Den Mother: Would you care to join us in our Rainbow Squirt Pledge of Purpose?
Rainbow Squirts: "To promote niceness. To make the world prettier. To share candy with everyone. To obfuscate the true nature of the Milkman. To protect the Milkman at all costs. To destroy all who would harm the Milkman, or threaten to reveal his secret objective."
A Milkman Conspiracy is any conspiracy operating from an organization so pathetically uninfluential that it should by all rights barely be able to overcome zoning regulations, yet is somehow able to sink its fangs into vast swathes of the Earth. Named for a level of Psychonauts in which the paranoid fantasies of one of the characters involve being a milkman-spy at the center of a war between an army of secret agents and... a troop of homicidal Girl Scouts.
If the organization is not secret, this becomes just a Weird Trade Union. If it is not powerful even in the story, this is a Brotherhood of Funny Hats.
Compare Almighty Janitor and The Dog Was the Mastermind.
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Anime & Manga
In Read or Die spinoff Read or Die the TV, the governments of the world are all merely puppets, secretly being controlled by that wretched hive of scum and villainy: The British Library.
In Steins;Gate, CERN—sorry, SERN—have secretly been trying to create time travel, killing at least 14 human tests subjects in the process, and have a network of armed agents called Rounders that are recruited through cellphone texts. In the timelines where they complete it they immediately use it to take over the world and turn it into an impossibly bleak dystopia.
The card game Illuminati occasionally displays this. While you typically need to have groups that would logically be powerful, small ones help you out as well; people can win by taking control of the Furries.
Indeed, a classic example in game is the "Secret Masters Of Fandom attack to control California."
In Hot Fuzz, a vast campaign of murder and intimidation is covered up by a conspiracy of a few village shops, the local pub, and the local Inspector, all for the purposes of ensuring they continue to win the "Village of the Year" award.
The 1967 film The President's Analyst features a plot to enslave all humanity masterminded by TPC (The Phone Company). This group, or at least its real-world equivalent, used to have a bit more power and influence than most in this list.
Hilarious subversion in the film The Stupids. The titular familybelieve they've uncovered one of these, involving the police, garbage collectors, the New York Times, the local deli, the local Chinese restaurant, and bees (my God) to steal all the world's mail and deliver it to a man called "Sender" (Christopher Lee!) (because the father, who used to be a mailman, got suspicious about all those letters that said "return to sender"). The twist is that, not only does this conspiracy not exist, but in their efforts to thwart it, the Stupids manage to mess up an actually dangerous conspiracy entirely by accident. Oh, and they find Sender, and he turns out to be, not Christopher Lee, but Bob Keeshan!
Auric Enterprises, an international jewellers, is engaged in gold smuggling, murder, nuclear terrorism and conspiracy with Red China.
On Her Majesty's Secret Service. A laboratory in the Swiss Alps for curing allergies is Blofeld's secret bio-weapons facility for developing bacteria designed to cause sterility in plants and animals of his choice, presumably including humanity itself.
Inverted in Diamonds Are Forever, where the billionaire Willard Whyte's enterprises have been hijacked by Blofeld to engage in diamond smuggling and terrorism... all controlled from a hotel in Vegas.
Drax Industries' Moonraker space shuttle programme wants to wipe out humanity and start over with a race of ubermenschen astronauts.
The Carver Media Group blackmails the President into signing bills, sells software filled with bugs to force buyers to constantly upgrade, may or may not have run Mad Cow Disease stories out of revenge because the boss was owed money from a British beef baron from a poker game who refused to pay (and then ran the stories for another year because the French paid him to do so), and engages in murder, conspiracy, and a plot to bring the world to the brink of World War IIIin a bid to get broadcasting rights in China, for which end it sinks a British navy ship (after sending it off course into Chinese waters), steals a ballistic missile from it, and frames them for shooting down a Chinese fighter jet, before shooting all the survivors with Chinese ammunition in time for the morning edition. Allegedly able "to topple governments with a single broadcast", and appears to engineer disasters regularly for the sake of ratings, which also allows them to be the first to report on events. The bosses' motto is "There's no news like bad news" which is exemplified in this little exchange:
Newsman: Floods in Pakistan, riots in Paris and a plane crash in California.
Greene Planet, a Greenpeace-style organization, is part of a grander Illuminati-like group and is responsible for setting up dictators and monopolizing Bolivia's water supply, causing massive drought, as well as accusing the government of selling thousands of acres of rainforest to greedy developers to cut down even though they actually sold them to Greene Planet, who then sold them to the developers. Manages to get the CIA involved too.
In Dr. Strangelove, General Ripper tries to start nuclear war with the Russians over one such conspiracy. While tampering with our water supply would be a good way to deal a lethal blow to major population centers in the United States, Ripper comes to the conclusion that the Russians are doing this because when he tried having sex his "essence" was denied exit from his body. If he had seen people dying or getting sick from drinking water then there would be some validity to Ripper's claim, but as it stands The General brought on nuclear war with Russia just because he couldn't get it up.
The International is about a corrupt bank that secretly has for clients everyone from democratic governments to dictators, criminals and terrorists, and considered so big and important that Failure Is the Only Option for the heroes trying to bring it down, as if they succeed another such bank will simply take its place. To make matters worse, it was inspired by true events.
The Grand Budapest Hotel features a benevolent one. M. Gustave is a member of the Society of Crossed Keys, a secret international network of hotel janitors. In a late part of the movie, Gustave requests their help to find Serge, the witness of a murder which main suspect is Gustave (he is also the victim's butler.
In The Illuminatus! Trilogy, the real Illuminati, the one of which Hagbard Celine is Primus, maintains its control over world affairs by operating through Discordians and anarchists, two groups of people who by their very nature are disorganized and individualistic.
Tom Holt's books feature a literal milkman conspiracy as imagined by Danny Bennett, a journalist hellbent on proving that the real power behind world governments lies with... the Milk Marketing Board.
The Crying of Lot 49 features a vast conspiracy which is either a secret postal service masquerading as a swingers' club, or an eccentric dead man's estate masquerading as an secret postal service masquerading as a swingers' club, for a prank. Needless to say, the protagonist's just as confused as you are. Don't expect anything to be explained.
And V.F.D. itself stands for Volunteer Fire Department.
In the book Michaelmas, the benevolent secret ruler of the planet is a respected TV journalist in the Walter Cronkite mode.
In Catch-22, Lieutenant Milo Minderbinder (magnificent bastard extraordinaire) is only the head of the mess hall, but manages to become more powerful than any of the generals by organizing a vast international trading company through the mess hall.
By the same token, ex-PFC (yes, ex-Private First Class) Wintergreen, the mail room clerk, is the most powerful man in the US Army and the de facto European Commander because he handles all significant communications between the brass and every time he sees an order he doesn't like, he chucks it in the trash. At one point it is claimed that he delayed the Normandy invasion until more armor was committed.
The Dark Heresy novel Scourge the Heretic briefly mentions this when it becomes apparent that a people-smuggling conspiracy has its hideout in a former mining shaft now in use for growing mushrooms (by the Fraternity of Comestibles for the Cultivation of Edible Fungi), though it's immediately noted that they probably just don't have any idea what goes on in their holdings.
In The Mysterious Island, only the arrival of the colonists saves Nemo from dying alone with all of his crew dead and the Nautilus trapped at Lincoln Island — and gives him a new, arguably more noble purpose.
Vaguely implied in Lord Dunsany's short story "Why the Milkman Shudders When He Perceives the Dawn". The Ancient Company of Milkmen seems to be hiding, or be aware of, some dark secret, but we're never told exactly why it is that the Milkman shudders when he perceives the dawn.
The DiscworldFools' Guild Diary reveals that jesters of the Guild regularly report the public and private doings of their respective royal patrons to Dr. Whiteface, leader of the Guild. In effect, it's a huge spy network that covertly monitors various petty kingdoms in the region, to its own profit and advantage.
Live Action TV
British TV show The Avengers featured another literal Milkman Conspiracy in the episode "False Witness", with the added twist that the dairy produced was absolutely central to their scheme. The series also featured, on other occasions, sinister cabals of nannies, window cleaners, hoteliers, romance novelists, secretaries, farmers and retired Vaudeville performers.
And don't forget the 'British Fanatics' who killed government ministers by tricking them into getting off trains at disused stations, and then murdering them. Why? Because the trains no longer run on time under the current government...
Community does this hilariously with the Greendale Air Conditioner Repair School, and one of John Goodman's greatest monologues.
Vice Dean Laybourne: Mr. Barnes, air conditioning repair is an elite, worldwide family dating back to the very beginnings of civilizations. Our predecessors were slaves, fanning the Pharaohs with palm fronds. Over time, we became expert at making our superiors comfortable. We made it our business. And along the way, we learned to make ourselves comfortable. No more palm fronds, Troy. Now we are the Pharaohs.
Vice Dean Laybourne: That's what we do, Troy. Incredible, invisible, inbelievable things. We're an unseen, unknown, unvincinble fraternity of craftsmen.
In the Devilfish episode of Mystery Science Theater 3000, Mike and the Bots start making fun of Dolphins, only to find out that Dolphins are a space-faring race that attack the Satellite. Later, Mike gets cocky and starts teasing an electrician, only for him to call in his dolphin buddies to start blasting the Satellite again.
The Milkmen of the town of the town of Eerie play a subtle roll in the towns very strangeness.
The Regents in Warehouse 13 have regular day jobs (one of them is a waitress at a diner), despite being in possession of the most dangerous artifacts in the history of the world. Subverted in that they are not evil and have no goals of world domination. In fact, their goal is to protect humanity from dangerous items and has been for thousands of years.
When Artie expresses surprise at who the Regents are, they ask him who he'd rather have this power. A person in power would be motivated by more power. And, of course, there's the revelation that Pete's mom is a Regent.
One episode of Monk featured a secret ring of chambermaids that used confidential information left lying around in hotel rooms to engage in insider trading. When one of their number wants out (or did she want more money? or was she a new girl who stumbled onto their secret? I don't recall), they kill her and use their position and near-invisibility to disappear the body and cover up the crime to the point where Monk looks like (more of) a lunatic for even trying to investigate.
In the "Secret Service Dentistry" sketch for Monty Python's Flying Circus, the hapless protagonist Lemming finds himself caught in the middle of an elaborate spy game between the British Dental Association and a conspiracy of evil dentists working under the employ of the Big Cheese. And then it turned out that Lemming was himself a member of the BDA
Breaking Bad: Los Pollos Hermanos. On the surface, a regional Chilean-influenced fried- and roast-chicken chain, with its head, the mild-mannered Gustavo Fring, a pillar of the community and a friend to law enforcement. Go deeper, and you find that Los Pollos Hermanos is a front for the largest and most sophisticated methamphetamine ring in the Southwest, with an industrial-scale lab producing large amounts of high-quality crystal meth to be distributed in the chain's buckets of fried-chicken batter. And Fring? A truly ruthless, devious, and vengeful kingpin.
The Blacklist gives us The Cyprus Agency, an adoption agency for the wealthy that offers to scour the globe in search of your "ideal" infant child- hair colour, ethnicity, sex, genetics...you name it, they'll find it. In reality, the babies are abducted from their mothers at birth, and the mothers are dozens of abducted women who fit the various genetic profiles and who are kept comatose in a fertility clinic, impregnated by artificial insemination and give birth all while unconscious. What truly makes it this trope is that while most of the agency is in it for profit (or fear), the boss is the father of Every. Single. Child. and he does all this because wants to leave a legacy.
The Amnesty Collective, a prison rights organization protesting the death penalty, was co-founded and run by The Judge, a Knight Templar who gets revenge for miscarriages of justice by abducting the officers or officials they hold responsible for the length of time the innocent (or "innocent", as the case may be) is themselves held. If the miscarriage leads to the death penalty, The Judge is prepared to execute in retaliation as well. While most of the organization seems entirely legit, The Judge is helped by at least a few members.
In French News Parody Groland, there is "Le Complot des Vieux" (the old people conspiracy). They are organized with secret cameras everywhere... To create everyday annoyances like filling buses to the brim so that young people have to stand up when going somewhere, always coming in front of younger people at the supermarket and taking as long as humanly possible to pay for their groceries... Stealing the elevator from younger people...
In Red vs. Blue, a bizarre Milkman Conspiracy is set off when Vic, the obnoxious dispatch operator back at "Blue Army Headquarters," is told, in the past after some time travel, that "Red and Blue are the same thing." Vic takes this literally and it eventually turned out that because of all this, the commander-in-chief of both Red and Blue armies is, in fact, Vic, who has been setting them at war with one another over one offhand comment.
The conspiracy deepens: Vic manages to do this because he's actually the computer that's running the Capture the Flag game that everyone is playing. At least, that's what the last episode implied.
It should be noted that in the end, it's not really a Milkman Conspiracy, it only appears to be one. The truth is even more complicated. In short, both the Red Army and the Blue Army are made up of rejects from the regular army on training bases controlled by the Freelancer Project. Scenarios are set up on these bases to train Freelancers, all of whom are aware of the deception while the "simulation troopers" are not. However, simulation troopers who do well enough are apparently shuffled back into the regular army, such as Donut (apparently?) and Tucker.
The title characters in the Modesty Blaise story "The Head Girls" are spies who are trained as secretaries, then placed with high ranking scientists and government officials, giving them access to their bosses' secrets.
The Mak Attax cabal in Unknown Armies who have infiltrated "the world's largest fast-food chain" in order to spread magic randomly through the population. It is also heavily implied that they saved the world from disaster at least once, by performing a powerful ritual on the stroke of midnight on December 31, 1999.
JAGS Wonderland has the Orange-Peel Men, Whirls who gather together to try to control Chessboard Zero, but only influence it in exceedingly strange ways, such as trying to get people to adhere to Red Shirt Tuesday.
In Exalted, one of Sidereal Charms allows them to create these on the spot. As long as she support it, it avoids being just a Brotherhood of Funny Hats by virtue of, well, being supported by a member of an Ancient Conspiracy that controls the entire world from the offices of Heaven. Should she abandon them and the conspiracy have disparate goals and capabilities, it quickly falls apart.
Killer7 has the United States government controlled by Japan. This isn't so bad, except their method of control is by hypereducating and brainwashing the students of a single elementary school. In Seattle. Oh, and the principal is Harman Smith. Not to mention the fact that US Presidential Elections are rigged by the Education Ministry, who also have the power to authorize global war against both the US and Japan.
In Resident Evil 4, los Iluminados, a cult led by Ozmund Saddler, are a bunch of Spanish farmers and zealots... with an island fully equipped and devoted to studying the Plaga parasite and creating many types of monsters. Still, they are only farmers.
The teams in Team Fortress 2 operate this way. Reliable Excavation and Demolition and the Builders' League United are fronts for two organizations that secretly control every government in the world and are constantly at war with each other. Signs in the game's maps reveal more fronts for these organizations, such as Red Bread and Blu Corn. It's hinted that every major corporation in the world ultimately has ties to one or the other.
Of course, it reaches a new level when you find out that they're both run by the same handful of people apparently out of misanthropy and spite.
In season 2 of Sam & Max: Freelance Police, the mysterious "Them" that has Bosco living in fear is revealed to be three mariachis (actually, three time-shifted versions of the same mariachi) who travel through time and space so they can perform at every birthday ever.
There is some truth in that Bosco is also being watched by Flint Paper. He was hired by Mama Bosco to find the one that ruined her store in the 60s. Someone's been spying on poor Bosco since before he was born.
Trope Namer: The famous Psychonauts level. Although in this case the conspiracy is all in the head of the one man who knows about it. No, literally; the conspiracy is carried out by constructs within his mind, who represent the mental blocks that prevent his destructively psychotic, hypnotically implanted alter-ego from surfacing until he's been given a code phrase, and challenged by other constructs which represent his attempts to sort out what it is he won't let himself know. Except he suspects himself as much as anyone else, so he fears both sets of constructs equally.
Narbonic features a vast conspiratorial organization made up solely of guys named Dave. All the guys in the world named Dave. At one point, protagonist Dave Davenport gets kicked out and his name becomes David. The other protagonists don't care and decide to keep calling him Dave anyway.
In The Adventures of Dr. McNinja, a rivalry between raptor-riding banditos and a man so ripped that he grew a fart-fueled jetpack is revealed to have been the result of a sinister plan orchestrated by the local Fox affiliate's 10 o'clock news. The plan is foiled, however, by the weatherman.
Parodied in Venus Falls with the Interstellar Society of Exceptionally Stupid Old Men in Togas who by some design of Twisted Fate decide who the last 2 "survivors" of a species/race will be and thus end up on Venus.
Also in The Simpsons, the Freemason-esque "Stonecutters" are shown to have infiltrated the Egg Council, for their own nefarious ends—and also claim to control the British crown, keep the metric system down, and keep Atlantis off the map.
Another episode had Dexter infiltrate a secret lair in pursuit of some masquerade-shattering photos his mother dropped off at the local photo development booth. (The zit-faced teen running the booth turns out to be The Man Behind the Man.)
Ben 10, at least before the Time Skip. The world's last, best defense against the alien supermenaces (apart from Ben) are "Plumbers", guys who spend most of their time in blue collar jobs such as crossing guards, electricians, school teachers and most likely, actual plumbers. When aliens show up, they drag the battlesuit out from the back of the closet and fire up the laser rays they keep in a false bottom.
In Teen Titans, Beast Boy discovers that the local burger chain hides a conspiracy of alien cows who are plotting to enslave mankind. The episode is called "Employee of the Month". Intelligent space tofu kidnaps cows to use as fuel while selling a "Meaty Meaty" substitute through a store front managed by an android made of tofu.
The villain in the final episode of the first series of Invader Zim masterminded her plan to wreck the earth from a hotdog stand. Which was bigger than an office building.
Imagine if Cobra Command was a real-life secret terrorist group as well as the famous fictional organization. This is the case in The Venture Bros., except replace "Cobra Command" with "The Guild of Calamitous Intent".
The storybook/audio tapes that came with the "Secret Army Supplies" toy line from the late '80s had one of these. The titular military organization is so secret that it officially doesn't exist. It is run from the headquarters of Electronic Export Services, and performs classified missions to kidnap scientists, prevent the Soviets from taking control of the world's oil market and so forth.
The Glasgow Ice Cream Wars of the 1980's were violent gang wars between rival ice cream truck drivers over different routes. The reason? The truck drivers were also drug dealers and they were fighting over distribution territory.