Mole in Charge

Simply put, this is when The Mole somehow ascends to the position of actually running the organization he, she, or it has infiltrated. In effect, they try to cause the organization or group to self-destruct, or they go completely drunk on the power this new position gives them and corrupts it to their own purposes. A popular variant these days is to let the heroes wind up in charge of the Nebulous Evil Organization they've been fighting, where they try to steer legions of Psycho for Hire types to good ends... usually with mixed results.

Unlike Les Collaborateurs, the 'Mole In Charge keeps those loyalties secret.

This sometimes overlaps with Good Running Evil. A common cause of Divided We Fall, since other subordinates don't realize it, and the requirement for the Ragtag Bunch of Misfits to save the day. Sometimes overlaps with Hired to Hunt Himself. May lead to the Mole in question Running Both Sides.

WARNING! There are unmarked Spoilers ahead. Beware.

Examples of Mole in Charge include:

Anime and Manga

In Code Geass, Lelouch, prince of Britannia, is also Zero, leader of its enemies. However, he isn't The Mole since he honestly opposes Britannia. However, this does occur when Lelouch succeeds Charles as emperor of Britannia. Too bad The Black Knights thought he was evil.
- In Code Geass: Tales of an Alternate Shogunate, this is played straight when Lelouch is Zero, head of the Black Knights rebelling against Britannia, and also head of the Shinsegumi, which are tasked with capturing Zero.
After the Time Skip in Death Note, Light is in charge of the task force investigating his mass murder spree.

Comic Books

This seems to happen to SHIELD depressingly often in Nick Fury stories.
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.
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 group of 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: Elseworld 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.

Film

G.I. Joe: The Rise of Cobra ends with COBRA agent Zartan having replaced the real U.S. President.
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 the Clone Wars. They're the same person, whose ultimate goal is the downfall of the Republic and destruction of the Jedi Order. And the Emperor, leader of the evil Imperial forces.
Viggo Mortensen does this in Eastern Promises.
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.
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 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.

Literature

Tinker, Tailor, Soldier, Spy by John Le Carre 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 the leader 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.'. He isn't their leader, though - if the group even has a leader, it's the Dealy Lama.
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 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.
- In the third book in Empire From the Ashes, there is the taking over of Safehold by the staff of the colony ships.^[context?]
- Wind Riders Oath in the Bahzell series has several of them with much of the backstory and the conclusion of Prince Roger.^[context?]
- The Honor Harrington books managed to avoid them for quite some time, but then came the Mesans, with an entire multi-generational network of moles.
Older Than Radio, it is. 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.

Live-Action TV

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!
Similarly, 24 has given us versions of President Evil who are really The Mole for hostile foreign powers.
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.
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.
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.
On Grimm, Nick's boss, Captain Renard is The Mole, and quite possibly the Big Bad.
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.

Professional Wrestling

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.

Video Games

In Sam and Max, the mole in the toy mafia has become this.
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 Seven Kingdoms 2: The Frythan Wars using your spy units, which look like any ordinary unit to everyone but the owner - the enemy treats it like an ordinary unit, including being eligible for being promotion to general status and running a fort, and even 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.
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.
The first Resident Evil game has Albert Wesker, in charge of the S.T.A.R.S. sent to the mansion.
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 them 1into removing one of the few obstacles left to his plan to destroy the House of Sorrows and claim its powerful magic for the Tuatha.

Western Animation

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).

Real Life

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. Part of it was that he was a superficially charming person, both to comrades and to women (whom he betrayed even more flippantly than he betrayed his country). However, another part which might have contributed is that he was often head of counterintelligence on a neutral station during World War II, where an under-the-table meeting with the Soviets is easily explained in an Enemy Mine context ("Hey, this informant is endangering my men and yours, etc"). He wouldn't have even had to hide the fact that he was meeting the Russians from his own team, and security would not have suspected him of giving something away that he shouldn't because English Boys Don't Do That.
- There were constant suspicions that 'the Fifth Man', the undiscovered Cambridge Spy and Philby's colleague, was actually whoever was the current 'C' of MI-6, a literal example of this trope.
- A similar story exists during World War II. Apparently, up until Franklin D. Roosevelt's fourth (and final) election, his Vice President was Henry A. Wallace, who in recent documents was indicated to actually be a Soviet plant. He was eventually removed in favor of Harry S. Truman, although that had less to do with suspicions of Wallace being a Soviet plant as it was due to them realizing that FDR was likely to die and wanting to ensure they had someone else for president.
Admiral Canaris who was actually head of the Abwehr while also being part of the German Resistance.
- In The Unseen War in Europe by John Waller, Canaris once took a tour with insufficient security and Philby suggested an SOE team assassinate him. His boss vetoed the idea without saying why, except for some vague idea about his usefulness. Philby later claimed that an intermediary had opened contact, and possibly thought that would be more useful to the Western Allies than the Soviets (or just that it would blow him personally).
At the height of the Red Scare, it was believed by some of the wackier Conspiracy Theorists that President Dwight Eisenhower was a Soviet plant.
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, he had already retired, and over a year of preparation did not even begin to repair the damage by the time World War I started. Redl's role? Director of Austro-Hungarian intelligence!
- 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.
Joseph 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.
As part of a plea deal Enriqque Tarrio, chairman of the right-wing white supremacist "militia" "The Proud Boys", worked as an informant for the FBI.