Good Running Evil

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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.

Anime & Manga

 * In Code Geass, Lelouch has been fighting Britannia's tyranny; later, he
 * Averted in Air Gear: Ikki is asked to take the position as leader of Genesis, but he turns it down.
 * 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.

Comic Books

 * For a while Daredevil ran the evil ninja assassins called the Hand.
 * 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.
 * 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 to 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.

Film

 * The end of Eastern Promises reveals that, and is likely to (at some point in the future,) end up running the organisation.

Literature

 * In Sword of Truth,
 * A Song of Ice and Fire features a variation where

Live Action TV

 * Angel: Taking over Wolfram and Hart in season 5.
 * 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.
 * 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.

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 Hell . As well as every single evil organization, evil person, or evil action, ever. This oddity is known as The Problem Of Evil.

Tabletop Games

 * In Magic the Gathering's Ravnica cycle, Jarad takes over as Guildmaster of the Golgari after Savra is defeated.

Video Games

 * The Mass Effect 2 DLC "Lair of the Shadow Broker" ends with Commander Shepard and
 * In the end of Mass Effect 3,
 * A variation occurs in Tales of the Abyss. The Big Bad is actually a Well Intentioned Extremist manipulating a Complete Monster.
 * Sub-Zero ended up taking control of the Lin Kuei, a clan of assassins based in China.
 * 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  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.

Webcomics

 * While Drow Tales is a Grey and Gray Morality, the Vloz'ress clan is pretty much the nation - equivalent of a Villainous Harlequin. After  Lavova tries to take over, only to find Ensemble Darkhorse Kiel waiting for her.