There's an altruistic group or organization, often run by an idealist or goody two shoes chock full of nice guys and girls and legions of people generally with a motto of We Help the Helpless. Often the group in question is a charity organization dedicated to adopting forgotten orphans, finding homes and care for discarded animals, curing disease, spreading peaceful spirituality, or advancing human rights in a peaceful manner.
And then one day or perhaps from the beginning, either as part of an Evil Plan, a cover-up, or just a FaceHeel Turn, a bad guy ends up running it. Often villains would refuse the chance because all those goody goodies would be consistently around them, but some take the chance to use it to their advantage. Rarely are these villains anything but a Bad Samaritan, Bitch in Sheep's Clothing, Treacherous Quest Giver, or Faux Affably Evil characters, but at times they may be genuinely polite, proper, and thoughtful folk. They just happen to have sinister pastimes on the side or a grand malevolent goal in the future.
The difficulty of this task varies depending on how closely the activity of the bad guy in question in monitored. Due to the circumstance of the good people being ignorant or unaware of the bad guy's activities, the organization is often turn into a front for criminal activity or just a Fake Charity. Most of the time, the plot is about the villain using their organization for a greater goal as a Manipulative Bastard or Chessmaster; occasionally, though, the villain may actually run the organization for personal reasons that are not related to their own malevolence.
Polar Inverse to Good Running Evil. Often a sister trope to Tyrant Takes the Helm if the figure in question is newly appointed after a benevolent boss has been removed. The malevolent figure in question is often a Mole in Charge if working for a separate sinister organization. If not, it is often a case of Conspiracy Redemption for a protagonist who has joined the organization. See also Running Both Sides.
Warning. Spoilers will be unmarked ahead.
- Franken Fran has a rather peculiar version of this trope with the Sentinel storylines. An organization bent on humanity destroying itself is actually behind projects like orphanages and bringing resources to poverty-stricken areas, because this will encourage a population boom that will drive mankind to extinction faster. The Sentinels are now wandering the world blowing up such projects, in the name of good.
- In Space Patrol Luluco, it's revealed that the leader of the Space Patrol is actually a Blackholian (an Always Chaotic Evil race of Impossible Thieves).
- Maxwell Lord IV (demonstrated in the main trope picture) would be a progressive example from the Justice League International series of DC Comics. Though always a manipulative snake and amoral businessman, he was a benevolent figure who re-formed the Justice League of America and established the Justice League International to genuinely make the Earth a peaceful and safe place for regular humans to live. Unfortunately the combination of the death of his father, ritual nagging by his mother to hate figures of higher authority and act for the benefit of non-powered individuals, sudden death of his mother in Coast City, and destroyed faith in superheroes caused him to take a permanent and murderous personality shift. As of now, his current incarnation is a manipulative mind-controlling sociopath with a goal to rid the Earth of any metahuman control that is not his own. His death caused by Wonder Woman and subsequent resurrection in Blackest Night only made him more determined and twice as ruthless.
- Both the comic-book Marvel Universe and the Marvel Cinematic Universe versions of S.H.I.E.L.D. were eventually showcased to have been run for a very long time by HYDRA (Depending on the Writer, the comic-book SHIELD was even led by HYDRA as far back as its inception).
- In Nextwave, H.A.T.E. (a parody of S.H.I.E.L.D.) is owned by the Beyond Corporation, which is secretly a front for the evil group S.I.L.E.N.T. (a parody of HYDRA). Note that this was going on for a few years before the SHIELD/HYDRA connections in the MCU or Earth-616 showed up.
- In the Spawn/Batman crossover, the main villain of the story, Dr. Margaret Love, would be an example. She's the founder and leader of the Heal The World charity foundation mentioned in the story that provided food and shelter to New York's homeless population along with social realignment. She also experimented on homeless men to turn them into robotic slaves and tried to start a war that would kill off humanity using stockpiled nuclear weapons due to becoming a Misanthrope Supreme after seeing the world fail to become the paradise she desired.
- Murdock from the comic Dark Gods is this. He was originally an early Cro-Magnon male who gained magical powers after establishing order among his tribe and creating a figure of worship for them. The belief of his tribesman opened a door for an Eldritch Abomination to possess his body and allowed him to live over the centuries as various god guises to combat malevolent monstrosities and eventually founded The Storm, an organization dedicated to stopping them. Unfortunately, by the modern day he has gone to believe he is the true God of humanity and vowed to rule them a tyrant after using his followers' belief to increase his power and destroy the monstrous god, Tiamat.
- In The League of Extraordinary Gentlemen, MI6 is run by a man known as "M", which they assume to be Mycroft Holmes. This causes some hilarity in M, who is actually Professor Moriarty.
- In the original Runaways, most of the kids believed that they'd been brought together by Alex Wilder to stop their supervillain parents from bringing about the end of the world. In reality, their parents' plans were already likely doomed, as the human and non-human families were planning to double-cross each other at the last possible moment. Thus, the real reason that Alex brought them together was to create a common enemy to force their parents to work together so that they would carry out their plan and bring about the end of the world, at which point he expected that his family would get special favors from their benefactors.
- In Aztek, the Q Society is an Ancient Tradition working to avert the end of the world. In the present day, it's heavily dependent on financial support from a wealthy sponsor who is revealed partway through the run to be Lex Luthor. To be fair, he genuinely wants them to succeed in their task of saving the world from Tezcatlipoca, but until Tezcatlipoca shows up he intends to take full advantage of effectively owning his own superhero.
- In Bulletproof Monk, Nina serves as an example. She is the granddaughter of a Nazi officer who works to help her grandfather obtain an ancient artifact so that he can commit genocide on a global scale. Her day job is running a human rights organization dedicated to working against hate and violence in all its forms as its newly-appointed executive director.
- In Thunderball, Emilio Largo is a member of the International Brotherhood for Assistance of Stateless Persons, a philanthropic organization based in Paris. He is also "Number Two" in the criminal organization known as SPECTRE Special Executive for Counterintelligence, Terrorism, Revenge and Extortion). The Brotherhood acts as a front group for SPECTRE.
- SPECTRE and its mysterious leader Ernst Stavro Blofeld is behind many criminal schemes involving Evil Plans of the Take Over the World variety. And its ruling council is a behind-the-scenes cabal of corrupt officials, politicians, terrorists and businesspersons SPECTRE is essentially a shadow government, whose members choose to operate in the dark but present themselves to the public as Villains With Good Publicity. Organizations such as Greene Planet, the Lord's Resistance Army, the International Brotherhood for Assistance of Stateless Persons, Centre for National Security/Joint Intelligence Service, and Osato Chemicals serve as mere fronts for the criminal organization.
- In the Star Wars prequel trilogy, Senator Palpatine is elected Chancellor of the Republic, which has kept a precarious semblance of peace since its inception. By the third film, he has almost absolute control over the Republic and is revealed to be the Sith leader, Lord Sidious, who has been manipulating both sides of Republic and the occurring wars since the first film.
- In Captain America: The Winter Soldier the heroes find out that SHIELD and other sectors of the government has been subverted by HYDRA. Some time after World War 2 a number of former HYDRA scientists were recruited to work for the agency and while they publicly renounced their former beliefs, in secret they were turning and recruiting people to their own cause and by the time of the movie they have hundreds of SHIELD operatives as well as a Senator in their ranks and the sitting Secretary of Defence as one of their leaders.
- In The Flash (2014), for the whole first season Prof. Eobard Thawne a.k.a the Reverse Flash was using S.T.A.R. Labs crew and Team Flash under the guise of Dr. Harrison Wells, who was Flash's mentor and boss of S.T.A.R. Labs, in the hope of escaping his Trapped in the Past state.
- In Agents of S.H.I.E.L.D. a number of storylines deal with the fallout of The Winter Soldier in which HYDRA was found to have infiltrated SHIELD, with the latter half of season 1 dealing with the civil war that broke out inside the agency as a result and subsequent seasons dealing with SHIELD loyalists trying to rebuild it. The third season also reveals that Gideon Malick, a member of the United Nations Security Council from the first Avengers movie, was yet another HYDRA leader.
- A variation forms the premise of The Blacklist, with notorious fugitive Raymond Reddington working with a secret FBI task force to stop other criminals. While he is hypothetically under their watch and certainly not in any position of authority that quickly proves to be a thin distinction as every other episode leads to him exploiting the arrangement to further his own criminal interests.
- Daredevil (2015): In season 1, Wilson Fisk owns many fronts, one of which is Union Allied Construction, with whom he's skimming on Incident reconstruction contracts in Hell's Kitchen. Season 3 sees Fisk manipulate the FBI into becoming his personal minions by selling out criminals involved in corruption and taking their connections for himself, all while painting the false picture that he's a reformed criminal.
- Luke Cage (2016): Mariah Dillard's Family First initiative is very much legitimate, and Mariah does genuinely want to help out her fellow Harlemites, though the source of the money for said initiatives and programs is illegal arms dealing.
- In Warhammer 40,000, there is a case revolving around the figure of worship and veneration in the Adeptus Mechanicus. Depending on the Writer, the Adeptus Mechanicus, which is responsible for running the Imperium's machines and starships, actually worships the C'tan star god called the Void Dragon as the Omnissiah (as opposed to the Omnissiah being an aspect of the God-Emperor, the in-universe explanation).
- In Azure Striker Gunvolt, we have Asimov. Asimov is the Rebel Leader of La Résistance organization QUILL, who, while cold and pragmatic, is very devoted towards the freedom of the Adepts and Gunvolt sees him like a father figure. Then, after you beat the Final Boss, it's revealed that his goal actually stretches further: he wants full supremacy of Adepts and to Kill All Humans. Gunvolt is understandably shocked and decides to go against him.
- Mega Man
- In the Mega Man Zero series, Copy-X, leader of Neo-Arcadia, would serve as an example. Neo Arcadia Army functions as the Hero Antagonist faction of the game dedicated to restoring the world from the marks of Elf Wars, maintaining the sole surviving human population, and protecting the empire against the threats of La Résistance (i.e the player's side). Unfortunately, Copy-X is a Knight Templar who thinks that slaughtering Reploids in the name of solving an energy crisis is a good thing to do.
- Downplayed in Mega Man Zx Advent where it is a case of evil "hiring" good, but Master Thomas has given the player orders to thwart the enemies'plans and also commands the Bounty Hunter organization to stop the Big Bad. In The Stinger, your benefactor reveals himself to have a similar goal as the Big Bad's (Restart the World), but he just did not like how the Big Bad tried to go about it.
- In Touhou, Yukari Yakumo seems to be a Pragmatic Villainy version of this, verging on Blue Running Orange. One of the leaders of the youkai, she also gives the human youkai exterminator Reimu training and resources, and may have appointed her to her position in the first place. Unusually, her nature is not a secret to Reimu - it's just that Yukari wants Gensokyo to have an impartial human sheriff to prevent the youkai from pushing humans too far and sparking a war, and Reimu agrees with this goal. While Reimu doesn't usually trust Yukari (and has even fought her in the past), she's willing to follow orders from her if the situation is serious enough.
- Rashid ad-Din Sinan aka Al-Mualim from Assassin's Creed is an example for the Levantine Brotherhood of Assassins. Despite having a highly positive effect on the progress of the Assassin Order and promoting the spread of peace in his homeland, Rashid's desire to obtain an Apple of Eden led to him secretly working with the Knights Templar, sworn enemies of his own Order, in an attempt to tyrannically secure power and betray the order. May count as an aversion as the Assassin Order is only seen as a benevolent organization from the viewpoint of the player while being in truth morally dubious at best.
- In Dawn of War, Azariah Kyras would be an example. It's revealed in Chaos Rising that the Chapter Master of the Blood Ravens fell to Chaos centuries ago. In the Space Marine campaign of Retribution, a major turn in the story is Apollo Diomedes coming to terms with the truth, as he has essentially spent more than four hundred years protecting a heretic.
- In The Elder Scrolls V: Skyrim, the leader of the Impartial Purpose-Driven Faction of the Greybeards (who are the good guys in the time frame of the game since they a) take you under their wing and b) facilitate peace talks for the ongoing civil war) turns out to actually be Paarthunax, one of the ancient dragons, a mass murderer, and a former top lieutenant of the Alduin himself, who became disillusioned with Alduin's goals but is otherwise quite morally ambiguous—the Blades, for one, still believe him to be an evil, manipulative schemer.
- Resident Evil
- The franchise has this happen constantly over the course of the series. This is mainly due to the Umbrella Corporation's bribes and/or associates.
- Played With in Resident Evil: Revelations 2. It's revealed that Terra Save, a anti-bioterroism peace group that Claire Redfield and Moira Burton work for, is actually good, but Neil Fisher, a senior staff of the company, used the company to help the Alex Wesker. Neil is revealed to be a Well-Intentioned Extremist but caused the main characters to lose faith in him.
- In the animated adaptation of The 99, the kids are first gathered by Rughal, the series' Big Bad. After realizing who Rughal is and what his intentions are, the kids break away and join up with the more benevolent Dr. Ramzi.