Somebody is involved in something dirty, or just did something nasty. Could be The Government, could be The Mafia or The Syndicate, could be General Ripper, a Corrupt Corporate Executive, or an Ancient Conspiracy. No matter what bad guy was involved, somebody saw it all, heard it all, or somehow caught wind of what's going down (or what went down), and the bad guy in question has found out about the witness.
Since the witness now knows too much, the bad guy's entire scheme may come crashing down, so they aim to "silence" the witness in some manner, through bribery, blackmail, intimidation, or even murder.
A common variant is that the person who purportedly knows too much doesn't actually know anything at all (or at least, doesn't understand what knowledge they have) — but the overly paranoid conspirators believe that they do, thus leading to their campaign of persecution. There's a good chance the hero will eventually get sick of being relentlessly hounded/threatened/shot at by the conspirators and start fighting back. In the process, they usually learn the "real" secret anyway by constantly coming into contact with said conspirators at every turn and eventually will find a way to bring the plan to ruin. The ironic conclusion, of course, is that if the Big Bad had just relaxed and left the person alone, they'd have succeeded.
If it isn't the hero getting persecuted, it will likely be someone the hero cares about, which will usually prompt either a bodyguard scenario as the hero tries to protect them against the bad guys, or a Roaring Rampage of Revenge if the loved one is killed. Either way, it's an excellent MacGuffin.
The most common motive for bad guys to go after innocent people and the reason that the FBI has the Witness Protection Program.
See Revealing Coverup, Killed to Uphold the Masquerade, Have You Told Anyone Else?, and His Name Is.... See also Leave No Witnesses for those situations where a roomful of people all Learn Too Much at once. Where the knowledge itself is harmful, see Things Man Was Not Meant to Know.
Sent in a message to Professor Eifman just after he figured out the true agenda of Celestial Being's founder, and just before the Thrones attack the base, killing him in the process. Either sent by Ribbons Almack or by Veda itself.
Eifman's computer screen: "You have witnessed too much."
Played with in the case of Kinue Crossroad. She is killed for knowing too much, but the guy who killed her is a violent sociopath, and deliberately gave her the information before killing her for knowing too much, apparently just because doing so amused him.
In Brotherhood, so did Isaac McDougall. He also gets offed for his efforts.
It's not until quite a bit later in the story that the audience is shown exactly what he had uncovered. At first it seemed that he'd discovered little more than that there was an Ancient Conspiracy, and his knowledge shouldn't really have been a threat to them yet. But in fact, he'd also realized that all of Amestris was a giant transmutation circle, a fact that was the lynchpin of the entire conspiracy.
Isaac: Do you know what shape this country is in?
The two brothers that Ed fought at Laboratory 5 were killed before they could tell him what they knew about the Philosopher's Stone.
In episode 13, Shirley Fenette gets shot to death for knowing that Rolo Lamperouge isn't Lelouch's brother. The fact that Shirley wanted to help reunite Lelouch with his real sibling, Nunally, eliciting Rolo's jealousy doesn't help, either.
In the first episodes of both the first and second season, Lelouch is about to be shot for having seen C.C., although the second time it was intentional.
In Suzaku of the Counterattack, this is why Schneizel had Marianne killed.
In an early episode of R2, Rolo murders a Britannian soldier who walks in on a conversation he's having with Viletta for hearing things he shouldn't. And all the guy heard was the word "Geass", which he couldn't possibly have even understood.
The scholars of Ohara got too deep in researching the Void Century (which is hinted at being a huge threat toward the World Government), and consequently the island, along with its inhabitants, was bombarded into oblivion by the World Government. It's also the real reason why Robin has a bounty.
Played for comedy in Luffy/Ace's flashback. Luffy discovers where Ace and Sabo keep their treasure, and they state that they're going to kill him to keep him from telling, only to realize that neither of them have killed anyone before.
In Gundam Wing, all five Gundam Pilots were ordered to kill anybody who sees the Gundams or who discovers their identities. Heero takes it to an extreme, assuming that Relena knows too much without any actual evidence (she found him washed up on a beach in a spacesuit) and threatening to kill her for most of the series. In the second episode, Duo's a bit more forgiving, using a road flare to block Relena's view of Wing and Deathscythe and telling her that it's in her best interests to look away.
In the Vampire Princess Miyu TV series, this partially is what prompts Dark Magical Girl Miyu to get the otaku Secret Keeper to fall to his death. The fact that he showed absolutely no understanding about Miyu's nature and what it means to be the Guardian really didn't help his case.
In the original manga of the Hentai series Bondage Fairies, main heroine Pfil is invited into the home of a trio of sisters while on a missing-stag-beetle case. While there, she accidentally stumbles upon a detached stag beetle leg. The sisters realize that they've been found out, and they knock Pfil out and take her captive, starting the plot.
In Future GPX Cyber Formula, Osamu Sugo leaves the Missing Link F-1 team after knowing of his boss Smith's plans to use Asurada, the computer system created by Hayato's father, as a weapon of mass destruction. He soon disguises himself as Knight Schumacher, in order to keep an eye on Hayato, as well as Smith and his men. During his racing duel with his rival Bootsvorz, Smith attacks Osamu from behind with his helicopter's missile for exposing said secret. Osamu gets better, but ends up injuring his eye.
Averted in Mai Hime. Akira is duty-bound to kill Takumi if he finds out she's a girl, but not only is unable to go through with it, but even saves his life by giving him his medicine.
Baki kills Hayate after he sees him meeting with Kabuto, learning that the Sand and Sound Villages are conspiring to destroy the Leaf Village.
This happened to Kabuto himself too. He and his mother figure were spies for Root, but Danzo decided they had become a liability and set them up to kill one another. This was the catalyst for Kabuto's Face Heel Turn.
Shinichi Kudo comes across a mysterious black man extorting from another man, but he fails to see the black man's partner, who sneaks on him and knocks him out cold with a lead pipe. The two tries to force feed him with a poison pill...but the pill only shrinks him into a body of a child and assumes the alias of Conan Edogawa.
In the Ski Lodge case, this was the reason for Minako Mochizuki's murder: she found out that two of her three favorite teachers (one of them being the one she adored) were involved in a fraud, so she tried to confront them... and the two strangled her to death and then made it look like she committed suicide. And the third teacher? She killed them as part of her plot to get revenge for Minako's murder.
The Non-Serial MoviePhantom of Baker Street reveals the immediate reason for Hiroki's death is because he found out Schneider was the direct descendant of Jack the Ripper.
In the Luxury Liner case, Tatsuo got beaten to death by his wife Aki's cousin Ichiro because Tatsuo saw him trying to drop the killing weapon (a knife which he used to kill his grandfather) in the sea.
In another Non-Serial Movie, Touma witnessed a murder committed by his mother's friend, who then kidnapped him and tried to kill him. However, Touma then fell off a cliff and fell in a coma, only waking up eight years later. The killer targets him again, fearing that if he ever recovered his memories, he'd denounce him.
Happens to Ran Mouri twice, once in the anime/manga and later in a Non-Serial Movie. In the first, she steps inside several rooms where guys are undressing, but one of them has a secret, so he decides to kill her... and he's the killer of the case. In the second, she clearly sees the face of a murderer who immediately tries to shoot her dead, and even when she has a huge Trauma Induced Amnesia he still attempts to murder her.
In Part 3, Enya is killed by Dio and Steely Dan (Dio supplied the weapon) so she can't reveal how The World works. The kicker: Even while dying, it was clear that Enya would never have thought to betray Dio like that. Steely Dan just laughs about that.
In Part 6, Whitesnake kills Jongalli as insurance against Jotaro and Jolyne learning who's really behind the latter's imprisonment — Enrico Pucci, the prison chaplain.
Almost happens twice in Orphen. First, Lai steps on who everyone believes to be Childman but is actually Azalie in Childman's body, and she turns him into a Human Popsicle. Later, Hartia finds the frozen Lai and sees Childman!Azalie's shadow in Azalie's form, so she snaps and almost kills him, but he barely manages to escape to Orphen and Co.'s side. In the end, Hartia survives and Lai is de-frozen.
Comic Books
In Top 10, pop star and former science-hero sidekick Glenn Garland is killed because he was going to tell the media about the illegal and repulsive actions of a group which he used to be a part of. The Vigilante from Venus also expressed concern that they were going to try to kill her before she went to trial, for fear that she would incriminate them in her testimony.
This trope is what sets the whole plot of the first Sin City story "The Hard Goodbye" in motion, as Goldie is killed on orders from another character after she discovered his nasty secret habit. Another character dies after mistaking a death squad for honest cops and telling them everything.
One is killed because he knows the details of a plan, even though he had no intention of revealing it; he had told Moloch, who simply didn't understand what he heard and would be no threat to its success even if he did understand it.
The other (not Moloch, by the way) is killed because he knows the plan and is going to reveal it. His murder may have been pointless, though, because he'd mailed his journal to the "New Frontiersman". Whether anyone of importance would believe what that Conspiracy Theorist tabloid reports is unclear, though.
This is essentially the reason that The Boys haven't been brutally butchered by ruthless 'superheroes' the Seven; the only reason they aren't dead is that they have even more damaging information on someone that The Seven fear more.
Fan Fic
Magnificent Kamen in Sailor Nothing allows no witness to escape to reveal the Masquerade. The fact that he's a Yamiko probably has something to do with that.
In Winter War, Hisagi kills Iemura for discovering that he is a Fake Defector, even though they were (theoretically) on the same side and Iemura was offering his support, because he didn't believe that Iemura could keep the secret. The guilt eventually drives the killer into Heroic BSOD to the point where his zanpakutou has to take over his body just to keep him alive.
In a movie about the presidential candidate Luis Donaldo Colosio's assassination in Tijuana called Colosio: El Asesinato, the main character is a police officer who works undercover and is asked by the president's former brother-in-law José Francisco Ruiz Massieu to investigate the murder. After a series of investigations, he concludes that the very same party killed Colosio. At the same time, someone is killing everyone involved with the case and murder, including the murderer and anyone who dares to seek the truth. As a result, the main character gets killed in the end as well as his pregnant wife, his partner, the police chief in Tijuana, and Ruiz Massieu, all because of this trope.
Snakes on a Plane: The catalytic event for the eponymous serpents upon the aircraft.
Subverted slightly in Adventures in Babysitting — one of the kids had taken a Playboy magazine that could get the crime boss put away, and the presumption the criminals made, of course, was that the kids had read it, plus the fact that they'd met at all meant they knew too much. The magazine was returned, and the crime boss' underling resigned, knocking him out along the way.
The Hong Kong action movie Sha Po Lang (known in the US as "Killzone") kicks off with the murder of a witness ordered by a Triad crimelord so that his testimony could not be given and the crimelord would be set free. This sets four cops against him, all with their own reasons for wanting to take him down.
In Lethal Weapon, Riggs is tortured by the bad guys to find out what he knows about their impending shipment, which is nothing.
In Serenity, the Operative is sent after River because she picked up the secret of Miranda, which has been buried for twelve years, from the heads of top members of the Alliance's Parliament who came to the Academy to see her. The nature of the secret in question means that Parliament wants more than anything to keep it buried, even if it means River must die.
This is a perfect example of the variant, since River was totally crazy, so she couldn't have communicated what she knew to anybody who could do anything about it. The Operative coming after her and the crew compelled them to find out the truth.
The Man With One Red Shoe has the scheming deputy head of the CIA trying to frame the actual head, so that he can have his job. The head knows this, and lets slip that someone who can foil this plan very simply will be arriving at the airport. He then sends his aide to meet any random person at the airport, so that the deputy and his men will follow them and try to find out what he knows. The aide picks a rather head-in-the-clouds musician, who's wearing a pair of mismatched shoes because of a practical joke.
It's pretty strongly implied that the "villain" of The Hunted was just acting in self defense, pursued by government assassins over his past black-ops experience.
Robert's justification for killing Leroy and Destiny in Mystery Team.
In Drive, a gangster uses a crew of low level criminals to rip off a Mafia boss with the intent to later kill them and take the money for himself. When the plan blows up in his face, he and his partner decide that everyone involved Knows Too Much and must die so the Mafia never finds out who was really responsible. Ironically, the only survivor of the crew actually does not know anything and was about to leave town.
Inverted in Diamonds Are Forever concerning the diamond smuggling ring. When one of your own passes you fake diamonds, he knows too much about the circumstances to die. This is demonstrated when Shady Tree rescues James Bond (who had assumed the identity of Peter Franks, a fellow diamond smuggler who Bond had killed) from a retort to question him about where he hid the real diamonds, only for Bond to use leverage against him to the tune of $50,000 ("You bring me the real money, and I'll bring you the real diamonds."), and then Zig Zagged when Albert R. Saxby reminds Wint and Kidd that they "didn't get the real diamonds. So we need Tree, alive." Wint and Kidd remark on how "that's most annoying" because they had already cut Tree down, as revealed when Bond shows up in his dressing room.
All over the place in The Fourth Protocol, about a Soviet plot to set off a nuclear bomb outside a US airbase in Britain and Make It Look Like An Accident. The implications of this plan being exposed are so serious that the KGB sleeper agent and the scientist who assembles the bomb are set up to be killed. The film takes this up to another level for dramatic purposes — it opens with traitor Kim Philby (who planned it) being shot, and an innocent bystander who walks in on an exchange of a smuggled component gets stabbed.
In American Beauty, Col. Fitts kills Lester to make sure he doesn't tell anyone that he's gay.
Literature
In Duumvirate, anyone getting too close to certain truths is most commonly fed misinformation, with options for inflicted insanity, death, and acquisition.
An interesting variant in Animorphs — the heroes consider this during the David Trilogy, when the eponymous character turns against them. It makes them pretty uncomfortable, though in the end, they decide on an even more extreme solution.
The Mote in God's Eye. After the three midshipmen crash land on Mote Prime, they wander around for a while and make a number of discoveries. The Motie decision makers decide to kill them to keep them from telling the other humans what they've found out. And it plays out the other way, too. The humans are about to be captured, but they decide that they know too much about human technology to allow themselves to be taken prisoner — so they kill themselves.
In Girlfriend In A Coma, Karen, the eponymous character, believes this was why she went into her coma in the first place — she caught a glimpse of the future, and it wasn't pleasant.
In Dan Abnett's Gaunt's Ghosts novel The Armour of Contempt, Ludd interrupts a No-Holds-Barred Beatdown intended to kill Merrt. The man ordering it assures him that the body would never be found here, and offers a bribe. Ludd says he could report it anyway, and the man admits he knows too much to live. Fortunately, Ludd had backup, even though Hark had been distracted for a minute before.
If you're a character in an Agatha Christie novel, don't ever try to blackmail a murderer if you want to live to the end of the novel.
Amberiotis of One, Two, Buckle My Shoe and Louise Bourget of Death On The Nile found this out the hard way.
Joyce Reynolds, the 13-year-old schoolgirl from "Hallowe'en Party" (1969). She tries to use her knowledge of a murder to her benefit. Instead, the murderers have her killed, drowned in an apple-bobbing tub. And what makes this worse is that it's not even her knowledge, really; she's overheard the child who really does know about the murder talk about it and has tried to pass it off as her own knowledge for attention.
Other would-be blackmailer victims include Miss Blanche from Cat Among the Pigeons and Leopold from Hallowe'en Party. Other characters who "knew too much" include Donald Ross from Lord Edgware Dies and Mrs Upward from Mrs McGinty's Dead — as well as the principal murder victims in Three Act Tragedy, The Murder Of Roger Ackroyd, Cards on the Table, Evil Under the Sun, and A Caribbean Mystery.
An example of the second variant comes in Why Didn't They Ask Evans?. Bobby Jones witnessed the death of a man who stumbled and fell off a cliff, then tells a woman claiming to be the man's sister that his last words were "Why didn't they ask Evans?" This is enough to convince the conspirators that Bobby has to be killed, which is in turn enough to convince Bobby that the man was murdered, "Evans" knows something important, and he should investigate...
An example that's neither a blackmailer nor the principle murder victim is Salome Otterbourne in Death On The Nile, who witnesses the murder of Louise Bourget (see above), goes to tell Poirot, and gets to invoke His Name Is... before being shot dead by the killer.
Syme in 1984 lauds the principles behind New Speak to Winston, explaining in great detail how it helps the Party perfect its control over the general populace. Despite being thoroughly loyal to the Party, he is eventually made an "unperson" due to this understanding. A fate Winston himself is able to see coming, predicting that Syme will be "Vaporized" several chapters before it actually happens.
Honor Harrington: Defied in Crown of Slaves. Some Solarians suggest offing Thandi Palane, but are warned away by the fact that she is connected to knowledgeable and hardened killers (read: VictorCachat, Anton Zilwicki, and Jeremy X) who would take bloody vengeance, compounding the fact that the person who knows too much is the one they would go to for assassinations in the first place.
Twenty Thousand Leagues Under the Sea: This is the reason why Aronnax, Conseil, and Ned Land will remain prisoners of the Nautilus and cannot come back to Civilization. Ever. (Captain Nemo lets them abandon the Nautilus and explore land, but is always in uncivilized shores). Captain Nemo explains:
"... You came to surprise a secret which no man in the world must penetrate — the secret of my whole existence. And you think that I am going to send you back to that world which must know me no more? Never! In retaining you, it is not you whom I guard — it is myself."
Pretty Little Liars: Hanna gets hit by a car when she recognizes A's number in Perfect.
Bran sees Jaime and Cersei having sex and is then pushed out of a tower for it. During the ensuing coma, he's attacked by an assassin. We later learn that the assassination attempt is a subversion — he was attacked because Joffrey wanted his father's approval.
Jon Arryn learned about Jaime and Cersei as well, and promptly died under suspicious circumstances. Interestingly, this is also a subversion — he was killed because Petyr felt like sowing some discord.
Petyr also has a habit of doing this, murdering Ser Dontos, whom he used as a catspaw in order to smuggle Sansa Stark out of Kings Landing, and his accomplice in Jon Arryn's murder, Lysa Tully.
Undoubtedly inspired by the assassination of Von Papen (see Real Life), Ian Fleming had two SMERSH assassins fall victim to this trick in his first James Bond novel Casino Royale.
The Emperors Soul; Shai is Genre Savvy enough to know she's going to be killed after she is no longer useful to her captors in part because she could blackmail them with the fact that the Emperor was almost killed and they resorted to forbidden magic to fix and conceal this. She doesn't actually want to blackmail them, but they won't believe that.
A constant danger for the protagonists in the Safehold series. Their knowledge of Safehold's status as a Lost Colony in Medieval Stasis would be blasphemous to the average person, so they have to be insanely cautious about who they let in on the knowledge. Those people are also told, if they don't work it out themselves, that if there's any danger of betrayal they'll be forced to take measures.
A specific instance occurs in the third book, By Heresies Distressed when an attempted assassination is foiled by the arrival of Merlin, who is supposed to be hundreds of miles away in a whole other country. Merlin then proceeds to kill every enemy there to prevent anyone from talking about his arrival.
River Tam from Firefly. We don't find out what it is that she knows until The MovieSerenity (see Film), but we know her handlers paraded her in front of many top-level politics and military leaders... without realizing that she is a mind reader, so the government definitely considers it too much. So much so that two government agents killed an entire building full of people for the crime of having heard her talk gibberish while she was under arrest.
Dr. Culix: The boy on the bike? He's seen too much. Get him!
Dollhouse: Rather than being "terminated" (one way or another), a "handler" who has been exposed for raping his assigned "doll" is offered a task more suited to his evident personality: eliminate a woman who has inadvertently learned too much about the Dollhouse from an FBI agent investigating the organization. Only it's subverted when it's revealed that the target is a doll herself, one with a "killer" sleeper personality, and he's actually being sent to his death as part of a larger scheme.
UFO. A continuing duty of SHADO (Supreme Headquarters Alien Defence Organisation) is to suppress information on UFO incidents to prevent worldwide panic over the knowledge that beings from another world are harvesting human organs. Their methods include intimidation (ranging from beatings to government pressure on the employers of the witness), conscription into SHADO, amnesia pills, and even murder.
In the Mission: Impossible episode "The Town", Phelps stumbles across a town of Russian spies and discovers the fact. They intend to make his death look like natural causes. Fortunately, he has four brilliant colleagues.
Implied in an episode after a teenage girl breaks into the Warehouse to coerce Artie to help her save her brother (as in, she knows about the Warehouse and now we have to do something about it). They seem like the kind of folks who consider death to be a (albeit viable) last resort, though.
Something very similar happens in the first episode of Season 3 — the warehouse agents run into ATF agent Steve Jinks on a mission, and their attempts to explain the situation away don't work because he's a Living Lie Detector. Since he's in on the secret and already a federal agent, he gets recruited.
In Battlestar Galactica, this is basically why Tory kills Cally, who has learned that Tory, Cally's own husband Galen, and Colonel Tigh are actually Cyclons. Important to note that Galen is not in on this, and kills Tory for it when he finds out.
NCIS: The episode "Witness" was based on this motive. It included a medium Tear Jerker, as McGee narrowly failed to save the girl, who he'd hit it off with just the day before.
Several (main and minor) characters on The Wire have been killed off because of this trope. Whether they do or don't know too much, the results tend to be tragic.
Stringer Bell: "But there go a life that had to be snatched, Avon(...) Twenty years above his fucking head. He'd flip, man! They got you, me, and Brianna! No fucking way, man! Hell, no! Now, I know you family, you loved that nigga, but you wanna talk that 'Blood is thicker than water' bullshit, you take that shit somewhere else, nigga! That motherfucker would've taken down the whole fucking show, starting with you, killer!"
Someone from Pretty Little Liars is in great danger in the Summer Finale of the show. A even sends a text to Emily which says 'She knew too much.'
In The X-Files, Mulder knows entirely too much right from the start, and then gathers more information along the way. When attempts to get him to come to the dark side fail, the Syndicate try to destroy him instead. Since Mulder is more valuable to them alive than dead, they tend to do terrible things to people he cares about. Arguably the worst was giving Scully an inoperable tumor that spelled a slow and painful death for a season (until a cure is found by Mulder's snooping ways, of course).
An interesting variant occurs with John in Farscape because, while he knows that the Ancients put wormhole knowledge in his head, he isn't able to unlock that information himself for a few seasons. This leads to Scorpius chasing him across the universe and mind-probing him to figure out information that John is still trying to discover himself.
Part of the reason why the teacher in "True Calling" was murdered was because she had proof that another teacher was using drugs and forcing a student to bring them to him. When she called him out on it, he simply snapped and chased her to the streets before finally killing her.
The victim in "Blood On The Tracks", who wanted to confess to the cops about a crime he and several of his friends had been involved in that left another friend dead. With only one other person in the group agreeing with him, two of the others conspired to kill them both in order to ensure their silence.
In the episode "Democracy", five people who had evidence of a voting fraud conspiracy "accidentally" die before they can reveal the fraud. Unfortunately for the conspiracy, one of them managed to get the list of their names to Charlie shortly before being killed, who determines that the odds of five random people dying in a given two week period are approximately a bajillion to one. Don orders a second autopsy on the one who gave Charlie the list, which confirms that she was murdered, and the attempt to tie up a few loose ends has now attracted the attention of the Federal Bureau of Investigation.
In "Disturbed", the episode after the credits opens with a murdered mailman who was last seen alive outside of a home where a woman was killed. He waves at the repairman entering the house. The repairman is a serial killer and he kills both his intended victim in the house and the mailman who passed by three hours ahead of schedule and saw the repairman enter the house. Nearly an aversion, since the mailman only possibly knew something.
This is why Jonah Gabriel and his partner were shot before the events of the series, in that they came too close to discovering the true extent of police involvement in Counterpoint.
Ross McGovern is killed for investigating the above incident too closely, because his investigations could have led to what Gabriel and Delaney discovered.
Even invoked in episode 6, when Glickman tells Gabriel to confront Commander Penney with the news that he knows about Counterpoint. They're counting on Penney then sending Gatehouse after Gabriel, because they want to lure Gatehouse into a trap.
In Season 1, Nina kills Teri because she overheard information that would have compromised her escape from CTU, though there are also other reasons considering both women's history with Jack.
In Season 2, Marie kills Reza just as he is about to clear his own name and find out who moved the funds for Syed Ali.
In Season 3, the reason why the Big Bad forces CTU to execute Ryan Chappelle.
In Season 7, the villains kill Dubaku after he is captured because he has information on them that he is using as blackmail to prevent being subject to You Have Failed Me and You Have Outlived Your Usefulness.
Parodied in The Black Adder. Edmund desperately tries to call off his plan to assassinate Dougal McAngus, who may have evidence proving his brother is an illegitimate child. When he tries to tell Percy that "He knows too much!" Percy, momentarily forgetting just why they are killing him (Dougal had stolen three titles from him), menacingly replies "That is why he must die!"
Rare (anti?)heroic example in Merlin in the series 4 finale. Merlin knows that Agravaine cannot be allowed to reveal to Morgana that he's Emrys, and so kills him off. Alright, he waited until the guy pulled a knife to actually do it, but it's heavily implied that he wasn't going to leave alive either way.
In the JAG episode "Someone to Watch over Annie", the ten year old son of Harm's Romantic False Lead by accident gets to see a murder at Andrews Air Force Base while slipping away from his school class when on a tour. It turns out the bad guys are weapons smugglers who don't shy away from trying to killing witnesses.
Ellery Queen: The reason that the title character in "The Adventure of Colonel Nivin's Memoirs" was killed.
The Home Guard Auxilary Units were stay-behind units trained in the event of a German invasion of Britain during World War II. Each patrol consisted of local men recommended by their Chief Constable. They had secret orders only to be opened in the event of an invasion. One man opened his anyway and found to his shock that his first mission was to assassinate the Chief Constable, as he was the only man who knew the identity of the unit members.
In a joke, a KGB agent is questioned by his superior: "How much is 2 plus 2?" - "Four." - "And how much is 3 times 5?" - "Fifteen." - "And how much is the square root of 9?" - "Three." At the moment, the superior draws his gun and shoots the agent. "Comrades, I had to neutralize him, he knew too much!"
Videogames
Max Payne: It turns out that the junkies who killed the title character's wife and baby girl were sent by Nicole Horne after a dossier about Horne's project found its way to the wife's desk and Horne decided to silence her by "any means necessary." Tragically, Max's wife was trying to tell him about this ("a strange memo, something about Vikings"), but he ignored it. In the third game, Da Silva is Genre Savvy enough to know this will happen to him if he digs too deep, so he points the much more combat-competent Max in the right direction instead.
The protagonist in Arcanum is an example of the second type: all he knows is a gnome gave him a ring and told him to "Find the boy," but due to the conspiracy's repeated attempts to murder you, you eventually figure out their incredibly convoluted plans.
Fire Emblem 8: Some characters know well what the hell is going on in Grado (the Cleric Natasha whose mentor, a well-respected high priest, was killed for discovering that the Emperor was dead and revived as an Artificial Human and the Shaman Knoll, Lyon's second-hand in the project to revive said Emperor). What does the Empire do? They frame both of them as traitors; Natasha has to flee from her homeland and Knoll is imprisoned and slated for execution. Subverted because, in-game, both survive and join Eirika's (in Natasha's case) or Ephraim's (in Knoll's) troupes.
Modern Warfare 2: After sending all of the TF 141 to both of Makarov's safehouses, General Shepherd betrays them all because he suspected that they knew about his plans to make the U.S. the most powerful country in the world.
Hawke and Lash from Advance Wars Dual Strike are attacked when Hawke figures out the Big Bad's true motive for starting a war. Of course, the allied nations save them and they all fight the Big Bad together. Hm. Maybe the Big Bad was planning on getting rid of Hawke and Lash anyways, since Lash is caught up in Hawke's problem for almost no reason.note A few missions prior, Kindle outright states that they don't think particularly highly of Hawke OR Lash, and basically implies that they never really had much of a need for either of them. The aforementioned overhearing of plans basically just gives them a convenient excuse to actually do something about it.
In Halo 3: ODST, an NMPD officer on Kinsler's payroll is instructed to make sure Dr. Endesha is dead, and to eliminate any witnesses. Unfortunately for him, you are a witness. Let's see: a corrupt cop versus an elite UNSC shock trooper. Guess who wins...
In the Hitman series, this is pretty much the only reason 47 will kill an innocent (in canon), as his existence is already very volatile and he cannot afford letting anyone (other than a select few) know about him.
In Half-Life, the Hazardous Environment Combat Unit are sent in to combat the aliens and kill all the scientists and security guards. Later on, Black Ops is sent in to kill the HECU survivors. Finally, the G-Man nukes the entire base at the end.
This sets up the plot of Robinsons Requiem: you and several other Robinsons have discovered that AWE banishes or kills any agents who have potentially contracted alien diseases or virii while exploring unknown planets. Unfortunately for you, AWE finds out that you've learned this Awful Truth and decides to send all of you to the Death World Zarathustra.
Before the Rank 8 fight in No More Heroes, Travis interrupts Shinobu's presentation before her class. She sighs, tells him to meet her outside, then draws her katana as he leaves. When they meet up, she's complaining about how hard it is to lead two lives... at which point Travis makes the connection: "You killed them, didn't you?"
Nine Hours Nine Persons Nine Doors: Ace's motivation for killing Clover, Snake, Musashidou, Nijisaki, and the Ninth Man are them knowing about his own past. Though, it was also to obtain his '9' bracelet which would put him at an advantage.
In Sonny, this is the reason the ZPCI board the White November in the first game and destroy the village in the second game. In the former, Sonny kills the soldiers after they take out Louis, escaping on a lifeboat after recieving the MacGuffin. In the latter, Sonny and his crew fight the leader of the troops briefly before fleeing on an old train.
In Fallout New Vegas, if you convince Veronica to leave the Brotherhood of Steel for the Followers of the Apocalypse in her personal quest, several fanatical Paladins will massacre a Followers outpost and then try to go after Veronica since they see her as a heretic (which to be fair, she is) who might end up spreading knowledge about the Brotherhood that they're devoted to keeping secret. After fighting them off, Veronica is left horrendously traumatized, but she's sure that she made the right choice in leaving the Brotherhood.
L.A. Noire: Dirty Cop Roy Earle sells out By-the-Book Cop Cole Phelps by revealing his affair with Elsa Litchmann as he knows that if he keeps on moving the ranks, the Suburban Redevelopment Fund and its conspiracy will be exposed. However, it only encourages Cole to investigate Elysian Fields, much to Roy's dismay.
In Oddworld: Stranger's Wrath, after being captured and revealed to be a Steef, Stranger immediately procceds to kill D. Caste Raider and his gang, using only his bare hands.
BlazBlue: Continuum Shift: This, coupled with Protectorate issues, turns out to be the big motivation behind Captain Hazama's attempt on the life of Makoto Nanaya in Jin's story. Makoto turns out to be big friends with Noel Vermillion and Tsubaki Yayoi, both of whom had big roles to play in Hazama's plan, so getting her as far away from them (like, say, Ikaruga) is high on his priority list. Unfortunately for him, she winds up finding out that Noel Vermillion is a Murakumo unit, an artificially created being with the purpose of using the Eye of the Azure to destroy the Master Unit. As if that wasn't enough, she winds up falling into an alternate timeline where Noel didn't exist and Tsubaki wound up dead, which ironically is fuel Hazama used to facilitate Tsubaki's Face Heel Turn, and the first thing she does is block an attempt on Jin's life by Hazama. The knowledge of Murakumo Noel is dangerous enough, but the possibility that the events Makoto witnessed could abort or reverse Tsubaki's change in alignment mean that, to him, it's not worth chancing her staying alive.
In Splinter Cell Conviction while Sam is interrogating Galliard, a man working for a mysterious group named Megiddo, he learns about Megiddo controlling multiple locations, but before he has a chance to obtain more information, Galliard is assassinated by a shooter to protect Megiddo's identity. The shooter responsible for assassinating him later dies in a car bomb explosion, assumed to be arranged by Megiddo, so the shooter can't reveal Megiddo's identity, if he is ever caught by Fisher.
The Walking Dead Episode 1 a good reason to not choose Carley to live, especially if playing Lee as a paranoid jerk ass.. Episode 2 Larry in episode 2 also falls into a weird inversion of the trope, as he threatens to tell everyone and he's being the antagonistic jerk ass, while you may play Lee to be a man of a gentle spirit.
In Mass Effect 1, on Noveria the volus, Han Olar, asks an asari commando about to kill him if he'll get a "you know too much speech?" Fortunately, Shepard saves Olar before the commando can kill him.
In Prototypethis trope ends up being the cause of the whole plot. After the real Alex Mercer was hired to make a virus ten times deadlier, his employers who were under investigation, decided to permanently silence all loose ends. Just as their assassins caught up with him, the real Mercer spitefully unleashed the virus to take the whole world with him just before he was gunned down.
The Nostalgia Critic: In his review of Full House, the Olsen Twins try and kill the Critic when he attempts to tell the world his new knowledge that they're evil.
Western Animation
Parodied in an episode of Jackie Chan Adventures, appropriately titled "The Chan Who Knew Too Much". A cabal of wizards repeatedly states that Jackie "knows too much" when he finds out any of the cabal's secrets... their name, their plans for Stonehenge, or even the location of the bathrooms in their secret lair. ("He's privy to our privies!") To make it even better, Jackie really didn't know anything at all about when he first accidentally dropped in on all of them — for all he knew, they could have just been wannabe satanists or something. They pretty much told Jackie everything themselves, e.g showing him that they knew magic by trying to kill him with it.
Gloriously lampshaded when Jade claims to know their magic words, but can't cast their spells. The man gloats that she 'knows nothing' and Jackie cries out, "That's what I've been trying to tell you!"
In Batman Beyond: Said in its entirety by Inque about Terry McGinnis. It is also motive behind Derek Powers's murder of Terry's father, which prompted Terry to become Batman.
Homer followed his coworkers to the Stonecutters' headquarters. He gets inside by falling through the skylight and is instantly surrounded. They declare that he has seen to much and must pay "the ultimate penalty". So they toss him out the front door.
In "New Kids on the Bleech", after Lisa discovers the Navy's conspiracy to recruit people via Subliminal Seduction, Lt. Smash says ominously "Well, know that you know, I'm afraid I can't let you leave." But Lisa already left.
Spoofed in the Looney Tunes short "Bugs and Thugs", where gangster Rocky decides that Bugs "knows too much" when he, among other things, correctly identifies Carson City as the capital of the state of Nevada.
Lampshaded in Scooby Doo And The Alien Invaders, where the villains say this as they prepare to kill Fred, Velma, and Daphne. Fred grumbles "That's always our problem..." in response.
In Futurama, a robotic toilet the crew is throwing away offers them "Happy Poopy Time" if they spare it. Fry simply says "You know too much."
An episode of The Venture Brothers has Dr. Orpheus about to reveal the truth of why The Monarch was arrested. As he's about to spill the beans, Phantom Limb calls in the Strangers to freeze everyone in ice and administer either memory wipes or hypnotic suggestions to the room, thereby making Orpheus declare that Monarch is guilty of crimes he didn't commit.
Nicodemus inverts this in a discussion with Mrs. Frisby in The Secret of NIMH; instead of using it as an excuse to die, he utilizes this fact as a reason to survive by leaving their colony. "My child, we can no longer live as rats... we know too much."
In 1942, the Russians arranged an assassination of Von Papen, the German ambassador to Turkey. They gave the would-be assassin a package which they said was a smoke bomb to cover his escape. The assassin decided that attacking under cover of the smoke was a better plan and so set it off early: it exploded killing the assassin but leaving von Papen unharmed except for the gore splattered on his suit. The Russians of course intended him to do this after shooting the target, thus preventing him from telling who was the guilty party.
This is the reason why, in a lot of urban neighborhoods, people won't talk to the police about crimes they saw, and is also the basis of the "snitches get stitches" saying.
Not at all helpful are the anti-"tattle tale" rules that are in most schools, teaching children the wonderful lesson to never bring a wrong doing to the proper authorities no matter what they see.
The scene in Goodfellas when Robert DeNiro's character systemically kills all of the participants in the Lufthansa Heist at JFK was an accurate representation of real life in which gangster James Burke did just that.
In Polish Resistance member Jan Karski's autobiography, he tells the story of being rescued from the Gestapo, and being told by his rescuers shortly after escape "We were given two orders. The first one was to save you at any price; the other was to shoot you in case we did not succeed."
