Good Running Evil
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! 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 Poisonous Friends. 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. This sometimes overlaps with Mole in Charge. Spoilers ahead.
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Anime & Manga
- 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.
- In Umineko no Naku Koro ni, 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 taken Up to Eleven 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 Na´ve 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 he 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, 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.
- 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, 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 Ghost Rider, Noble Kale takes over Mephisto's realm, which effectively put an end to Mephisto and Blackheart for good, or would have if StatusQuo wasn't was 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.
- 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.
- 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 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.
Live Action TV
- Angel: Taking over Wolfram and Hart in season 5.
- 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.
- In Chuck, Mary Bartowski is right-hand man of Alexei Volkoff, head of Volkoff Industries.
- 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 organisation when its previous leader went mad after seeing the future and killed everyone.
Mythology & Religion
- 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.
- 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 rebuild all the damage they caused.
- A Light side Smuggler in Star Wars: The Old Republic 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.
- 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.
- 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.
- How "good" you are is up to you, but you can become the leader of the Dark Brotherhood (an Assassins' Guild) and/or the Thieves' Guild in most games in the Elder Scrolls series. A certain amount of stealing and, well, assassination is required to do so, though at least a couple of the assassination targets really deserve to die.
- Played straightest in Oblivion, where completing the Knights of the Nine storyline wipes away your infamy and is supposed to offer redemption for evil characters. You could be the most thoroughly cruel Dark Brotherhood assassin, head of the Thieves' Guild, start the quest, and wind up the noble paragon.
- Prince Zuko of Avatar The Last Airbender 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 its 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 (though canonically he at least survived long enough to abdicate his position to his daughter).