There's a Nebulous Evil Organization, often run by an Evil Overlord and chock full of Psychos for Hire and legions of mooks. And then one day, either as part of an Evil Plan or out of dire necessity, our heroes end up running it! They may have inherited the position or they may be going through a "Freaky Friday" Flip or some other situation. Either way this casts the organization as less than impenetrable to outsiders. Often they jump at the chance because now all those resources can be turned to good, or simply out of a belief that nothing else works: if you can't beat 'em, join 'em.
This is rarely an easy task, of course: the bulk of the conspiracy is still made up of evildoers and scum, and solo heroes may well end up with True Companions who are all Psycho Supporters. Sometimes the hero will even need to hide their real motives from their assorted underlings. This plot can also often involve the hero becoming the Man In Front of the Man and having to answer to The Omniscient Council of Vagueness.
Most of the time, the plot is about the heroes risking corruption; occasionally, though, the hero is playing a Batman Gambit of their own, banking on either crippling the evil organization or genuinely making it a force for good.
- Averted in Air Gear: Ikki is asked to take the position as leader of Genesis, but he turns it down.
- In Code Geass, Lelouch has been fighting Britannia's tyranny; later, he succeeds Charles as emperor, and plays the part of Evil Overlord in a Genghis Gambit for world peace.
- Go, Go, Loser Ranger!: At some point during the 13 year war between alien Invaders and human Rangers, the Invader Executives all fled or were killed and their flying castle was abandoned. The Rangers moved in and forced the remaining footsoldiers to hold mock-battles against them once a week or be Killed Off for Real, so the Rangers maintain their popularity.
- The Crossbone Vanguard from Mobile Suit Crossbone Gundam are the same faction that had previously been the antagonists of F91. After the events of the movie, Berah assumed command and changed them from the military wing of The Empire to a secret force defending the Federation from the second, even eviler empire that had secretly been funding the first. The change is relatively smooth, but it's mentioned that many of the rank and file still believe in the old guard's aristocratic principles and only follow Berah out of loyalty to her family, and the only named holdover from the Cosmo Babylonia days eventually betrays them to the bad guys because he recognizes that they represent his ideals better.
- In Umineko: When They Cry, for several reasons, Battler ends up arguing for the Witches' side in Episodes 5 and 6 of the Visual Novel.
- Puella Magi Madoka Magica The Movie: Rebellion has a self-inflicted version with Akuma Homura - the evolution of Dark Magical Girl Homura into a Satanic Archetype out of the belief she needed to do so in order to save her friend and probable lover. Played With, in that it's also implied her motive was a misunderstanding (the conversation that convinced her to betray Madoka was with her pre-Character Development Naïve Everygirl version who was trying to cheer her up) and it's made quite clear that part of it is still massively selfish (she links her own happiness to Madoka's safety so utterly she dismisses the idea of letting her be free out of hand).
- For a while Daredevil ran the evil ninja assassins called the Hand.
- This is the entire premise of Agents of Atlas.
- In Superman & Batman: Generations, Bruce Wayne accepts Ra's al-Ghul's offer of succeeding him as the head of the League of Shadows, then changes it from a legion of assassins into a benevolent superpower. This turned out to be fairly simple; it was just a process of taking the cover organizations they used to aid in their evil plans and making them legit.
- 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.
- Currently in the comics, Lex Luthor is in prison for murdering Manchester Black. After he went away, Luthor signed over control of LexCorp to Superman. Without his knowledge. Supes doesn't find out until the L on top of the tower turns into an S. Superman has no interest in going along with Lex's nonsense and initially refuses, but Lex wrote into the deal that if Superman tried to hand over control of the company to someone else it would be dissolved and half of Metropolis would lose their jobs.
- After "The five books of Blood," DC heroine Renee Montoya finds herself the leader of the "Religion of Crime" that she had been hunting down for more than a year because she (accidentally) caused the death of their previous leader.
- In the Marvel Universe, the Shroud set up a gang called the Night Shift. The other members thought they were preying on the organised crime gangs of LA so they could take over the city. Actually, he was just using them to shut down organised crime in LA.
- In The Sandman (1989), after Lucifer quits, throws everyone out of Hell, and hands the keys over to Morpheus, God decides that Hell will be run directly by Heaven from now on and appoints two angels to be his overseers there.
- Later it's revealed that only one of these angels was properly good. The other was indecisive, having stayed impartial from the original War in Heaven and picking the winning side as soon as it came apparent. He develops some serious Smug Snake and Holier Than Thou tendencies soon enough after taking charge of Hell.
- The good angel was also the one who had the courage to take the key to Hell. The other one whimpered, wailed, and even considered following Lucifer's example by rebelling against God before resigning himself to his duty.
- In the League of Extraordinary Gentlemen, it was revealed that Moriarty was a member of British Intelligence who took over Britain's organized crime networks as part of a plan to keep crime in the country within limits. Unfortunately, he ended up Becoming the Mask, at which point he was stopped first by Sherlock Holmes, and then by the League.
- "Good" is a stretch in this case, but at one point The Punisher took over a mafia family so use their resources to take even worse criminals out. In 2022, Frank gets another go at this when he's made a leader of the Hand, a cult of demon-worshipping necromantic ninjas and as a sacred figure to certain factions, he's using their loyalty to steer them into hunting criminals.
- In Ghost Rider, Noble Kale takes over Mephisto's realm, which effectively put an end to Mephisto and Blackheart for good, or would have if Status Quo wasn't so prevalent in Marvel comics. So he was kicked out of hell by demons for being too benevolent for their tastes and later disappeared into comic book limbo while Mephisto and Blackheart returned.
- Advanced Idea Mechanics are a long-running evil corporation that were bought out by billionaire Roberto da Costa, aka Sunspot, after he joined The Avengers. He converted them into the Avengers science division, then into the government-sponsored American Intelligence Mechanics, while weeding out any of the rogue A.I.M. employees trying to rebuild the organisation from the ground up.
- At one point it was suggested that S.H.I.E.L.D. was allowing HYDRA to believe they were secretly running S.H.I.E.L.D., while actually S.H.I.E.L.D. was secretly running them. It may have got even more complicated than that.
- The end of Eastern Promises reveals that Nikolai is an undercover law-enforcement agent, and is likely to (at some point in the future) end up running the organisation.
- In The Chronicles of Riddick (2004), Riddick becomes the new ruler of the evil Necromonger army after he kills their leader, although it's debatable just how "good" Riddick actually is.
- A Song of Ice and Fire features a variation where Daenerys conquers a slave city using an army of slaves she bought and then freed, and then decides to settle down and rule rather than leave its people to starve. She then has to deal with the city itself, whose entire economy depended on slavery. Like in most of Martin's works, institutional problems prove hard to fix from the top down.
- In Sword of Truth, Richard
CypherRahl is given control of his ancestral nation of D'Hara, as well as an entire legion of Cold Blooded Torturing Broken Cuties, the Mord-Sith.
- In Atlas Shrugged, the looters eventually capture John Galt because they want him to be their new leader. He refuses.
- The comedy of There Was No Secret Evil Fighting Organization comes from the threat of the murderous World Shadows...a threat that doesn't actually exist, but is carefully orchestrated by older espers to look real, so that younger espers will have fun fighting them and learn valuable life skills. (Hence the title. There is no secret evil-fighting organization, but there is an organization that believes itself to be one.) In reality, there are no supernatural monsters in the world, or any inherent meaning to the espers' power at all...something that causes Amaterasu's founders no small amount of frustration.
- A Practical Guide to Evil: In a setting where the Theory of Narrative Causality and Black-and-White Morality are objective reality, one of the previous rulers of Praes was Dread Emperor Benevolent, the first and only good-aligned Dread Emperor in history. He's described as having been at war with half the realm for the entire duration of his rule, which racked up a gargantuan body count, yet was so successful that later rulers had him Unpersoned for fear of what he represented.
- Angel. In Season 5, Team Angel are put in charge of the Los Angeles branch of supernatural law firm Wolfram & Hart. It doesn't work well, with our heroes finding themselves increasingly morally compromised and demoralized. Wolfram & Hart were fairly open about this being the point of giving them the job. The lead-up to the Grand Finale had Angel exploit this by pretending to be corrupted in order to infiltrate the Circle of the Black Thorn, the Co-Dragons of the Wolf, Ram and Hart.
- The Prisoner (1967) episode "Free For All": Number 6 is elected to the position of Number 2, technically putting him in charge of the Village.
- In Chuck, Mary Bartowski is right-hand man of Alexei Volkoff, head of Volkoff Industries.
- Kamen Rider Gaim has two examples.
- Takatora Kureshima is the head of an evil Mega-Corp, but at worst he's a Well-Intentioned Extremist committing what he believes to be necessary evils to save the human race. When a more positive solution is put in front of him, he immediately switches over to that from his original Evil Plan. The issue though is that his inner circle doesn't share his ideals and only want to claim power for themselves, and when Takatora jumps ship from what they were plotting, they begin plotting to remove him by force.
- Rosyuo is the ruler of the Overlord Inves, but he's long since given up on being an Evil Overlord after his Darwinistic regime destroyed his whole civilization. Now he only plays the part of being one to keep his bloodthirsty minions all in line.
- In Torchwood, Captain Jack was pressured into working for Torchwood Three back when it was still a conspiracy to seize alien tech for the British Empire and hunt down the Doctor. He was given the opportunity to reinvent the organization when its previous leader went mad after seeing the future and killed everyone.
- In Arrow, Ollie nearly ends up running the League of Assassins after the current Ra's al Ghul makes him his heir (in their duel, he'd handed Ollie a total Curb-Stomp Battle but considered Oliver's survival proof of his worth.) Oliver is told that when he's officially in charge, his desires will be law, even if it's to become a lawkeeping force under the Arrow. What keeps him from taking over and trying to turn the League into Heroes "R" Us? Mainly, their tradition to destroy the hometown of a new leader in order to sever all past ties. Uh-oh.
- In Supergirl (2015) the Department of Extranormal Operations was founded specifically to act as a counter to Superman if necessary, which evolved into a Knight Templar organization that considered all extraterrestrials as threats, run by rabid bigot Hank Henshaw who saw its responsibility as protecting humans from aliens at almost any cost. When J'onn J'onzz secretly replaced Henshaw, he was obviously able to quietly adjust its mission and personnel to the point that when Supergirl became active the DEO aided her, and when he was outed as a Martian the majority of people within the organization took it in stride and cheered when he was formally re-instated as director under his true name. The DEO has since become one of the biggest protectors of law-abiding and innocent extraterrestrials in the United States.
- There is one train of philosophical thought that proposes this is how Heaven and Hell work. If God is all powerful, and if He created everything, and if He has a plan for everything, then logically Hell operates because God wants it to operate. And since God's plan predetermines everything that happens in the universe, this includes everything that happens in Hell, too. Thus, God is actually running Hellnote . As well as every single evil organization, evil person, or evil action, ever. This oddity is known as "the problem of evil." Traditional Calvinism took it to the extreme of saying God had predestined everyone's fate, including what actions they would take to save or damn them, and that one could guess who "the elect" (i.e. those going to heaven) would be by their upright, successful lives, versus the damned having the exact opposite.
- In Magic: The Gathering's Ravnica cycle, Jarad takes over as Guildmaster of the Golgari after Savra is defeated.
- In the 3E Mutants & Masterminds Freedom City setting, Seven defeated Una, Queen of the Netherworld, and by ancient rules of conquest, now rules the Netherworld. This is a bad thing for her because she is barred from Earth, and giving up the office would lead to the Netherworld dissolving, killing all of its inhabitants.
- Command & Conquer: Tiberian Sun: At the start of the Nod campaign, the good GDI is secretly running the evil Nod as a puppet government. The initial goal is to break free and restore Nod to being an independent evil organization.
- Heroes Chronicles: The Sword of Frost has Tarnum disguise himself as a Nighon Overlord and lead its Always Chaotic Evil inhabitants to save the world.
- The Mass Effect 2 DLC "Lair of the Shadow Broker" ends with Commander Shepard and Liara T'soni killing the Shadow Broker and Liara deciding to take over his organization and use it to help Shepard fight the Reapers.
- In the end of Mass Effect 3, one of the three options to stop the Reaper threat is to upload Shepard's consciousness to control them. The consequences of this are never shown though in the original ending, with the exception of the Reapers leaving. In the Extended Cut version of this ending, the resulting Reaper-Shepard consciousness has the Reapers repair all the damage they caused and vows to honor the sacrifice the human Shepard made by defending the galaxy.
- At the end of Outlast, Miles ends up becoming the new host for the Walrider, and is last seen during the Whistleblower DLC using his newfound powers to take vengeance on all the bastards at Murkoff who put him and the other inmates through a living hell.
- Star Wars: The Old Republic
- A Light side Smuggler is a Republic patriot and fairly honest person...who still gets to run most of the criminal underworld. Likewise, their companion Risha gets her own empire to run.
- A Light Side Sith Inquisitor will be one of the two most powerful people in the Empire by the endgame, and the closest they get to being evil is immense sarcasm.
- In the Open Palm ("light sided") ending of Jade Empire, the thief Sky takes up running his archenemy's criminal empire. Seems BioWare has a soft spot for this trope.
- A variation occurs in Tales of the Abyss. The Big Bad is actually a Well-Intentioned Extremist manipulating a monster.
- Mortal Kombat: Sub-Zero went from being a renegade on the run from the Lin Kuei, a shady assassin clan from China, to becoming the clan's leader and changing its purpose to protecting Earthrealm from outside threats.
- At the end of Wrath of the Lich King, the titular Lich King is defeated. But somebody has to be in charge of the hordes of ravenous undead crawling around the planet, or the effects will be worse than the original war. So Bolvar Fordragon takes on the mantle of the Lich King, proclaiming himself the "Jailor of the Damned."
- Depending on how you play Mike Thorton of Alpha Protocol can end up running Halbech... or all sorts of organizations really, at the end of the game.
- The Elder Scrolls
- Throughout the series, you can choose to play as a good character, an evil character, or any shade of gray in between. If you choose to play as a "good" character, you can still rise to the top of multiple "evil" organizations, such as the Dark Brotherhood (an assassin's guild doubling as a Religion of Evil) and the Thieves' Guild (which has rules like no-killing but is still a group centered around stealing the property of others). This also works in reverse, as you can be an outright evil character who murders unprovoked and steals everything that isn't nailed down, yet rise to the top of several "good" factions like honorable warrior guilds and temple organizations, as long as you don't kill or steal from your fellow members.
- In Oblivion's Knights of the Nine expansion, a certain quest wipes away your infamy and is supposed to offer redemption for evil characters. You can be the most thoroughly cruel Dark Brotherhood assassin and head of the Thieves' Guild, but complete the quest and be seen as a virtuous, noble paragon.
- In The Last Sovereign, the heroes invent an Evil Overlord and stage an invasion of a country (with its ruler's consent) to gain a base and resources to improve the world. Original plan is to get rid of the overlord later (hence this being called the Doomed King Plan), but he becomes so prominent and respected that they have to keep the ploy running.
- Fallout 4: The Sole Survivor will become Director of the Institute if they choose to side with them, though despite The Institute's impressive technology, they won't actually provide much of it to help people with.
- Touhou Project: Her true moral alignment may be up to audience interpretation, but despite being one of the most powerful youkai in Gensokyo, Yukari Yakumo has little interest in actually antagonizing humans and goes out of her way to make sure the Human Village stays protected, in order to use their fear and superstitions to keep the youkai population sustained.
- Avatar: The Last Airbender: Prince Zuko technically ends up in this role in the finale. While the Fire Nation is an evil, corrupt, warmongering empire, it's explicitly pointed out that this is because propaganda has raised everyone to believe it's necessary, even good. They aren't Always Chaotic Evil. Zuko himself spent about two and a half seasons realizing it was wrong, and eventually pulled a Heel–Face Turn. When the finale comes around and Team Avatar places him in charge, he's more than happy to rebuild the nation. Follow-up comics make it clear how very, very hard this is, especially when everyone has been conditioned to hate you and you're simultaneously trying to fix an entire nation while not being as authoritarian as your father (though canonically he survives, abdicates his position to his daughter, and is still traveling as an ambassador at ninety-three, as per the sequel show).
- Captain Planet and the Planeteers: In "The Unbearable Blightness of Being", Dr. Blight pulls a "Freaky Friday" Flip on herself and Gaia. The latter, after some initial confusion, manages to fool Blight's computer assistant MAL into believing she's the real deal, and takes command of him and their aircraft, so that she can gain the Planeteers' trust and undo the mind switch.
- The Simpsons: Discussed by Homer in "Whacking Day", though given the source, it's pretty obvious this wouldn't work as intended.
Homer: Lisa, if I'm part of the mob, maybe I can steer it in wise, productive directions. Now, where's my foam cowboy hat and air horn?