Super Registration Act

Any law that requires Super Heroes (or, really, anyone with superpowers) to be registered with the government in a national database (including the name and residence of each hero's Secret Identity) or face penalties. This originated with the Marvel Comics' X-Men in the form of the "Mutant Registration Act", where it provided a metaphor for discussing racial and/or communist themes. Since then, it has been used and re-used, and needs a fresh twist thrown in to be usable at all.

While sometimes the act can take the benevolent, unobtrusive form of a government-sponsored Hero Secret Service complete with Hero Insurance, in most cases the law is an antagonist in and of itself, whose only purpose is to prohibit superheroes from using their powers recklessly (if at all), or in the worst case scenario, is the first step to full-scale Super Human Trafficking. Of course, no supervillain in their right mind would bother obeying the terms of this law, which makes it comparable to American Gun Politics in that the "outlaws" know in advance that their victims will be forbidden to defend themselves. In fact, enforcement of the act often permits the supervillains to do even more damage than usual, giving the 'real' heroes a chance to defy the act by stopping the Big Bad the registered crimefighters missed and hit the Reset Button on the whole thing without exploring the long-term consequences of registration.

It's not often that the law comes about purely as a result of normal civil processes, intelligent debate, or genuine public outrage, even though there's not a government in real life that would tolerate unregistered crime fighters with concealed identities, especially superhuman ones. This is because comic books, like most serial works, operate on Rule of Fun, being escapist fiction where the stakes depend on one lone individual or a small group, which is hampered when your favorite character punches a clock and answers to The Man.

Actually implementing such a system is of course a tricky proposition, given the fact your targets can do things like erase your memories or blow up tanks by pointing at them, and depends on whether you're registering super humans or super heroes. Options include:

For policing super-humans:
 * A: Create a non-superpowered combat force with top-of-the-line training and the best equipment money can buy. Sometimes these agents act as a special crimes unit; other times, it's a superspy/black ops agency.
 * B: Recruit a group of right-thinking, like-minded Supers to enforce the system.

For policing super heroes:
 * C: Recruit a group of evil, criminal-minded supervillains to police the heroes. The local Tailor-Made Prison filled with the heroes' Rogues Gallery should provide no shortage of potential Boxed Crooks for your Badass Crew. Some of the less bloodthirsty and more sympathetic ones might pull a Heel Face Turn from the allure of working on the side of the angels; for the rest, it would be a smart idea to secure their loyalty with an Explosive Leash implanted in the base of their spinal columns.
 * D: Create a PR campaign and outreach program that emphasizes the perks of registration: Hero Insurance to repair collateral damage and protection against civil lawsuits, a possible government salary and training to develop your powers and people-saving skills. Works best to draft/enlist the top tier superheroes, so that second and third stringers that look up to them will be inspired to register. However, if any of the A-listers decide to go against it, the hero community could be embroiled in a Civil War that makes both sides look bad.
 * E: Don't make a big deal out of it; trying to force a large number of superhumans into doing something is a pre-emptive measure. Instead, wait until you have a suspect safely under the Power Nullifiers, then ask if he has registered his powers. It works for the cops in Powers.

Anime and Manga

 * A positive version appears in the manga and anime Somedays Dreamers, where in current-day Japan, magic users are registered with the government, trained to control their abilities and use them responsibly, and licensed to offer their skills for hire.
 * Used as part of the setting of the anime/manga Zettai Karen Children. Schools regularly scan students for psychic powers and give mandatory psychic power suppressing limiters to those who have them (which marks them as espers to the general populace, who often discriminate against them). For the people too powerful to be completely limited, it is illegal for them to attend school unless they're part of a military organization that guarantees that they're under control. Presumably this extends to adult society as well, although it's never shown. Unlike the other examples, registration is portrayed as a good thing, or at least as the best compromise that can be achieved when there's both humans and espers advocating genocide.
 * Espers with future predicting powers have predicted that this will directly cause the downfall of humanity, by inciting a muggle vs esper civil war (which the espers will win, by destroying everything). A major ongoing plot is whether it can be averted via positive relationships between the main characters (the 3 strongest espers and their muggle "handler")
 * The Super Registration Act has been implemented in the Tiger and Bunny universe for at least several decades and generally works without a hitch. The Justice Bureau approves all heroes and allows them to sign up with a sponsor company and serve as private law enforcement/celebrities (technically, it's possible to be a free agent without a sponsor, but it's almost unheard of). While only NEXT have been shown to be active as heroes, presumably anyone without a criminal record has the opportunity to become one. Any hero under investigation for criminal behavior is suspended until they're cleared of all charges. Damages are handled either by the sponsor company or, if a judge rules that property damage was necessary in order for a hero to do their job properly, by the state.
 * It appears more reasonable than others, but the execution is marred by

Comic Books

 * Back during the "Acts of Vengeance" Crisis Crossover, a Super Registration Act was proposed, though it was defeated by the political power of the Fantastic Four and The Avengers; this was pointed out later as something that eventually led to...
 * Civil War: The big 2006 Crisis Crossover from Marvel Comics, centered around the Super Human Registration Act and the superhero community's reactions to it (an all-out slugfest). The X-Men stayed out of the whole conflict, perhaps so that attention wouldn't be drawn to the trope's overusedness. What's especially problematic here is that the meaning of the SHRA seems to change from comic to comic—sometimes, it's just a matter of heroes registering their identities and powers with the government, but other books treat it as a sort of superhuman draft. This inconsistency and the political climate at the time (the whole thing had parallels to the freedom/security debate surrounding the Patriot Act) make the event's slogan, "Which Side Are You On?", much more difficult to answer. Ultimately, the pro-reg side won out but at the cost of the respect of the public, leading to supervillains taking over SHIELD/HAMMER for a while.
 * Part of the reason for all this chaos in-story seems to be that the registration act itself is only part of the picture. At the same time, there's a general government push to co-opt the superhero community and rein in its rogue elements. So while the SHRA itself may not mean anything but "anyone with superpowers has to register with the government," you still have creepy black ops types drafting supersoldiers.
 * Perhaps lampshading how overblown the concept was in Civil War, the spin-off series Omega Flight noted that the Marvel Universe's Canada had had a Super Registration Act for years, but it was never a problem because it didn't involve forced outings, secret prisons, conscripting teenagers, or supervillain mercenaries.
 * Another big problem with Civil War was the pro-reg side being led by people who actually had means to make normal law enforcement and military agencies less than near-helpless against metahuman criminals and de-facto private armies (never mind the diverse array of alien, extradimensional and time-travelling conquerors threatening the Earth), means not requiring dangerous experiments on people or production of notoriously difficult to control robots, but pointedly refused to do so.
 * In a neat bit of historical reference, The Bronze Age All-Star Comics series revealed the reason the Justice Society had broken up in the '50s: they were called before a thinly-disguised version of the House Un-American Activities Committee and asked to reveal their identities. Unwilling to do so but also unwilling to go against the law, they stopped operating for a time. (In a Post-Crisis Retcon, this was changed to the actual HUAC.)
 * In the Post-Crisis DCU's background (related largely in the short-lived series Chase), the act passed by the HUAC actually kept any superheroes from operating openly from 1951 until at least the '80s or '90s, but by the time Superman showed up it had been largely forgotten by the public at large and quietly abolished with no fanfare.
 * In The Dark Knight Returns continuity, however, the government prohibitions on superheroes are stronger, with Superman himself having been strong-armed into being an operative of the US government.
 * In the Reboot version of the Legion of Super-Heroes, people from Titan, a race of natural telepaths, are forced to wear a Saturn emblem when interacting with other species.
 * Pre-Crisis, several heroes were granted exemptions (due to their "special status" or "special relations with law enforcement") from Congress' demands, and allowed to continue to operate: Superman, Batman (and Robin), and Wonder Woman. In reality, of course, these characters were among the few superheroes continuously published through the 1950s (while the rest of their JSA cohorts weren't), a time when superheroes weren't as popular as other genres (Westerns, horror, etc.).
 * In the critically acclaimed series Watchmen, the rise of costumed vigilantes in the '30s resulted in Congressional legislation authorizing superhero activities - which was repealed in The Seventies after fed-up police went on strike nationwide and mass rioting ensued. After the "Keene Act" is passed, the only superheroes permitted to ply their trade legally are those who work full-time for the government, including the world's only genuine superhuman.
 * The Minutemen also faced the House Un-American Activities Committee. They came up with a compromise to the request to identify themselves to the committee: Each member was to reveal their identity to one member of the Committee. That member was to put their name into the enormous stack of names they wanted the FBI to do a background check on without any flags reading 'this person is '. Then they would speak to the committee as a whole in their costumed persona. As a result, the heroes were investigated in their true identities, while limiting the number of people who knew who they really were. The only member of the Minutemen to not accept this compromise, Hooded Justice, resigned.
 * This is a central point in the comic series Powers. The main characters are Buddy Cops who investigate crimes related to registered and unregistered superpowered heroes and villains. The registration is in effect from the start, and being caught unregistered has a lot of legal woes tied to it. In fact it's even illegal to own a COSTUME unless you're registered which must make fancy dress parties a nightmare in this world..
 * It then lampshades this as of course the ONLY people who follow a law as ridiculous as that are the HEROES. The psychotic supervillains still run riot, the only difference is that now only badly unerqualified humans are left to try (and fail) to stop them. In the end the heroes return, realizing that justice is a lot more important than "The Law".
 * A Darkwing Duck comic where several superheroes led by a Mr. Fantastic Captain Ersatz arrived in St. Canard city and tried to enforce a Super Registration Act. Darkwing, of course, didn't like this. This comic became much funnier after Civil War came out.
 * In Astro City's "Confessions" arc, the government of the titular city starts a registration act. It does not go well.
 * This happened when reality got changed so that Superman, Wonder Woman, and Batman never existed in the 2009 series Trinity. The alternate Flash delivers an epic What the Hell, Hero? when he orders the solders trying to arrest him (in the middle of a battle against supervillains!) to do something useful and actually be heroes.
 * The X-Men have brought this up as a plot every few years. Considering that the titular team's most prominent member is a short, bad-tempered Canadian with unbreakable claws that can cut through almost everything, with a Healing Factor that makes him close to invincible, the Have You Tried Not Being a Monster? angle most of these stories go for kinda falls apart.
 * Except when you consider how much he's mellowed and how often he's worked with various governments.
 * The Captain Carrot and His Amazing Zoo Crew 2007 miniseries featured the United Species of America's government, under new President Beneduck Arnold, pass the "Collar ID" law, which was designed to neutralize the powers of the US' superhero populace, with the heroes either retiring (as the Zoo Crew did) or losing their powers. At one point, the President notes to the Crew "thanks to [the law], there are no more superheroes left on Earth!" Of course this came at Earth-C's Darkest Hour---a global flooding created by Starro---and ignores the US-centric nature of the law. Apparently the heroes moving to places like Earth-C's Cornada or Loondon to avoid the law weren't options, though simply moving out of the US rarely seems to be a considered option under this trope...

Film

 * The film The Incredibles inverts the situation: After a series of successful lawsuits against Super Heroes leads to a wave of anti-hero sentiment, the government relocates them a la the Witness Protection Program and helps them lead normal lives. Note that the agency keeping track of the supers also existed in what seems to have been a regulatory/support role before these events, and none of the supers seemed to mind it.
 * It's implied in the DVD extras that at least some members of the agency think the heroes have gotten a bad rap, and hope they can return to active service someday.
 * It's not all positive—supers in the program are expected to refrain from heroics (hence the ski masks worn by Mr. Incredible and Frozone when they rescue people from a burning building), and those caught using their powers must relocate and assume a new civilian identity.
 * Again, like the Witness Protection Program, that requires them to keep the low profile.
 * It also made it easier for the Big Bad to keep track of surviving heroes.
 * The Generation X made-for-TV film deals with a harsh mutant registration act. Any mutant who doesn't register before their powers first flare up is imprisoned and considered a terrorist threat. Considering that most powers in the film are small-scale, low-budget and don't cause nearly as much property damage as you see in comic book panels, the knee-jerk reaction falls partly into Adaptation Explanation Extrication.

Literature

 * The Wild Cards books had the Senate Committee on Ace REesouces in the 1950s, in an alternate-history version of the anti-communist hysteria of the time. Its target was "Aces," rare people given superpowers by the Wild Card virus. In 1954, all people with super powers were required to register with the Federal government under the Exotic Powers Act, and were drafted into government service under the Special Conscription Act.
 * After the emergence of the psychic Talents in Anne McCaffrey's Pegasus and Tower books, the first thing they do is preempt what they see as the inevitability of this, creating their own registration organization and making sure it's used only for good.
 * Telepaths in Katherine Kerr's Polar City Blues and other books in the same universe are marked with a "P" tattoo on their jaw. No coercion or punishment is mentioned; however no telepath can go unnoticed by another for long, especially if they haven't been trained and the only place to get the training is at the school which does the branding...
 * Subverted in the two Temps shared world anthologies, in which all British "paranorms" are required to register with the Department of Paranormal Resources and, in exchange for a monthly stipend and a cheap suit, can then be called up as government operatives and penalised for vigilantism. Mostly, the paranorms view this the way most people view government interference in their lives; annoying, but not worth making a fuss over.
 * Imagers (basically mages) in LE Modesitt JR's Imager Portfolio are required to join the Collegium. This organization is run by and filled with Imagers, and occupies a venerable but somewhat precarious place in the local power structure. It trains imagers, keeps them out of trouble, and acts as something of a special ops/intelligence/research agency for the governmental council—something like option H, but with an emphasis on avoiding publicity.
 * The Ministry of Magic in the Harry Potter universe, which regulates the wizarding world in the UK, forces Animagi (wizards with the rare skill of being able to transform into a specific animal) to register with the government or face prison time.
 * This is one of the core elements of Shadow Ops. If you're a Latent (magic-using human) in the United States, you've got three basic options. the first: a fairly comfortable (or uncomfortable, if you force the military to come after you) imprisonment while having your abilities fully suppressed for the rest of your life. The second: join the military. Again, for life. Third: Bullets, lethal injection, or the electric chair, depending on area. Unless you're rich, related to a senator, or a famous celebrity. And if you're unlucky enough to manifest powers in one of the "prohibited" schools (necromancy, sentient elemental conjuration, gate magic, negramancy) or use a "legal" school in an illegal way (a physiomancer ripping apart human flesh, or a terramancer controlling animals) then you've only got the former two options. The ethics and morals of this system are debated extensively over the course of the book, with security versus freedom being a core theme. Ultimately, the protagonist decides he can't support a government that effectively imprisons and enslaves its own citizens for something they have no control over, and effects an escape.

Live Action TV

 * Babylon 5 did a heartbreakingly thorough examination of this with the PsiCorps, a government started program and organization that registered, brainwashed trained, and hunted down rogue telepaths. It seemed to work well enough that its highest-powered and most loyal members eventually got to run it themselves. In the words of Garibaldi, "The Corps got started because we were afraid of telepaths. Now they're victims of our own fears. We took away every right they had and shoved them into a big black box called PsiCorps. Now look at them. Black uniforms, jackboots, giving orders..." Telepaths had only three legal choices: imprisonment, chemical nullification of their powers (often leading to death), or joining PsiCorps. It should come as no surprise that PsiCorps became a cloak and dagger organization with dozens of evil schemes, eventually leading to a teep civil war.
 * They also do things such as breeding telepaths against their wills.
 * This seems to be part of one possible future in the Heroesverse.
 * It was the plot of an entire season.
 * The government agency "Checkmate" is attempting to do this in Season 9 of Smallville, willing to use kidnapping and murder to try to force superheroes under their thumb.
 * In Season Ten, the government passes a "Vigilante Registration Act" with some help from  Several episodes later, efforts spearheaded by Senator Martha Kent get it repealed.
 * In the short-lived, live-action sitcom version of The Tick (animation), superheroes are required to have a hero license to operate within the City. However, the application process for such is simple and requires no background check, so the Tick easily makes up a false name to be listed as his secret identity. Furthermore, the consequences for not having a license are nonexistent.
 * The 4400 in one ep mentioned that a politician crafted a law forcing all 4400's to register their powers with the guv'ment.

Tabletop Games

 * The Champions 5th Edition Tabletop Games has a Superhuman Registration Act in its game universe Backstory. It uses it in an uncommonly sensible fashion—widespread public protests were unable to get it formally repealed, but it's now a law that the government virtually never tries to enforce, let alone use as an excuse for metahuman conscription. Several of the most prominent superhero teams of the Champions Universe have officially registered and sanctioned themselves, but many superheroes have chosen not to, with little official interference in their lives. It still remains on the books, but it's normally used only as the legal authority to demand (and record, and distribute) the true identity of any metahuman already being arrested on another criminal charge. However, the lives of registered metahumans are made easier in several ways as compared to unregistered ones—they can testify in court without having to reveal their secret identities publically (as those identities have already been revealed to the government and are thus available to the court, if not the public), they are offered opportunities for basic law enforcement training and certification as deputies, etc. They do need to follow certain guidelines - not killing opponents except within standard law enforcement rules of engagement (modified to account for the fact that a bulletproof hero's life is not actually in danger from a thug with a gun, and suchlike), making good-faith efforts to avoid collateral damage, etc.
 * Technically, those that are not registered are considered to be vigilanties and, as such, criminals. This is rarely enforced except in extreme cases; Vigilantes who kill opponents are considered criminals and are hunted by the law.
 * Supervillains get no such option; those that are cpatured have their identity, powers and abilities recorded by the government, with that information being, in turn, sent to law enforcement agencies and registered superhero groups to help them. This is compliant with real-world law in that people being booked for an arrest have no expectation of privacy re: their fingerprints, vital statistics, and other identifying measures.
 * All countries have theiy own, sometimes radically different ways with the Registration Act: In China, all Supers, as soon as they notice their powers, have to register and "voluntary" join the Tiger Squad, China's official super team - or be hunted down and killed. Japan, on the other hand, has a number of Superheroes working with and for the government, but no Registration Act at all.
 * In Paranoia, being an unregistered mutant is punishable by death. Since just about every player character and NPC is a mutant of some sort or another, and very few are registered, things can get interesting very quickly.
 * In Warhammer 40000, the Imperium of Man makes a point to hunt down psykers, humans with psychic powers. The majority are killed, while the remnants are 'sanctioned' after much conditioning to serve the Imperium in various fashions, or used to power their giant space beacon. (Justified in that untrained psykers minds are open to the Warp, which can make them dangerous).
 * By "dangerous", he means that rogue psykers tend to unwittingly summon or even create monstrous Cosmic Horrors known as daemons wherever they go, as well as other horrible things. A single rogue psyker can cause soul-eating daemons to overrun an entire planet, forcing the Inquisition to come and deliver an Earthshattering Kaboom to the unfortunate world.
 * And if the beacon were allowed to go out, the Imperium would collapse and humanity would be eaten by Eldritch Abominations.
 * The Moore Act in the "Iron Age" setting of Mutants and Masterminds made superheroes illegal in Freedom City. Named after Mayor Franklin Moore (who, in turn, was named after Alan Moore, creator of the Keene Act in Watchmen).
 * White Wolf's Aberrant had a rather underhanded variety. While there is no official law requiring Novas to register, their powers tend to be hard to control without specialized training and medical care. Both are available only from Project Utopia, so most of them end up there, policing their "unenlightened" brethren. In the process they're also
 * on a lighter note in the world of Aberrant there also exists image firms like Appellate Lexington, that will register a super identity and make up a costume for you
 * Practically speaking, the main reason that the major world governments did not press for a super registration law was twofold: a) voluntary compliance would 'out' most novas anyway, as there were a myriad of perfectly legal ways to make a ridiculous amount of money using nova powers and b) between their freely wiretapping everything to a degree that would make the NSA weep in envy and their own nova investigators, the multi-national intelligence agency known as the Directive could pretty much break any secret ID short of Divis Mal's in about a week -- and routinely did.
 * Taken to extremes in Forgotten Realms. The nation of Cormyr requires all adventurers to register with the government, not just mages and clerics.

Video Games

 * In the MMORPG City of Heroes, where super-powered individuals are, indeed, required to register their powers, identity, etc. with the local authorities in order to get their superhero license. This makes the superheroes official agents of the government, and gives them full rights to beat up anybody who wears gang symbols, black hats, or hooded robes. There is, however, a Shout-Out to the trope in the game's Backstory: a "Might for Rights" act was passed during the Cold War, drafting super-powered individuals to "fight against communism", but it was overturned as unconstitutional after massive protests from said super-powered beings and their supporters. This lead to the formation of the Malta Operatives, who intend to kill any super who will not work for them and have developed weapons to fight them with.
 * There's also a number of variations on the theme: villains are required to register their identities and powers as well, but their IDs are (depending on who you ask) either the property of the government, as all villains have to break out of prison as their tutorial, or property of Arachnos, which controls the Rogue Isles. There's also a number of references in the game to various histories of the "registered superheroes": some fought in World War 2 voluntarily as heroes, especially against German superpowered squads; a group of heroes led a harsh and ultimately controversial rampage against drugs; and so on. The latest incarnation of the Superhero Registration Act as it exists in the game today wasn't passed until the mid-to-late eighties, at which point sanctioned vigilantism in Paragon City began to skyrocket. There's also a number of logic extensions of the existence of such an act, most notably Hero Corps. After all, if vigilantism is legal...why not make a profit off of it?
 * Of course, roleplayers in the game are free to interpret the laws as they see fit, much like every other part of the game, even if their opinion goes counter to established canon. Some characters have identities which are secret from everyone, even the government. In fact, there exists every level of publicity for a character, from identity-secret-to-everyone-no-exceptions, to my-hero-name-is-my-real-name.
 * For Champions Online, see Tabletop -> Champions above.
 * A program similar to the above Babylon 5 example exists in Starcraft, where any telepath born within Confederate space must be taken to the Confederate training centers, where they're turned into the Ghosts (psychic commandos). One of the most famous being Sarah Kerrigan.
 * This program was continued by the Dominion.
 * In the third Mega Man Star Force game, it becomes impossible to EM Wave Change without first joining up with the Satella Police and getting a "Transcode." As Geo demonstrates in the beginning of the game, trying to Wave Change without a Transcode locks up the Hunter-VG and makes it impossible to use.
 * Suprisingly even a kids online game, Poptropica, has this in effect on Super Power Island.
 * In Dragon Age it's mentioned in one of the codexes that the Tevinter Imperium at the height of its power maintained a registry of every mage/potential mage in the Empire. This system kind of broke down after the first Blight reduced the Imperium to its current Vestigial Empire state. The present day Circle of Magi and the Templars lack such a system; making it that much harder for them to find potential mages before they become demonic Abominations.
 * Mass Effect: Specifically, if you do the sidequest in the first game where you're trying to rescue Chairman Burns from biotic extremists and he ends up dead, there will be a news feature in the second game saying that lots of people are in favor of registering biotics. If the chairman lives, Kaidan talks about the government keeping track of biotics anyway, and that he figured "why not?" and joined the military.

Webcomics

 * Registration in the webcomic Antihero for Hire exists, but is optional; Crossroads was actually rejected when she tried to join.
 * The Webcomic Fellowship of Heroes offers a world with a voluntary superhero registration project to give heroes official sanction, with an organisation that doesn't hunt down unregistrated heroes. Still, "Indie" heroes are considered rather controversial.
 * In Everyday Heroes, only those superhumans who are active crime-fighters are required to register with the government. For a while Mr. Mighty held a series of civilian jobs. (He couldn't be a crime-fighter after marrying a former villainess.)
 * In HeroesOfCrash registration is an optional thing that helps superheroes get assistance from the government if necessary. It's possible to be a non-registered superhero, but it involves trade-offs.
 * The Webcomic Sidekick Girl has this but it's a bureaucracy (for both heroes and villains) making it even more evil.
 * The Ciem Webcomic Series has in its expanded universe a Judge Belliah of the 9th Circuit Court of Appeals, a Complete Monster who tries to start one via judicial activism. And political mobs. In the end, all he succeeds at doing is winning over two supervillains to join La Résistance in freeing an Emotion Eater Reality Warper powerful enough to save all of them; and gets said Emotion Eater Reality Warper banned in Belgium.
 * Averted and discussed in Spinnerette. The supreme court has evidently decided that superpowers fall under second amendment protection, and laws have been passed enabling superheroes to act within the legal system without revealing identities to anybody, but there are also groups that oppose this state of affairs and want to take this trope more literally.

Web Original

 * This is basically the status quo in the Whateley Universe, where mutants are required by law to have a Mutant ID card and present it at customs or when boarding commercial flights. Students at Whateley Academy can choose to either 'voluntarily' get one or be expelled.
 * Fine Structures reaches this level of conflict around year 11.
 * "The Company" in The Return takes a mixture of the first three options. Only author-fiat has prevented the inevitable disaster.

Western Animation

 * Also appears in the early-'90s X-Men cartoon, though the "Mutant Control Agency" in that series is "a private organization, occasionally supported by the government", and the registration is seemingly done voluntarily. Later, the government tries to shut it down when they notice the X-Men breaking, determining that if mutants were taking violent action against the organization than it was getting too extreme. Apparently nobody in the government checked to notice that the control agency had plans to send giant robots out to abduct any mutants that registered, and likely cause more damage than the mutants they were supposed to protect the common humans from.
 * And Later in X-Men: Evolution when Former Principal Edward Kelly is running for Mayor and one of his plans is for a Mutant Registration Act, to essentially segregate Mutants from humans and treat them like an inferior race. The X-Men are unwilling to get involved due to the way it could backfire. The Brotherhood, not so much.
 * The Mutant Response Division in Wolverine and the X-Men is charged with finding mutants and "registering" them-this often means holding them indefinitely. The creators mention in the commentary that the "Mardies" actually have good reasons to exist and would be a positive thing if they weren't led by a General Ripper and caught between Senator Kelly and Magneto's bids for all-out war. Their success rate is pretty abysmal against the Brotherhood and the X-Men until they build the Sentinels and Master Mold, which causes its own problems.