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.
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.
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.
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.
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.
In the Star Wars 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 theCloneWars. 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 Civl War in the original trilogy (Episodes IV-VI).
The Man in the Iron Mask: The Jesuits are actively opposing the king, so he decides to put a man in charge of finding their general and killing him. Of course, he chooses one of his close allies: Aramis, who turns out to be the Jesuit general.
Though that was after he had built up his empire as a self-defense measure. A better example is Sullivan, Frank's mole in the State Police, who's put in charge of finding the mole in the State police.
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.
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 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.
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.
Tinker, Tailor, Soldier, Spy by John le Carré 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).
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 Arsčne 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.
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.
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 Presidents 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.
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!
In another case, the right-hand-man of the Big Bad took over CTU in the final season to capture and kill Jack Bauer.
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.
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.
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.
Scorpius from Farscape probably counts, being in charge of the Peacekeeper's wormhole weaponization project while being a double agent for the Scarens.
Except, 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.
On Intelligence, a seasons-spanning storyline involved the discovery of a CIA mole in the highest echelons of the Canadian Security Intelligence Service and its fallout.
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 The Hour , the rumoured Soviet mole in the BBC ultimately turns out to be Clarence.
In 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.
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 andEights 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 thePresident of the Aces and Eights.
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, Sophia 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 caseis 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 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.
Albert Wesker, in charge of the S.T.A.R.S. sent to the mansion, in Resident Evil.
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, he still becomes one of the most powerful people in the Triad hierarchy and if he wanted to and found support, he could become Dragon Head.
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.
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.
In Worm, the Undersiders eventually help Coil become this, as his civilian identity replaces the local PRT director, putting him in control of not only every supervillain but every superhero in the city.
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.
Transformers Animated. The head of Autobot Intelligence is Shockwave, a shapeshifting Decepticon spy. Nice going, guys.
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).
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.
Soviet Agent Kim Philby ended up as the head of British Intelligence's anti-Soviet branch, Section IX, for a brief time before he was suspected of being The Mole and moved to a different position.
There were constant suspicions that 'the Fifth Man', the undiscovered Cambridge Spy and Philby's colleague, was actually whoever was the current 'C' of SIS, a literal example of this trope.
It has been claimed that Sir Roger Hollis, former head of MI-5, was a Soviet mole, but little evidence has been produced for this (apart from the MI-5 agent in charge fo the investigation publishing a candid, for a time censored, tell-all account of the investigation and MI-5 publicly admitting that Hollis remains the prime suspect) and the historian allowed access to the most of their files for an official history disagrees with the theory.
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 One 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.
Josef Stalin has been accused of this, with some historians suggesting he may have worked as a spy for the Czarist secret police in the days before the Russian Revolution. If true, given that he would later become absolute dictator of the entire country under the movement he spied against and the virtually unchallenged head of the Communist world, it would probably make him the most successful example of a Mole in Charge ever. However, most historians have now dismissed this, as he was always referred to in Czarist police documents as a revolutionary terrorist, whereas their moles were always identified as moles.
There were actually plenty of moles recorded in no document at all. In fact, there are reasons to believe the Flock of Wolves trope was played more or less straight with just about any underground... well, that and Double Reverse Quadruple Agent.
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.