Heroes-R-Us

Like almost everyone else, heroes can achieve greater things when they band together. Heroes R Us is a group that recruits, trains, equips, and funds heroes and directs their efforts where they are most needed. They can be clandestine or public, governmental or not, and the scope of their powers may vary from fighting some single, specific enemy to being some sort of benevolent Ancient Tradition; the crux of the trope is that if The Hero isn't a member, they'd at least like him to be.

There are two major types of Heroes R Us: organizations of heroes, and heroic organizations. In organizations of heroes, every member has a skill or power that sets them apart from the Muggles. Owing to the natural rarity of such extraordinary people, these tend to be Oddly Small Organizations where even perfectly good action heroes are forced to take on administrative duties. Stories following such organizations tend to focus on The Squad of which the hero is a member, featuring the aforementioned promoted heroes as The Captain or the Four-Star Badass.

A heroic organization fields only a small number of highly competent agents, backed up by a staggering number of faceless assistants tasked with conjuring up fake identities for the heroes, escorting them to their targets and equipping them with fancy gadgets. Depending on how narrow the ratio between super and muggle employees in organization gets, it may even become a Hero Secret Service. Stories following heroic organizations generally follow the hero as he works alone, with only his Mission Control and possible partner/GirlOfTheWeek for company.

Though the word "hero" is used throughout this article, "protagonist" might be more accurate. While the intentions of the majority of the examples below are genuinely good, Da Chief might be forced to make tough decisions and butt heads with a Chaotic Good hero every once in a while; indeed, precisely this sort of ideological schism is frequently an element of stories featuring a Heroes R Us.

Common types of Heroes R Us include The Chosen Many, The Order, Artifact Collection Agency, NGO and La Résistance.

Anime and Manga

 * The Royal Order of Protestant Knights, or the Hellsing organisation.
 * BABEL in Zettai Karen Children, a government ESP organization dedicated to stopping crimes before they happen.
 * The Worlds Welfare & Works Association, better known as the 3.W.A., are the unfortunate employers of the Dirty Pair.
 * The Alien Exterminating Global Intercept System (AEGIS) from Gate Keepers.
 * The vampire hunting Red Shield from Blood Plus.
 * The Pandora organization in Pandora Hearts.
 * The Black Order of D.Gray-man collects Innocence and the people capable of using it to fight Akuma.
 * The Alchemists' Guild in Busou Renkin.
 * In Ga-Rei Zero, the Seeker Squad of Defense Ministry is a heroic organization, while the Exorcists are an organization of heroes, being Ancient Tradition converted into modern framework.
 * The Hero Association from Ratman.

Comics

 * Marvel Comics' S.H.I.E.L.D. is essentially the CIA for a weird world, complete with bizarre supertech and Nick Fury.
 * S.H.I.E.L.D. is a strange case; originally, they answered to a mysterious trio, and had international authority; but during Civil War, they acted pretty much as an American Law Enforcement branch, answerable to the US President. It's possible the organization has been redesigned (as was the case with DC Comics' Checkmate)... or somebody Did Not Do the Research.
 * This is almost certainly a case of Canon Immigration from the Ultimate universe, where S.H.I.E.L.D. is very definitely and contentiously a U.S. intelligence agency. Since that continuity's version of S.H.I.E.L.D. in general and Nick "Samuel L. Jackson" Fury in particular were wildly more successful with audiences... Whether it's intentional or the writers' mental picture was just infected by the more prominent adaptation is another question.
 * Confusion over exactly what S.H.I.E.L.D. was considerably predates the Ultimate Universe. From its creation, it was a basically American entity, notwithstanding it supposedly being international (which was mainly an excuse for why it could operate anywhere with impunity).
 * S.H.I.E.L.D. did have foreign agents, however (e.g., Contessa Valentina Allegra de Fontaine). A plausible explanation for S.H.I.E.L.D. might be that it's a NATO organization. Since NATO is an international alliance, but one where the United States largely runs the show, it would fit S.H.I.E.L.D. as it was depicted.
 * Technically S.H.I.E.L.D. is a UN agency that the US (as the Superhuman capital of the world) administers over. The jurisdiction conflict between the UN and US was actually a major plot point of Dark Reign (before Siege set in.
 * Comic book example: The trope is toyed with in  Ultimate X-Men, where the Hellfire Club provides funding for Charles Xavier -- as a means of getting to Jean Grey and unleashing the Phoenix Force.
 * The Ultimate X-Men were subsequently funded by the Church of Shi'ar Enlightenment, who are quite open about their interest in the Phoenix, but see it as a force for good. Too bad they've been infiltrated by Hellfire members.
 * From the Nextwave comics, we have the Nick Fury parody Dirk Anger, who leads up the organization known as H.A.T.E., which has such bizarre technology as "Ptero-assault troops" -- soldiers in bright yellow pterodactyl suits -- and "Drop Bears" -- Koalas with razor-sharp teeth. Nextwave is a strange, strange comic-- but it's got the name "Warren Ellis" on the cover, so you get what you came for.
 * Nextwave is not in continuity, however.
 * Wrong. Nextwave is the only thing in continuity. Everything else is Anal Skrulls.

Film

 * Another non-government agency, the titular agency from Men in Black.
 * The Soldier (1982). The title character is the leader of an elite unit formed after the "Iranian fiasco" and reporting only to the Director of the CIA. Which causes problems when he's assassinated.
 * The Jedi Order of Star Wars.

Literature

 * American Teens Against Crime (ATAC) from the most recent incarnation of The Hardy Boys.
 * The Executioner. Stony Man handles anti-terrorist and anti-crime operations beyond the capacity of established agencies like the CIA, NSA, and FBI. This usually means a mission that the U.S. Government can disclaim any knowledge of if it goes sour, or something that is just too dangerous for regular agencies to handle. Led by Hal Brognola and answering only to the White House, its primary weapons are Vigilante One-Man Army Mack Bolan, and his black ops units Able Team and Phoenix Force.
 * The mercenary unit Soldiers of Barrabas (or SOBS) (a Gold Eagle series by Jack Hild) is ostensibly lead by a mercenary who's 'soft' on his native country, and so willingly seeks contracts that advance its interests. In truth they work directly for the US government as a deniable dirty tricks team.
 * The Knights of Maidenhead in The Faerie Queene.
 * Tiger Mann (created by Mickey Spillane) was an early version of this trope, working for an espionage organization funded by a radical right-wing billionare. The character was first introduced in the novel DAY OF THE GUN (1964).
 * In Bad Monkeys, the protagonist Jane Charlotte works for an organization that is the second type. The organization has many branches, and the one that she works for is Department for the Final Disposition of Irredeemable Persons ("Bad Monkeys" for short), which is devoted to ending the lives of irredeemable evil persons. The various branches do almost anything you can think of, such as Panopticon, which has cameras in any picture with eyes and also in library bindings, or Catering, which will always answer if you pick up any phone.
 * In the Destroyer series, Remo Williams works for CURE, an agency whose very existence is known only to Presidents, and which has only three members: Remo himself, his mentor Chiun, and their boss, Dr. Smith. Chiun insists that Smith is the de facto emperor of the US, as the agency appears to have essentially unlimited authority and resources, even denying Presidential requests when Smith deems them unwise. Of course, an uber-hacker and two sociopathic assassins with superhuman powers WOULD be able to get away with a lot.

Live Action Television

 * The Phoenix Foundation, MacGyver's employer from the second season onward, though the DXS (a government department) also fits the type.
 * The Foundation for Law And Government in Knight Rider is an organization of exactly the same sort.
 * The Blackwood Project of War of the Worlds is an example with a narrow scope and clandestine affiliation with the government.
 * Very common in Invisible Man series. The Scifi Channel's The Invisible Man used a clandestine government department, while Gemini Man and the McCallum series both used private companies.
 * Power Rangers Lightspeed Rescue, Power Rangers Time Force and Power Rangers SPD all used this setup.
 * Super Sentai also used this setup several times. The earlier series were in fact much more likely to have an organization than a Ragtag Bunch of Misfits.
 * Denji Sentai Megaranger proves you can combine the two: none of the Megarangers were part of the organization before being the only ones around to suit up and stop the attack in the series premiere.
 * In Kamen Rider Dragon Knight, the Riders were apparently originally part of one of these, but as their doppelgangers in our dimension - the only ones who can use the Loyal Phlebotinum assigned to the original owners - had different lives, it's not how it works in the show proper.
 * Speaking of Kamen Rider, we've gotten this approach twice in a series that seldom works like this: Kamen Rider Blade had an organization called BOARD that was wiped out early on, leaving our heroes on their own with what little tech they could recover (there's basically the shiny suits and the monster radar.) Kamen Rider Kabuto has the ZECT organization - which is quite shady and our heroes are definitely with them but not of them.
 * The United Nations Intelligence Taskforce (UNIT) in Doctor Who is a (not very) clandestine government organization -- though it isn't always clear which government they answer to. The "United Nations" part of the name implies that they work for the UN, but there are many examples of the wishes of the UK government taking precedence, without a very clear sense of whether this is by the organization's design or a side-effect of UNIT's officers also being members of the British army.
 * During the time of the new series, the real life United Nations had complained. The organization's name is now the Unified Intelligence Taskforce, which makes who they answer to even less clear.
 * Also The Torchwood Institute in Doctor Who (where they start off as grey area "bad guys") and in Torchwood. It was set up by Queen Victoria and was for most of its history directly answerable to the Monarch but Queen Elizabeth's current position on them isn't very clear.
 * International Rescue from Thunderbirds makes it a point to keep their secrets and technology away from the governments of the world. This one dates to the '60s, ahead of its time.
 * We're never told exactly how or where the heroes of Mission Impossible get their hands on all their useful gadgetry, fake IDs, financial resources, and so forth. All we know is that they're connected to The Government, but not very closely; as the recordings we hear Once an Episode imply, the CIA (or whoever it is) can cut their whole organization loose if necessary, in order to maintain plausible deniability.
 * The line is "The Secretary will deny all knowledge of your actions", implying they answer directly to someone at the cabinet level.
 * The 4400 has the US governments National Threat Assessment Command (NTAC) which was pretty much completely redirected to handling issues caused by the 4400.
 * O2STK in The Middleman apparently are behind the Middleman Organization's bankroll and Applied Phlebotinum supply. In an interesting subversion, not even the Middleman himself knows who they are--the name is a joke meaning "Organization Too Secret To Know", and Middleman '69 called them WTHWWF, "Whoever The Hell/Heck We Work For."
 * In Heroes, Nathan Petrelli, a man with the ability to fly, and a candidate running for congress, finds that one of his biggest backers is the Linderman Group, headed by a Mr. Linderman, who has a special power in the form of healing living things. Possibly subverted in the fact that Linderman is the season's Big Bad.
 * Airwolf's heroes get a fair degree of support from the F.I.R.M.- they must get Redeye missiles from somewhere, but also have Santini Air (a chopper hire company) for other money and occasionally get paid for rescuing a Jailbird of Panama.
 * The A-Team's weaponry source is unclear and they have no organisation backing them up, averting this trope in one of the most Eighties of the shows.
 * The Dollhouse may be for hire, but most of the agents and administrators display the best intentions for their work.

Toys

 * This is the basic premise for LEGO's new Bionicle-replacement, Hero Factory.

Tabletop Games

 * Department 7 in d20 Modern (Most Player characters are members by default). Department 7's depictions vary from GM to GM, but it's always an organization that gives the players missions, provides them with payment (and cool equipment). It also provides assistance in other ways as well. Depending on the campaign, it could function as a mundane Law Enforcement/Anti Terror agency, or a UNIT/Torchwood style agency for dealing with the supernatural. It's also very mysterious, and may or may not have government connections.
 * The Mutants and Masterminds setting of Freedom City has AEGIS (American Elite Government Intervention Service), which is a clear expy of Marvel's SHIELD, or at least the "American Agency" version of it. It also has UNISON, the UN International Superhuman Oversight Network, which fills in for SHIELD's "UN Operation" version, combined with Doctor Who's UNIT.
 * The Conspiracies and Compacts of Hunter: The Vigil gears toward one end or another of this trope; for example, the Task Force Valkyrie is closer to heroic organization (made of normal humans fighting monsters), while the Lucifuge is closer to organization of heroes (made of super"humans" fighting monsters).

Video Games

 * Predictably, there are SEVERAL of these in City of Heroes, including the for-profit Hero Corps, the non-profit Freedom Corps, and several more-or-less clandestine groups, including The Vanguard, Longbow, and Wyvern.
 * And those are just the official ones in the game backstory. Technically, anyone who starts a supergroup (this MMO's version of a guild) has begun their own Heroes R Us organization.
 * There are also the official Villains R Us groups like The Council, Arachnos, and the Malta Group. Any player can start their own villain group as well.
 * The VSSE in Time Crisis. They're one of only two plot elements that connect the games together.
 * The Heroes Guild in the original Fable.
 * The Assassins of Assassin's Creed are engaged in a Secret War with the Templars.
 * The Grey Wardens of Dragon Age were formed to guard against the Blight.
 * The Ad Libitum guild in the Tales of the World: Radiant Mythology series.
 * The Skylanders in Skylanders: Spyro's Adventure are such a group, existing to defend the Skylands against evil with the help of the Portal Masters. Though interestingly enough, previous acts of heroism isn't a requirement so much as just being Badass and willing to fight for good. A few members are even of species which are enemies in game who defected, such as Boomer the Troll and most of the Undead Skylanders. Ghost Roaster isn't even really a hero and had to promise to only eat evil ghosts when he joined.
 * The Institute Of War in League of Legends is an interesting example, as it accepts Champions and Summoners from every qualifying city-state, several of which view each other's Champions as decidedly un-heroic. The Institute supervisors have to be very careful to avoid conflicts of interest, since its primary purpose is to allow every faction to hire heroes against each other to solve political disputes.
 * The Bracers' Guild in Legend of Heroes VI.

Web Comics

 * The Order of Orion from the Web Comic Rumors of War is an example in a world based on Greek Mythology. The main cast is one of several groups retained by the Order, though the role they play in the organization has yet to be revealed.

Web Original

 * The Justice Brigade of the Whateley Universe, a world renowned team of superheroes. The Knights of Purity are supposed to be this, teams of baselines in power armor protecting regular people from supervillains, but most mutants see them as the enemy. (They may be right, or it may be a mixed bag: in "Loose Cannons" a Knight is trying to kill the protagonists to hide his screw-up, but in "Ayla and the Birthday Brawl", a team of Knights saved Chaka from The Lamplighter.)

Western Animation
"OSI!! We fight for freedom and the little guy! OSI!! We'll tear a new hole in your sky! When it time to start the war You'll hear our mighty engines roar We're an army of super spies Look out Sphinx, you're gonna die! OSI!! We'll shatter your skull and make your children cry! OSI!! Here we come, look up in the sky! OSI!! Mass destruction comes your way!"
 * Global Justice on Kim Possible is a S.H.I.E.L.D. knockoff, right down to an eyepatch-wearing Fury equivalent, Dr. Director (who happens to be a woman).
 * WOOHP in Totally Spies exemplifies this trope.
 * The Rescue Aid Society from Disney's The Rescuers is a Mouse World version of this.
 * Inter-Nation Security from Birdman was never that developed - its only members seemed to be Birdman, Falcon Seven, Avenger, and possibly Birdboy - but it seemed to be a legitimate government (or inter-governmental) agency.
 * The Office Of Secret Intelligence (OSI) from The Venture Brothers, who even have their own theme song. It's a cross between G.I. Joe, S.H.I.E.L.D. and Village People.

- The OSI's theme song

Real Life

 * A real-life flaw of such units is exposed in the non-fiction book See No Evil. Former CIA agent Robert Baer tells how he was attached to a special unit, authorised by the President to track down terrorists. The unit failed because the CIA station heads kept refusing to share information with it, so they spent all their time running about trying to develop their own sources instead of doing the job they'd been created for.