, the leader of The Resistance is actually one of the 5 main leaders of The Order. His actions vary between giving his men suicide missions designed to get them killed, and genuine strikes against the Order which are really power grabs in an attempt to gain dominance over the other 4 leaders.
- In Call of Juarez: The Cartel, the Mendoza Cartel's high-ranking mole inside the U.S. government turns out to be Department of Justice Deputy Assistant Director Shane Dickson, the head of the special task force assembled specifically to deal with the Mendoza Cartel. In fact, the task force was designed to fail from the beginning, which explains why all 3 members work together so poorly and are so obviously corrupt and/or insane.
- This is an alarming problem in Resident Evil:
- Albert Wesker, in charge of the S.T.A.R.S. sent to the mansion in the first Resident Evil is also working for the company that made all the zombies in the first place.
- In Resident Evil: Revelations head of the Federal Bioterrorism Commission Morgan Lansdale is responsible for the monster outbreak on board the Zenobia so the world will be more afraid of bioterrorism and give the FBC more power. He is opposed by the head of Bioterrorism Security Assessment Alliance Clive R. O'Brian, who sent in Jill, Chris, Parker, and Jessica to the Zenobia with incredibly lacking intel in an elaborate plan to expose Lansdale, which, while well-meaning, was such a dangerous Gambit Roulette that he deserves a little bit of scorn.
- National Security Advisor Derek Simmons is the one responsible for the president's assassination and the zombie outbreak in Tall Oaks in Resident Evil 6.
- In Kingdoms of Amalur: Reckoning, the Big Bad of the House of Sorrows Faction questline is the faction's leader who is actually a Tuatha agent. He is even the one who recruits the Fateless One into the faction and successfully manipulates him/her into removing one of the few obstacles left to his plan to destroy the House of Sorrows and claim its powerful magic for the Tuatha.
- In Romance Of The Three Kingdoms II, you can hide officers in enemy territory to lower the loyalty of his officers. If his ruler dies, one of his officers (a relative if possible, the highest Charm officer otherwise) becomes the new ruler — which means that your mole may become their new ruler (and, if he does, he will promptly stop being a mole.
- In Sleeping Dogs, Wei Shen becomes a Red Pole in the Sun On Yee after Winston is killed. While he doesn't reach the top of the Sun On Yee overall, he's still this trope for the subsidiary Water Street Boys gang, making him one of the most powerful people in the Triad hierarchy, and if he had wanted to and found support, he could have moved to become Dragon Head. Ultimately however, he goes back to being a cop and the new Triad boss lets him walk away out of respect for eliminating her enemies.
- The Federation storyline in Escape Velocity Nova features this (Only the Federation storyline, mind — despite the Rashomon-y tendencies of the game, certain things only make sense if Schrödinger's Gun is in effect here): Frandall, head of Rebellion intelligence and former head of Federation Intelligence, turns out to be the real head of the Bureau.
- A comedic example in Pajama Sam 2. Carrot infiltrates World Wide Weather believing it to be economically oppressing employees. A puzzle solution requires that Sam needs Carrot to get himself on the Board of Directors, and Sam leaves Carrot to act in his stead. Carrot quickly becomes very popular by introducing seating for all the board members and then he starts implementing employee benefit programs. In the end, when Sam returns to see Carrot running the company by himself, Carrot explains that he thought management was top-heavy and downsized the entire board of directors except himself.
- Middle-earth: Shadow of Mordor: THE WHOLE DAMN POINT. Your goal as a Ranger with Wraith powers is to build an army out of Sauron's forces through mind control, thereby causing an Enemy Civil War strong enough to take down Sauron himself. Bad News: his army numbers in the millions. Good News: Sauron uses a mind control hierarchy, so that mind-controlled warchiefs have limited mind control over their lieutenants, and the lieutenants have limited mind control over the grunts. You either need to dominate a lieutenant and kill his warchief, thus allowing your mole to be instantly promoted to warchief, or dominate the leader himself.
- In Snatcher, the JUNKER chief Cunningham is revealed to be this when you discover his corpse in the morgue of Queen's Hospital. When he's exposed, he kills Harry and takes Mika hostage.
- In addition to being a Dirty Cop, Gates from Policenauts is this because he's the leader of the police force on Beyond Coast.
- Subtle occurrence in Mass Effect 3, where the Illusive Man is leading Cerberus against both the Reapers and the Council whilst trying to gain control of the former, but ends up indoctrinated by the Reapers instead.
- It's revealed in the True Mastermind Edition of Time Crisis 5 that Robert Baxter, the one leading the investigation on finding a traitor within the VSSE, is the traitor all along.
- In The Legend of Heroes: Trails of Cold Steel II, Rufus Albarea, the chief of staff of the entire Noble Alliance, is actually trying to undermine the very same alliance for his real boss, Chancellor Giliath Osborne.
- Yu Han-Sung and Augusgus from Tower of God are test directors of the regime of Zahard, supervising two of the most important floors of the Tower, yet in secret, they are working for the terrorist syndicate FUG and know how to use their positions to their advantage.
- The Avengers: Earth's Mightiest Heroes!: After Iron Man and Black Panther leave the team, Skrull Captain America takes charge.
- In an episode of Captain Planet Gaia gets body-switched with one of the bad guys, leaving one of them to run her organisation and Gaia to "run" the bad guy organisation (by tricking them into acting in eco-friendly ways).
- In Codename: Kids Next Door, we discover in the last few episodes that Numbuh 274/Chad, who became a very high-ranking member of the Teen-Ninjas was a Fake Defector still loyal to the KND.
- G.I. Joe Extreme ended at least one season with the villain Iron Klaw masquerading as the military official in charge of G.I. Joe itself.
- The Modifyers had Agent Xero acting as a Double Agent to infiltrate Baron Vain's operation, by using her Lacey Shadows cover identity. In the pilot episode, she's already become his right-hand, which gives her authority over Rat.
- In Phantom 2040, the enforcers' chief turns out to be on the payroll of Maximum, Inc..
- Star Wars: The Clone Wars: In the Umbara arc from Season 4, Anakin is called away to a Jedi meeting in the middle of a battle. His unit is temporarily commanded by Master Krell. Krell has secretly fallen to the Dark Side. He intentionally gives his troops reckless orders that get them killed, and at one point even tricks two groups of clones into shooting at each other before he is found out. It should be noted that Krell has not yet linked up with the Sith. He's hoping to get Count Dooku's attention by sabotaging the operation on Umbara so that he will be picked as Dooku's apprentice. He doesn't know that Dooku himself is the apprentice to Darth Sidious, AKA Republic Chancellor Palpatine (see above).
- Star Wars Rebels has this occur in season three with Agent Kallus as the new Fulcrum due to a Heel–Face Turn. Their high rank in the empire's Lothal garrison, specifically as an intelligence agent makes them a valuable ally, however this was also the season Grand Admiral Thrawn was put in charge of the Lothal situation and Governor Pryce took more of a commanding role, limiting Fulcrum's abilities making it closer to a "mole who would have been in charge if higher-ups hadn't gotten involved."
- Transformers Animated. The head of Autobot Intelligence is Shockwave, a shapeshifting Decepticon spy. Makes you wonder about Ultra Magnus's character-judging skills.
- Young Justice. Aqualad/Kaldur, Black Manta's second in command is really a Fake Defector trying to get closer to the Light and their new partner. The show doesn't shy away from the moral dilemmas the mole has to face to maintain cover.
- Heroic example in Gargoyles: Detective Matt Bluestone is an ally of the Manhattan gargoyle clan, and gets appointed to the NYPD Gargoyle task force sent out to capture them. It puts him in a position to keep the odds high that his gargoyle friends elude capture.
- Infamous Soviet Agent Kim Philby ended up as the head of MI-6's anti-Soviet branch, Section IX, for quite some time before he was suspected of being The Mole and moved to a different position. He was well aware of the irony of this, and commented on the farcical nature of his position.
- Admiral Canaris who was actually head of the Abwehr while also being part of the German Resistance. He was caught after the July Plot and was executed a few weeks before the war ended.
- Alfred Redl was the most devastating spy Austria-Hungary ever had, giving Tsarist Russia virtually every scrap of data he could get his hands on to the point where by the time he was found out and forced to commit suicide, over a year of preparation did not even start to repair the damage by the time World War I started. Redl's role? Director of Austro-Hungarian intelligence!
- Though he was retired when he was found out. Interestingly, he was only found out because he had been so good at his role as a spy master for the Habsburgs: his reforms to the intelligence service had made the counter-intelligence branch quite effective at its job.
- Israeli spy Eli Cohen, using the alias "Kamel Amin Thaabet", became Chief Advisor to the Syrian Minister of Defense and was third in line to succeed as President of Syria before he was caught and executed in 1965.
- None other than Adolf Hitler, who was sent by the German military to infiltrate what would become the Nazi Party when it had less than 60 members. Nice Job Breaking It, Hero! doesn't even begin to describe it.
- José P. Laurel, the 3rd President of the Philippines, was, unlike the others on this list, a Reverse Mole (for the exiled government of the Commonwealth of the Philippines), with a good measure of Promoted to Scapegoat thrown in. A Reverse Mole who was supposed to be at the top, at that (so, he was The Quisling too, albeit subverted).
- Yevno Azef, head of the Socialist Revolutionary Party's Combat Organisation in pre-revolutionary Russia, was also a double agent in the employ of the Okhrana. He got the top job by selling out his predecessor, who was arrested and sentenced to death (but escaped by hiding in a barrel of cabbages).