"Ever since I was a kid, I'd have this dream where somebody would find out what I could do. It starts off with lots of ice cream and balloons, and ends in a small white room where little bits are cut out of me until there's nothing left to cut."
A standard justification for any unusual character to maintain a Masquerade, because The Government is Evil and Science Is Bad and if the authorities got their hands on them, they'd stick them in a concrete box and perform all sorts of cruel experiments to find out what makes them and/or their special powers tick, either destroying their quality of life, or killing them outright in hopes of getting all sorts of goodies.
Scientists will usually be portrayed as too obsessed to care for anyone or anything who might be used to further our knowledge of the universe or make a cool new weapon, caring only about the fame or payment they'll receive from their higher-ups. Only one bad scientist is enough to spoil your day, but in settings that use this trope the majority of encountered research workers are likely to be like this.
The oddest part of this trope is that the danger may never even materialize within the story — but the certainty of it happening will never be questioned by anyone concerned. Humans Are Bastards after all, Inhumanable Alien Rights be damned.
Sadly, there is a lot of Truth in Television to this trope. There is a long and dark history of human subject research and the early days of biological science can best be summed up as: "Let's see how many needles we can stick in this dog before it stops making noises!".
Modern research works a lot less intrusively as sonography, MRIs, and other medical imaging techniques have made hands-on vivisection less necessary for the internal examination of research subjects. Given sufficient funding and resources, there should be no reason for slicing off a limb just to see how it looks on the inside. The Playing with Syringes mentality of fictional "research" also happily ignores the fact that when you only have one specimen, it is a good idea to take care of it because once it stops working it'll be much harder to figure out how it used to. Of course, this is cold comfort to said specimen - it just means the torture will be of a greater duration, and would still result in them being locked away somewhere against their will. Just because they aren't cutting you up doesn't mean they ever intend to let you wander off (or that you won't wish they were).
Then there's the question of medical ethics. In Real Life, medical researchers have to follow very strict testing standards to be able to publish their results. Getting caught violating them can easily end their careers and leave them facing civil or even criminal charges. It should be noted that the Not Even Human excuse some scientists love to use in fiction would not be much of a defense, as no law explicitly says only Homo sapienshave the right to refuse to be gutted against their will. The Real Life instances where people have donated their bodies (or blood samples or whatever) to science in order to help research of particular conditions were, after all, voluntary.
Of course, these considerations only apply to scientists who intend their results to be publicly documented. It can be expected that various black ops organizations that either suspect or already know about The Masquerade won't care at all about any of this. (And crime is only punishable if one is caught.) So, you'll probably want to do your best not to get caught by them just the same.
Compare Alien Autopsy, in which the fantastic creature being studied is usually dead when human scientists find it in the first place, which would make such an up close and personal study sound significantly less unethical; Medicate The Medium, in which the special ability would be dismissed as psychosis and treated as such.
See Also: Playing with Syringes, when they really do cut something up.
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Anime and Manga
Agito, the short-tempered fire fairy from Magical Girl Lyrical Nanoha, can only remember being confined in a lab, which had left her almost completely broken, physically and mentally. According to her, she was only days away from death by exhaustion before being rescued.
A variant is Alphonse Elric from Fullmetal Alchemist. Mustang advises Al not to continue with the State Alchemy exam because there is often a physical examination involved, at which point they would discover his armor is empty and cart him off to a laboratory for study. However, Al doesn't have a masquerade; people who don't know the truth simply assume he likes armor/feels safe inside it.
Later on in the 2003 anime version, at least, it's implied that most people know he's a living suit of armor, but since the government already knows how to create those, nobody really gives a damn. At the time of the exam, Colonel Mustang wasn't quite high enough in the chain of command to realize this.
Which, given the series' tone and setting, is is probably 100% accurate (or worse).
Ryouta attests that this is why the escaped Magic Users in Kiwaguro No Brynhildr (who received their powers through Playing with Syringes in the first place) can't simply go public. They'd just end up back in the lab again. Which is odd considering the efforts the antagonists themselves go to to make sure that ordinary people don't find out about the existence of the Magic Users.
Dr. K-ko's antagonist status in Magical Pokaan comes from her intent to fool around with the girls in a lab.
She needn't worry though, because it turns out her brother wasn't there — the Lemures fished him out to use as a bargaining chip.
Tsukihime: In her backstory, Ciel was subjected to a very thorough "examination" after The Church discovered her bizarre ability to automatically, completely regenerate from any injury. No matter what they did, she just wouldn't die, but that didn't stop them from trying over and over again. In her route in the game, she attempts to kill Shiki after he is possessed by Roa to keep him from suffering the same fate.
Durarara!! has an interesting variation on this: instead of capturing Celty and performing a forced vivisection, a doctor approaches the supernatural entity in question and asks her if she would be willing to undergo such a procedure in exchange for a permanent place to stay — and she agrees. The results are still rather traumatic for her though, as it turns out that The Fair Folk are resistant to drugs and anesthesia. She then lives and falls in love with one of the scientists who did the work, and it's implied that she even works for the organization even after she learns they're holding her head.
Tessla in the Trigun manga didn't have a chance to run away. Her life and death make up Vash and Knives' tragicbackstory.
Subverted and justified in Digimon Tamers: the local Men In Black's leader Yamaki has an all-consuming hatred for Digimon, and really would cut them up. At one point, he sadistically destroys a Digimon on-screen over the mon's pleas for mercy. Takato worries about this for Guilmon and at one point imagines the army brutally gunning down his dinosaur buddy. Yamaki eventually sees the error of his ways, at which point the Tamers stop caring about keeping their Digimon hidden.
Dr Ni has expressed his interest in research of the slightly odd characteristics of the youkai-ness of most of the sanzo party in Saiyuki. Given who this is, it's safe to assume this research wouldn't be pleasant.
Darker Than Black has references to PANDORA practicing experimentation on Contractors. It's mentioned that initially, various countries did this, until a U.N. treaty intervened. Not to stop this, but to demand that countries would share their research. The manga provided some glimpses into one of such research facilities.
One has to wonder at the sanity of these scientists as well, because running human testing of an... unethical persuasion on a test subject whose only priority is their own survival, and is quite willing to go to any extreme to stay alive and is superpowered doesn't seem like the best idea. The only reason any Contractor would have (willingly) stayed in those facilities was because they thought that their chance of survival was better if they did, but that doesn't necessarily mean they enjoy what goes on there. The instant they felt that staying in the testing was more likely to end up with them dead than escaping, they would have put their all into leaving. And we are talking about a group of people who could do anything from literally just teleporting out on a whim, to creating a firestorm to escape, to causing a flood, to crushing the walls with gravity, etc. That said, any testing facility that treated its Contractors well could very easily have a Badass Army on demand if there was ever a threat to the facility.
In Witchblade at some point the wielder was captured and examined, but it turned out that while she was kept sedated, they wouldn't dare do anything that could look like an attempt to harm or remove its host (it can mince heavy machinery in an eyewink even against her will) before killing her outright. Manga, on the other hand, contained flashbacks about genetic experimentation with demon remnants as a source for creation of Super Soldiers (this didn't end well).
Averted: When Special Agent Axel Hughes finds out that Joey is the Kid With The Remote Control for Heroman, Joey asks him what's going to happen to him. "The U.S. Government is going to lock you away and do experiments on you for the rest of your life." Upon the look of horror on Joey's face, Axel laughs and tells him, that no; a friendly alliance is more beneficial for everyone. "You really thought we were going to do that?"
Mayuri Kurotsuchi in Bleach wants to cut up and experiment on anybody who demonstrates abilities he's unfamiliar with. He's equal-opportunity, though; he also cuts up and experiments on himself.
In Nichijou, miss Nakamura wishes to do this to the robotic Nano, so she can take credit for inventing her. If Nakamura weren't so inept at her repeated attempts to kidnap Nano, this would be quite dark for such an upbeat show.
In Vögelein, this is one of the arguments the Duskie gives for why Humans Are Bastards, saying that they'll take the title character, lock her up, and take her to pieces to see how she works. Considering that she's a clockwork Faerie...
A different example has Deadpool supporting character Montgomery at the mercy of a corporation that keeps him hooked up to machines, the better to utilize his precognition to their advantage.
In G.I. Joe vs. the Transformers, the Joes are ordered to do this to Bumblebee and Wheeljack by their superiors, who only see them as machines. They almost carry them out, until a stunned Wheeljack reveals that the army's plans of nuking Cobra Island will have disastrous consequences...
This was the motivation behind mutated child Batwing's rampage in Untold Tales of Spider-Man. When Spider-Man discovers him and promises to get him help, he freaks out completely because, as he put it, "Not going... get cut up by scientists... like mom said!"
The Planetary/JLA crossover oneshot is set in an alternate reality where the Planetary organization controls the advancement of science and technology the world over. By the time of the story, they've already cut up Barry Allen and Ray Palmer (the Atom) in order to create super-fast couriers and shrinking technology for Fantastic Voyage-style medical procedures.
Nikolai Dante refuses to report back to the the Makarov Dynasty after the Romanov Dynasty Weapon Crest fuses with his body for fear that the Makarovs would cut him up to learn how to design a similar Weapon Crest for themselves.
The Sandman: One of the reasons Hob keeps his immortality a secret from most people he knows, including the mortals he falls in love with. It's too easy for him to imagine a bunch of "Noble-prize wannabes examining slices of my pancreas."
Superman: Secret Identity - Clark is captured and experimented on by shady military types, and only narrowly escapes. On his way out, he finds the bodies of other superhumans who weren't so lucky, some of them children. When he learns he's going to have kids of his own, he makes it clear that he could have taken the entire government apart a long time ago if he wanted to and is prepared to help them out on his own terms.
Subverted in Ultimate Spider-Man. Nick Fury explains to Peter Parker that since he is technically an illegal genetic experiment, he will become government property when he turns eighteen. Peter freaks out and assumes this trope is in effect, but Fury later clarifies that Spider-Man will simply become a SHIELD agent and a government-sanctioned superhero.
Paul Chadwick's Concrete plays with this trope extensively. For one thing, the title character is just as eager to understand his transformation as the scientists are, and therefore he cooperates with them. For another, he is a world-famous celebrity, and it would be quickly noticed if he vanished mysteriously, or if some overzealous scientist got carried away with his studies. Furthermore, scientists in Concrete tend to be sympathetic characters who want to stay on the right side of the law. In fact, Concrete cooperates with the government and the military to create his cover story.
First, blanket statement: we're not going with your ridiculous military scientists. No poking, no prodding, no examinations, no experiments. If you're that curious you can ask nicely, but we reserve the right to say no. And especially don't do the cliché kidnap-them-in-the-middle-of-the-night-when-they're-off-guard thing.
In With Strings Attached, Shag points out that John can't go home with wings because he'd be dissected; Paul unknowingly echoes this when he tries to talk John into finding a way to change back. Much later, after he really is facing the return home, John sourly reflects that at least the scientists won't be able to hang onto him.
Also, Jeft refers to extremely powerful psionics as suffering this fate while Shag is yelling at him for apparently inducing psionic powers in Ringo.
One of the many reasons Shirou wants to keep the Magic Association away from the Sekirei in In Flight
If you are defeated, the best you can hope for is death, and your corpse will most likely be violated and experimented on.
An interesting variation in Arads Stardust. Funnily enough, Twilight Sparkle is already in the captivity of XCOM, an organization where this trope is their typical MO. However, the Council has also recommended sending Twilight to another base where only painful experimentation awaits her, which many XCOM personnel recognize as a horrible possibility and seek to prevent it.
Films — Live-Action
Subverted in ET The Extraterrestrial: Despite their initially sinister appearance, the scientists pursuing E.T. show no sign of wanting to cut him up, and even try to save his life when he's dying. They do want to cart him off and lock him up in a secret location while they study him, though.
Averted in Close Encounters of the Third Kind. Both humans and aliens always planned to return everyone unharmed at the end, except for volunteers who agree to be taken to the aliens' planet.
In Phenomenon the government is almost totally upfront about wanting to do this to George. Because George's mind is working at near 100% efficiency, it takes him no time at all to realize what they're not saying is that the exploratory surgery they want to do would kill him, and that they think they'd get less data doing the same surgery after his death.
At least they're willing to take no for an answer, unlike many of the other examples on this page.
Not really. When he says 'no', they have him declared insane and get a court order to perform the surgery. By claiming it's a treatment, they create a plausible legal excuse for vivisection.
Transformers: They're actually shown experimenting on Bumblebee. And by "experimenting", we mean basically torturing him.
In The Incredible Hulk movie, knowledge of what Thunderbolt wants to do with the gamma power is why Bruce keeps running because he knows they'll dissect him and try to weaponize the gamma power.
In Beneath the Planet of the Apes, Cornelius warns the fugitive astronaut Brent against speaking if captured by the apes— "If they catch you speaking, they will dissect you. And they will kill you. In that order."
In Splash, an "internal examination" was the next thing on the to-do list of mermaid Madison's scientist captor.
In District 9Wikus is nearly vivisected (without anesthesia and fully aware) when it turns out his mutation into a Prawn makes him capable of operating the aliens' weapons. It turns out his employers secretly have been dissecting and experimenting on the aliens for years for that same purpose.
"Disassemble" is practically an arc word in Short Circuit. Except that NOVA had little interest in Number-5's sentience; they saw it as a bug that needed fixing at best and a potential threat to innocent civilians at worst. At no point in either movie does any organization have any deliberate intention of doing any unpleasant experimentation on him.
Nobody wanted to disassemble him, but they did want to deactivate him because he still had a powerful and dangerous laser weapon on him and was out of their control. (Number-5 didn't reveal he removed the weapon and turned that space into a harmless toolbox until the end of the movie.)
A kid-friendly version appears in the Swedish children's movie "Pirret" (approximately "That Bubbly Feeling"). The movie is about a little girl who can fly when she's particularly happy and has "that bubbly feeling". Her mother asks the family physician if there's anything wrong with the girl, and the girl is whisked off to the hospital where a very unsympathetic doctor tries to find out what makes her fly. No actual cutting up, just MRI scans and stuff. Of course, since the doctor is constantly scaring her, she doesn't get "that bubbly feeling" in the doctor's presence, and in the end she's released.
Pavlov: "You bastards... you are all under arrest for murder, sedition, for treason against the Federation. Oh! Your going to pay... because we're not going to kill you... oh no... you see, we got special places for things like you... where they cut you up, but they keep you alive when they cut you up... so they can see what makes you tick, and then what makes you sick! And I will be there, oh yeah! I'm going to be there when they see ACK!" (threat cut short by infected soldier cutting his throat).
Arachnid dissection and vivisection occur in the first film as well- particularly pay attention to the captured brain bug in the epilogue.
Jack Frost (1998). Jack Frost's son is afraid (and to his credit, more Genre Savvy than his dad) that Jack will be experimented on by the government if he'd ever been discovered. Jack says he doesn't care, as long as he gets to spend some time with his son.
In The Man Who Fell to Earth, this issue comes up when Thomas (an alien) is captured by the U.S. government and experimented upon for years, no matter how much he begs. Oh, the prison is a nice hotel suite, he never wants for food, etc. and he even has a final tryst with his Earth mistress...but his imprisonment seals the fate of his dying race back home, and he is finally released a broken, stranded soul.
Literal example: In Creepshow, Jordy Verrill decides not to call a doctor about the alien green growth on his hand because he imagines the "cure" will be to chop off his afflicted fingers. Without anaesthetic.
The Goose that Laid the Golden Eggs. Its owner killed it to know how it worked, didn't learn anything, and now no longer gets golden eggs. Poor sucker.
Used as a proverb when it looks like somebody might end up cutting off a vital source of long-term gain (be it information or money) in their greed for short-term gain: "Don't kill the goose that lays the golden eggs".
Subverted in Singularity Sky when an ignorant citizen of a backwater world asks a Sufficiently Advanced Alien for a goose that lays golden eggs. No-one thinks about how it works until they start suffering radiation sickness... transmutation in real life is a nuclear process, after all.
Explicitly averted in the Isaac Asimov short story "Belief". The protagonist is a physics professor who discovers that he can fly; the entire story is about his attempts to get the scientific establishment to take him seriously. (His claims of antigravity get written off as a hoax, even on at least one physical demonstration.)
Asimov also wrote an SF version of the Golden Goose story (Pâté de Foie Gras) which averts this. Even though it's just a goose, the government scientists were extremely careful not to harm it, and were terrified when it developed a fever. They weren't interested in the goose so much for the traditional reason ("Gold! Gold! We're RICH!!!") so much as they were interested in how a frakking goose was accomplishing nuclear transmutation of the elements inside its reproductive system.
In Mercedes Lackey's urban fantasies, this trope is out in full force. The secret government facility or evil corporations are more than happy to track down people with psychic or magic talents and do nasty things to them in the name of controlling them and/or using their powers.
This is why Cris from the Philip K. Dick short story The Golden Man never stays in one place too long. In the case of the movie, however, the threat wasn't scientific experimentation but rather the possibility that the FBI would imprison Cris for life and force him to use his predictions to their advantage. He willingly goes with them in the end to prevent a nuclear attack that would kill his love interest.
Stephen King writes of The Shop, a government organization which does paranormal researches, into a lot of his stories. Charlie from Firestarter was on the run from them because of their desire to use Charlie as a weapon. This is mainly because her powers were entirely due to their Playing with Syringes with her parents, and they wanted to see the only really militarily useful result of the experiment. And by "militarily useful," we mean "potentially able to crack the planet in half."
Used in the Maximum Ride series, where the main characters are running away from one of these types of labs.
Similarly to the Twilight Zone example, the first humans to encounter the aliens in Pandora's Star by Peter F. Hamilton are dissected. The sequence, told from the alien's point of view, is pure horror even with death being (usually) a minor inconvenience in the Commonwealth.
In one of the Halo novels this is the reason given by Doctor Halsey for why the data on how Sargent Johnson survived contact with the Flood can never be told to anyone (even the good Sargent himself, who would likely turn himself in). Ironically, she tells this to the Master Chief . . . who later crushes the data crystal containing aforementioned information.
The backstory in The Stars My Destination has shades of this with the first man, a scientist, to learn to Jaunt, or teleport. The first time it happens is under the stress of a fatal situation, and the scientist knows that, to replicate the phenomenon, his colleagues are going to do their best to kill him. Subverted because he actually goes along with this, and after saying his goodbyes, does replicate it. The result is, by the time the novel takes place, all of mankind can teleport at will.
The reason that Nancy, heroine of Lois Duncan's A Gift of Magic, gives for wanting to keep her psychic powers a secret. She's isn't afraid of being dissected, but she is afraid of being dragged off by the government and being turned into a lab rat. The government already knows about her powers and respects her right to keep them to herself if that's what she wants.
In China Mieville's Perdido Street Station, Isaac visits the garuda (eagle people) ghetto and tries to bribe some of them to come to his lab so he can study them. The garuda leader loudly informs his flock that "they'll take your wings away, kill you dead!" even though Isaac protests that's not his plan.
to be fair this is such a crapsack world that this is an entirely reasonable assumption.
Invoked in Robert A. Heinlein's The Star Beast by John's ancestor when he acquires a native pet (or rather, inadvertently kidnaps a native princess) while exploring an alien planet.
Flinx of the Humanx Commonwealth series was genetically manipulated by the Meliorare Society as part of their secret program to produce supermen. When their more spectacular failures came to light, they were outlawed and hunted down along with all their experimental subjects. Those that could be "made normal" were corrected; those that could not were destroyed. Despite being superficially normal, Flinx is possessed of strong Psychic Powers, which alone would be enough to get him put in a fishbowl and studied for the rest of his life, but that plus his affiliation with the Meliorares means he is exceedingly careful to reveal his talents only to people he absolutely trusts. Even then, he runs afoul of this trope on several occasions, most specifically in Flinx in Flux, where not just one but two separate antagonists join the hunt — one to "fix him" and the other to "study him". On several occasions, he also runs afoul of surviving members of the Meliorares who see him as an opportunity for vindication of their cause.
Michael Crichton's Next revolves around the Real Life legal precedents that could be interpreted as this. Yeah, that's right; current biotech laws are vague enough that if a doctor harvests cells from you, not only can they sell them to researchers without compensating you, whoever buys those cells might own your "cell line" - AKA you and your children. ...At least if they have a skilled Amoral Attorney.
According to the Mi-go of the Cthulhu Mythos, the Brotherhood of the Yellow Sign hunts down and torment them for knowledge.
In The Hitchhiker's Guide to the Galaxy the pan-dimensional beings also known as mice try to obtain Arthur Dent's brain to perform experiments on ("Diced.") to find out the question of Life, the Universe and Everything.
In a novel a small group of people are captured by aliens who have been living in an underground complex in South America. The aliens then take one of the group to cut them up to see their intestines, for predicting the future, rather than for science. Turns out the 'cutting up' was an assumption on the part of the humans and in fact the aliens got all the information they wanted with sophisticated, and harmless, scans.
In Correspondence From The Goddess, after Lydia starts developing super-powers and Albert Pharmaceuticals expresses interest in studying her, Elana rejects the idea entirely, citing this trope. Lydia then goes to see them secretly, and it doesn't seem to go badly at all.
The six psychic boys in Hidden Talents swear a blood oath never to tell anyone else about their abilities, for fear of this trope. Readers find out in the sequel however, that this doesn't exactly work out.
This is pretty much the reason the Diffy family in Phil of the Future try to hide the fact that they come from the year 2121.
In Pushing Daisies, this is why Ned doesn't want anybody to know that he can bring people Back from the Dead. Given Ned's neurotic personality, it's not really surprising that he would think this.
Besides which, if anybody found out how his powers worked, he'd be arrested for murder for reviving Chuck when he knew that it would result in an innocent person dying.
This show is a good example of this trope done right. For Ned, who really has no idea why he can do what he can do and who's had no guidance whatsoever on how to deal with it (meaning for most of his life he had no outside feedback to help keep him grounded), and who has numerous issues with abandonment, emotional intimacy, and social anxiety on top of that, this fear is a logical extension of his character and life story, rather than merely being a nebulous threat meant to justify The Masquerade.
In a less extreme example, the main character of Kyle XY keeps his abilities a secret because he wants to live a normal life, rather than spending all his days being tested by scientists.
In Heroes, HRG tells Claire that this is what the company would do to her if they found her, presumably in order to test her regenerative properties.
Also, while not exactly cut up, Elle was treated to some rather unpleasant tests to figure out how powerful she was as part of her Back Story.
In the pilot episode of Alf, what finally convinces the family to hide the titular alien is being told by the researchers themselves what they plan to do to him.
Subverted in the later TV movie, where it's shown that Alf's doing all right after turning himself in, when he is not shooting his mouth off at least.
In an episode of Farscape, Crichton thinks he's returned to Earth. It's a world constructed from his memories, and when the aliens running the show introduce a copy/clone of Rygel dead on a dissection table, it's implied this is what Crichton subconsciously expects to happen. And he's a military scientist!
Ironically, when the crew actually does arrive on Earth, they're all treated as honored dignitaries and celebrities. Moya arrived at Earth several weeks before Crichton did (Note that Crichton's father and several other humans were already aboard when Crichton steps out) so the aliens actually managed to do fine by themselves.
In the first case, Crichton also angrily points out the hypocrisy of sending out invitation to alien life to come and visit only to murder and vivisect them when they do. Of course, he fails to realize that people who send out these invitations are different from the people who will be dealing with hypothetical alien visitors, who will likely have a "kill them before they kill us" mentality.
In Babylon 5, Talia's telepathic abilities had been enhanced to an unknown degree by her A God Am I ex-boyfriend, Jason Ironheart. A while after she left the show due to being revealed to have a sleeper personality, Bester mentioned that the Psi Corps had learned a lot when they "dissect—that is, examination" her. This is probably Bester trying to put people off their guard and/or just being a Jerk Ass, as the sleeper agent program was initiated by the Shadow-allied faction of the Corps, and he's not part of that, nor was he aware of Talia's sleeper personality before it was exposed.
Much later in the series, Bester offers to help Lyta Alexander find employment by providing fake Psi Corps credentials... in return for her body. After she's done using it, of course, and the contract would be void if she died of anything other than natural causes.
In the episode when Talia got her upgrade, Bester and his partner were trying to apprehend Jason Ironheart for just this purpose. When they finally do find him he's become so powerful that he accidentally kills one of them and then turns into a god.
The Sarah Jane Adventures. Sarah thinks that if UNIT ever found out about Luke, they'd consider him a threat and lock him up. She's not keen on them knowing about alien supercomputer Mr Smith, either.
In The Secret World of Alex Mack, this is one reason that Alex keeps her powers secret. Since the chemical plant really does want to cut her up and/or kill her lest the knowledge of the chemical's danger get out, her fears are somewhat justified. In the last episode, they do finally catch her, but rather than cut her up, they leave her to die in an exploding chemical plant. Danielle Atron also rubs this trope in Alex's face in the last episode.
This was somewhat subverted in regards to her parents. When they discovered her powers in the same episode (due to her confessing after said parents were left for dead in the exploding plant as well), they were quite understandably offended by Alex's belief that they would turn her in.
At the beginning of Power Rangers Dino Thunder, Kira suggests they go to the authorities about their new superpowers and the Mooks that attacked them. Hollywood Nerd Ethan argues that in movies, people with powers tend to end up in a lab with wires in their head, and Jerk Jock Conner agrees that even he's Genre Savvy about that part.
Which brings up some nasty Fridge Logic about the fact that Data had already been admitted to Starfleet Academy, been granted a commission and rank as an officer, and even decorated with medals for valor in the line of duty; none of which would or could apply to a piece of property rather than a legal recognized individual. The scientist's argument is essentially just "ignore that stuff because it would be cool if I could figure out how to make lots of new androids that we can treat like disposable slaves".
Given that Data is called to testify in his own trial, the whole thing seems moot. After all, if he wasn't an individual, he'd have been "submitted into evidence" (like a video recorder) instead.
In a Lois and Clark episode, Lois travels to an Alternate Universe where Clark never became Superman due to his adoptive parents dying when he was little. His fiancée keeps berating him using this trope as a warning whenever he covertly uses his powers to save people. This world has also gone to hell after the arrival of Tempus, who gets himself elected President and removes all gun regulations. Cue the chaos. Fortunately, Lois fixes the situation by making Clark a suit identical to her Clark's.
In Smallville, Memoria, Clark is captured and experimented on because the scientists have the blind luck of messing with kryptonite liquid at the time. In Ryan, Ryan is also sent to the same research facility. In Freak, Lex Luthor captures Chloe and has his team experimenton her in his secret lab.
The aliens of 3rd Rock From The Sun lived in constant fear of this and it was brought up whenever they thought they might be found out. Subverted in that, despite their fears, the idea of them being aliens never occurred to anyone other than Kathy Bates and her character was portrayed as insane. This is despite their occasional Suspiciously Specific Denial to being aliens.
In the first season of Roswell, the FBI is pursuing the aliens, presumably to do sinister experiments on them. In the episode The White Room, Max is captured, and narrowly escapes vivisection after being tortured. Though Pierce, the head of the Special Unit, was after information, not scientific knowledge.
What Wolfram & Hart want to do with Connor in Angel. Given that the main thing that separates him from the many people with superpowers in the world is that he's a focus of prophecy (presumably ones that will be defunct if they kill him) it seems a bit of a waste.
The Initiative on Buffy does this with any species they deem Hostile Sub-Terrestials (non-humans) to create Super Soldiers. It goes horribly wrong, of course. Riley thinks this is what would happen to him if the Initiative gets hold of him again. Of course, the real reason they're trying to bring him in is to remove his modifications, which are causing severe mental and physical breakdown, so he's not exactly being rational. Then again, Riley witnessed first-hand his former employers have no trouble experimenting on beings that are human most of the time, so his fears might not be ungrounded.
In an unusual twist, the Tam family in Firefly presumably laughed off this possibility, if it even occurred to them at all, when the government expressed interest in their 'gifted' daughter, River. Disaster ensued, and her brother Simon had to sacrifice his medical career to get her away from the scientists post-cutting up and take her on the lam to prevent it from happening again.
Sort of the catalyst for the whole series in Red Dwarf. In the first episode, the Captain tells Lister his cat will be cut up and have tests run on it, prompting the response, "Would you put it back together when you were done?"
Hollister: Lister, the cat would be dead. Lister: Well, with respect, sir, what's in it for the cat?
Doctor Who: This trope is why Rose didn't call a doctor for the Doctor in "The Christmas Invasion".
Quite justifiable, considering what happened to the Seventh Doctor the last time a medical "professional" got a hold of him, during the TV Movie. "Wow, this man has a double heart beat! Let's ignore that bullet wound and poke his arteries with our scalpels and see what happens!" He promptly dies.
Especially since Henry van Staten does it to him in "Dalek" in an earlier season.
And then Torchwood get their hands on him. And promptly avert things; the squad with trained guns lower them and applaud, and while he's captive he's told he'd be kept comfortable, and is in no way actually restricted. The Doctor proceeds to ... act civilised (aside from breaking a window to make a point).
This happens to a human captured by Silurians in "The Hungry Earth". Alive, and without anesthetics.
When short-lived companion Adam has future technology installed in his head in an attempt to set up a Timeline-Altering MacGuffin situation, the Doctor drops his useless ass back on earth and tells him that now he has to live quietly, less this happen to him. Which isn't going to be easy, since now his skull opens up every time someone snaps their fingers in his vicinity.
The Daily Show spoofs this with a John Oliver story about two politicians who decided to campaign together while running against each other to send a message of civility. John concludes that in the world were to learn of their existence, "they would be poked and prodded until there was nothing left." The story ends on an homage to E.T., with Jon Stewart playing the part of the evil scientist.
Henry from Sanctuary is captured by the Cabal, who attempt to turn him into a werewolf permanently, kill him and study him — all in the name of science, of course. He's even promised it'll be a noble end for him.
In the UK Being Human, the group encounters a zombified girl (who is in total denial of her status and appearance as a rotting corpse). When they go looking into her origins at the hospital they find evidence of several other living dead individuals who met this fate at the hands of doctors and scientists trying to discover what made them tick. The video they find even includes the final disposal of the still aware remains of these individuals (by cremation).
The Invisible Man: One of the episodes features a plot by the Chinese to get the quicksilver gland. Darien ends up getting his head drilled into so they can drain the quicksilver.
In The Outer LimitsRevival series episode Last Supper, an immortal woman finds this out the hard way when she's discovered by the US government and experimented on. Thankfully, she's rescued by a military guard who can't stand to see it happen, but the scientist who conducted the experiment finds out years later she's still alive and wants to finish his work...
Misfits averts this entirely, revealing their super powers to the general public seems only to result in mass media fame, with a notable lack of scary scientist dissections.
Torchwood: Miracle Day: An extremely disturbing example occurs when Jack's immortality is discovered by a family of butchers in the 1920's. They repeatedly stab him to death in front of ever-growing crowds. Eventually, the whole crowd starts hacking away at him.
This is the fear of para-psychics in Cthulhu Tech — completely justified since the government of their Bad Future doesn't even keep the fact that they sometimes do this a secret.
Considering how dangerous uncontrolled para-psychics are, the general public doesn't have a problem with this either.
And then there's Promethean: The Created, where several of the antagonist monsters demonstrate why you don't want an alchemically-reanimated corpse with incredible power and an inborn Uncanny Valley effect getting anywhere near a Morally Ambiguous Doctorate. The reasons range from a Galateid whose tissue was broken down and utilized to create living sex dolls to a cloning program that practically turns Prometheans into genetic soup.
In City of Heroes, Crey Industries does this so often, it's a pretty legitimate fear for the meta-humans in that universe.
At least according to the backstory, Crey never actually tries to do it to the player. The most they ever do is attempt to ruin your public image for getting too close to their CEO's big dark secret.
Resident doctor slash nuttybar Shiro in Siren does this to the Shibitofied Onda twins, experimenting on what, exactly, it would take to kill them. The answer is: nothing. Made especially Squicky when he tugs an unborn fetus out of Mina, the girl he had KILLED earlier in the plot and proceeds to stamp on it. Lovely.
In one of the bad endings of H-GameMadou Souhei Kleinhasa, Roze is experimented on by enemy scientists to find out how her magic works. It's implied that she doesn't survive their experiments.
In the X-COM series, it's the standard procedure when dealing with captive aliens but the only dead ones. Live ones are interrogated and then disposed of.
In the Firaxis remake, after the first interrogation (apparently, very painful), Dr. Vahlen tells your Number Two that the alien didn't survive the procedure. Indeed, none of the interrogated aliens do.
Toyed with in Harvest Moon DS. Local Mad Scientist Daryl has been chasing the strange creature Mukumuku for years in an attempt to figure out how it works, and given the long and fantastic family history of genetic experimentation he brags of, it seems It Runs in the Family. So when chance favors him, and he happens upon an injured mermaid girl? He takes her home to his basement, and... diligently cares for her until she recovers. And if you befriend said mermaid, she openly chastises you for daring to think Daryl would experiment on her.
In Infamous, Cole receives several warnings that the government wouldn't treat him kindly if they got their hands on him. It turns out to be a subversion: they already know how to endow someone with superpowers, they just want to control Cole and choose what direction he's pointed in since his powers are already very offensively oriented. Between the games, every government agent who has this goal for him is killed anyway. The mentalist Alden Tate, however, is vivisected.
Sector Seven has the reoccuring issue of hiring lunatics to deal with scientific discoveries. In fact, everyone that was offically hired by Sector Seven that's major to the story has this at some point. Lambda-11 comes to mind, but Relius gets a prize for using his own daughter and wife as experiemnts.
"Since when did people start expecting science to be humane? To study the body, you cut it open. To study the mind, you isolate it by crushing the heart. Historically, that's how science has advanced."
Girl Genius: This is one of the things sparks needs to worry about. Especially from the Baron himself, in Othar's case.
However, Agatha once acknowledges that it's sometimes better than some alternatives.
This is why Roland has to keep Sadachbia's presence on the down-low in Not So Distant, since Sadachbia is a large alien, who'd probably look great cut up on a table to Earth scientists.
Though she's a little confused about it on their first encounter with the FBI, this is later a thing Aylee in Sluggy Freelance fears. The humans she's living with assume the government would automatically perform a secret alien autopsy on her if they ever found out about her.
The talking raccoon, Woo, of Sandra and Woo mentions this when he first reveals this gift to Sandra, saying that he's kinda' attached to his vocal cords, and asking her to keep it quiet. The danger is never mentioned again.
When Vexxarr is first captured, the lab geeks started running tests on Minionbot, mostly consisting of finding out that none of their tools can affect his casing. They get as far as hammers before Minionbot gets mad.
This is the objective of The Coroner in Sidekick Girl. He's already killed one superhero by vivisection that we know of. The one he's most interested in (And has already captured once) is the title character, whose Healing Factor means that he can dissect her infinitely without her dying, allowing him more time to figure out how her powers work.
In Maggot Boy, resident Mad Doctor Sutton vivisects the rare sapient zombies to study how they work. Since they're undead, it causes no lasting physical harm, but it's still prettytraumatic.
"I'm not going to hurt you. Extensive testing has shown that's a physical impossibility!"
When Jix, Caligos, and Heleatra are captured by Area 51 the scientists attempt to vivisect Atra, despite one of them pointing out they could use an MRI, but her Healing Factor keeps closing up the incisions. Then it turns out the scientist who wanted to do the vivisection has a grudge against Jix stemming from the time they captured her android and attempted to take him apart.
Largely averted or subverted by the SCP Foundation, who largely take the place those traditionally experimenting on the Monster of the Week's corpse would. The Foundation tends to be interested in observing and containing subjects, destroying those too dangerous. It helps that they really don't want more of most SCPs, but the rare helpful ones avoid vivisection simply because there's no way to be sure it'd provide useful information, and there's usually only one. Of course, when that's not the case...
Phase doesn't believe that this is a prevalent problem in the Whateley Universe. Even after his own family lets a Mad Scientist trank him and slap him on an operating table. Part of the backstory of The Verse is that Phase is wrong about this. Really wrong.
In the backstory to Red vs. Blue, this was the fate of the Alpha AI. The entire series plot thus far is (sometimes loosely) based around dealing with the repercussions of cutting it into pieces.
Averted twice in The Salvation War: once, the National Security Advisor attempts to get a succubus so that he can vivisect her, but George W. Bush prevents this — the succubus had already been offered sanctuary for defecting — so the advisor has to "make do" with dissecting corpses of daemons killed in war. Later, Abigor offers some of his soldiers so that they can vivisected and humans can understand how demons are on the inside, but the general he is talking to tells him that it would be against their laws and doesn't follow on the offer.
Blackarachnia left the Autobots in Transformers Animated because she was afraid this would happen to her after she became technoorganic. Given the xenophobic nature of the High Command, she might not be too far off the mark.
One of the justifications for the Gargoylesmasquerade. Given that several of their bitterest enemies have discussed (or done) nasty things involving Gargoyle genes, it's quite justified.
Goliath:Look at me, human! I would spend the rest of my life in a testing facility. Was my crime against you so horrible as to make that an equitable punishment?
The Teenage Mutant Ninja Turtles take this trope to heart. Given that in the 2003 cartoon the first thing government agent Bishop did when he captured them was to take their genetic material and try to dissect them, their fears are more than simple paranoia.
Justified in Danny Phantom, where his ghost-obsessed parents aren't getting ethics approval for their research and have explicitly said they'd like to dissect or kill any ghost they find "molecule by molecule". However, it's odd that Danny was so certain they'd do the same to their own child, a half-ghost.
Well, with Jack constantly shouting that when he catches the ghost kid, he will rip him apart, molecule by molecule, it's reasonably understandable. One episode has them find out and accept him, only for him to wipe their minds for no reason, causing them to go back to hunting him.
Also the Guys in White, and their famous quote from Reality Trip: "You're coming in for questioning-" "-and experiments. Lots and lots of really painful experiments."
Very nearly carried out in the pilot episode of Street Sharks, to the point in which the doctor has Slammu tied down to an operating table and heavily sedated before the others escape and save him. They then try to perform the same "explorative surgery" on the doctor with what is essentially a chain saw before they have to escape.
The Mad Scientist in the Mickey Mouse short ''The Mad Doctor" actually sings a song about how he's a master at cutting bodies up and grafting parts to each other. He's first introduced as having planned to cut Pluto's freaking head off and graft it onto a chicken's body, just to see what sort of noise it would make. And he nearly cuts Mickey's stomach open with a HUGE buzz saw.
Specifically, the Mad Scientist wants to graft Pluto's head onto a hen's body and then breed the result with a normal rooster to see if whatever hatches from the egg will cackle, crow, or bark. Talk about Artistic License - Biology...
The main reason Roger in American Dad! hides from the CIA. In one episode, he actually does get captured and is about to be cut up, but Stan saves him.
Happens to Zoidberg in Futurama during the events of 'Roswell That Ends Well.' Fortunately, he has enough spare organs that he's not too bothered about it. He's also apparently conscious throughout this entire procedure.
Surgeon: Contents of stomach: one deviled egg...
Zoidberg: Deviled egg?! *gobbles the egg right out of the surgeon's hand*
Surgeon: Contents of stomach: the same deviled egg...
Referenced and averted in Hop. Fred says that this would happen to E.B. if he just went around talking in public. This is immediately followed by E.B. complaining to their waitress about his order, and her acting as if this is perfectly normal.
The Nazis, most infamously Mengele, whose "experiments" almost never produced any actual, useful scientific data (the main exception being the research on freezing injuries, which formed the basis of medical practice in that field for decades after the Nazi experiments ended), and didn't seem to have any purpose other than "how many more horrible things can we do?" Even Mengele's contemporaries were baffled.
During World War 2, Japanese Unit 731 did this to Prisoners of War and Chinese civilians without anesthetics while vivisecting. They also tore babies out of pregnant women, tested how much damage bombs and various diseases did on the prisoners, and tried out chemical weapons, all without anesthesia or treatment. Unlike Mengele, they actually did produce some useful data, which led to the Allies letting them go free in exchange for the information. Why the Allies didn't just say "We Lied" after getting the data is unclear.
Because lying about accepting a surrender would violate the Geneva Conventions (and, even if not, it'd just encourage people not to surrender at all and go down with the ship). Beyond that, the argument can be made that there's a certain ethical choice in lying about granting freedom in exchange for information.
Benign example with exploratory surgery. "Something's gone wrong inside you so we need to cut you open to see what we need to fix." Of course, this is the non-torturous example with the testing standards.
Then there is Animal vivisection of course. The United States, UK, and Australia at least have rules in place where they often need to be approved by both scientists and people interested in animal welfare. Anesthesia is usually required.