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The villain has betrayed his team, or his country, or the entire human race. Now, he's been defeated... but there's just one complication. If the traitor's guilt is revealed, there will be consequences -- perhaps his friends will seek revenge, or perhaps good people will also be dragged down, or perhaps the people's confidence in the whole system will be shaken.
One solution: cover the whole thing up. Perhaps the traitor can be punished discreetly or persuaded to eliminate himself rather than be disgraced, or perhaps the heroes just have to suck it up and accept that he's untouchable, at least for now. Often, the question is rendered moot, as the villain's defeat lead naturally to his death. In such cases, it is not uncommon for them to be reported as having died a hero, often with the implication that they were killed stopping the very evil they had, in reality, unleashed. (Note that if the character really did die stopping it, it is Redemption Equals Death, and while the heroes are likely to soften or hide his crimes, the motive will be different.)
Note this is also a useful plot device so "fictional" stories can pretend to have really happened, it was just "covered up".
Compare Never Speak Ill of the Dead.
Anime and Manga
- Ghost in the Shell: used frequently. 
- The second Death Note movie ends with a coverup. Light's family is led to believe that he died trying to stop Kira.
- Inverted with the end of Code Geass. The few people who were in on it/worked it out are covering up the fact that rather than a Complete Monster, Lelouch was actually creating world peace.
- And evidently played straight several episodes prior when the Black Knights betray Lelouch and attempt to cover it up.
- Inverted in One Piece. After the supposedly-government-allied pirate Crocodile was exposed, the World Government didn't bother to cover it up. They did, however, cover up the fact that another pirate crew resolved the issue by giving credit to a marine who had conveniently been tailing the heroes, because a rogue pirate beating a government-aligned pirate, traitor or not, would be a source of deep embarrassment.
- Played straight with Gecko Moria later on, possibly because his actions weren't quite as serious a betrayal as Crocodile's were.
- At the end of Fullmetal Alchemist, the Fuhrer was credited as having been a major force against the generals supposedly orchestrating the "alchemic experiment". In fact, he had been one of the driving forces for its completion and had brought the generals into the scheme. However, he was far too popular with the people and the evidence against him was lacking.
- Patlabor: The Movie: The true source of the malfunctioning labors is whitewashed so the Japanese government will not be disgraced. The corporation that built the faulty labor robots has given the government massive support and money.
- In Magical Girl Lyrical Nanoha A's, Admiral Graham's plan to seal the Book of Darkness away with Hayate is largely overlooked outside of the upper echelons of the TSAB, and he merely resigns, only being officially accused of breaking into Bureau systems and interfering with the investigation. In Striker S Sound Stage X it is mentioned that many parts of the Jail Scaglietti incident are classified, presumably including Jail's origins and connection to the Bureau, which had created him.
- Un-Go - Only reason why is Shinjuurou called "Defeated Detective"
- This happened in Naruto with the planned coup by the Uchiha clan. Itachi killed them without exposing their treachery in order to keep their reputation from being tarnished, and to give Sasuke a target for his anger. It... didn't work out so well.
- Watchmen, even if it is a little more complicated...
- Teen Titans: Even though she was The Mole, the Titans gave Terra a hero's funeral and kept her betrayal of the team a secret after her death.
- The Invisible Man's decision to sell out humanity to aliens was covered up in The League of Extraordinary Gentlemen. "covered up" means Hyde raped him to death.
- In The Rock, a threat by a much-decorated Marine General to use chemical weapons against San Francisco was covered up, helped by the fact that the General threatened to launch the gas if the FBI alerted the media.
- In xXx2, the Secretary of Defence and a General plotted to overthrow the government and kill the President.
- The Blue Max: General Count von Klugermann whitewashes or covers-ups Bruno Stachel's crimes because Germany needs a war hero since revolution is becoming more likely. Otto Heidemann is outraged at these cover-ups, but agrees to stay silent since the military and political leadership agree with Klugermann. Heidemann knows that very few officers will take his side if confronted with political pressure. , 
- Telefon: Grigori Bortsov is sent to kill Nikolai Dalchimsky so the KGB will not have to reveal the fact it failed to shut down a network of sleeper agents. 
- Assassination: The mastermind behind the assassination attempts on the First Lady is a high-ranking White House official. His death is reported as a medical condition to avoid a scandal. 
- The ending of the Jet Li movie Hero indicates that the would-be assassin was killed as a traitor, but buried as a hero.
- L.A. Confidential: once in the movie, twice in the book. Ed has to cover up Dudley's identity as the Big Bad, but his father did it back in the day by helping Dieterling frame Atherton for the murders his son committed.
- The ending of The Dark Knight. With Harvey Dent/Two-Face dead on the ground, Batman willingly allows the madman's crimes to be blamed on himself so Gotham won't lose an inspirational example.
- At the end of Tomorrow Never Dies, M orders the coverup of the death of media baron Elliot Carver, a bit of karmic irony considering his mass-media manipulation based plan, and has it reported as him committing suicide on his yacht. (What had actually happened is that Bond killed Carver with his giant drill after foiling his attempt at War for Fun and Profit.)
- By the end of Iron Man, the government has concocted a story to cover up most of the final battle, including that Treacherous Advisor Obidiah Stane disappeared in a plane crash whose wreckage was never found. It's doubtful that their Treachery Cover-Up story ever got a chance to play out, though, since Tony completely breaks their script at the press conference and outs himself as Iron Man.
- In the film The Art Of War, Wesley Snipes's character is set up for the murder of the Chinese ambassador in the middle of US-China trade talks. After finding out that a congresswoman involved in the talks is the mastermind, he reveals the truth to the Triads. She is murdered by a member of the Triads and is lauded as a hero, who gave her life to ensure the success of US-China trade relations. Of course, this also serves as a big "fuck you" to her, as she was secretly working on sabotaging the talks.
- The Man Who Shot Liberty Valance ended on an inversion. The reporters chose to cover up the fact the protagonist, a famous Senator and Vice-Presidential prospect, confessed that he did not kill the eponymous outlaw which made him a legendary figure.
- In Seven Days in May, the President decided that what had happened must never become public knowledge, in order to preserve the idea that a military coup against the United States government is simply unthinkable.
- John Ringo: used in the Paladin of Shadows Series. Information on a rape/sex slave ring is entrusted to the Kildar since public exposure will topple several governments.
- James Bond
- The death of Le Chiffre in Casino Royale is published as a suicide to focus attention on his trade union. Destroying the communist supported labor union and the French communist party is more important than confronting the Soviet Union. The Soviet assassin who kills Le Chiffre says that the publication of his gambling and embezzlement has undermined communist prestige in the NATO nations.
- When Drax's habit of cheating at cards is found out in Moonraker, James Bond is put against him to teach him a lesson instead of causing a scandal out of it, as it could jeopardize the Moonraker project.
- Clive Cussler: Many of the villains have massive influence and wealth; the Vigilante Man man only stops them.
- U.S.S. Seawolf: The president of the United States prevents his son, Linus Clark from being court martialed for negligence. Despite the official story, many in the military know the truth and lose all trust in the current administration. 
- Tom Clancy
- The Hunt for Red October: The defection of the Red October is covered up so the American military maintains a strategic advantage.
- The Cardinal Of The Kremlin: The defection of Nikolay Borissovich Gerasimov is covered up by the American and Soviet governments to avoid political problems with an arms control treaty. Several Soviet characters state that the court marital of 'Cardinal' might not be possible since he is war hero.
- Prince Serg in Lois McMaster Bujold's Shards of Honor.
- In H. Beam Piper's story "The Mercenaries", the leader of a freelance scientific research team executes a traitor in their midst. The death is passed off as a suicide to protect the team (and incidentally assures that the deceased will be remembered for his genuine scientific contributions). It's understood that the real story will be read between the lines... thereby protecting the team's reputation for trustworthiness and ability to take out its own trash.
- David Weber frequently uses this trope.
- Path of the Fury (In Fury Born): Alicia Dierdre De Vries of the Imperial Cadre “drop commando” unit resigns after Wadislaw Watts is allowed to escape a court martial in exchange for his assistance in destroying a Rishathan espionage network. Nobody in the imperial government wants a court martial since it will humiliate the Cadre. Later averted when terran emperor tells De Vries that: Fleet Admiral Subrahmanyan Treadwell, Vice Admiral Amos Brinkman, and the rest of the secessionist conspirators will be court martialed.
- Honor Harrington
- Many of the genetic slavery incidents are ignored or whitewashed due to political considerations. The high-level criminals escape while the low-level criminals are convicted.
- Several of the people in the High Ridge government escape a trial since the Grantville government cannot afford to risk accusations of a political vendetta. , 
- The North Hollow files are destroyed rather than published since publication would result in political chaos and 33% of the information is a forgery.
- Pavel Young avoids the death penalty due to political influence.
- After Arnold Giancola and Yves Grosclaude are killed in air car accidents, Eloise Pritchart refuses to cover up the public revelation of diplomatic forgery in the long term. Nevertheless, she orders a short-term cover up until reliable evidence can be obtained. The primary problems are obtaining legal evidence and avoiding accusations of the government arranging convenient accidents for the main suspects.
- After Operation Hassan causes chaos in the Manticorian and Grayson governments, only the Masadan and Grayson ( Samuel Mueller) conspirators are convicted. Haven is not accused because the only credible witness, Randal Donizetti, is killed to ensure secrecy.
- Samuel Mueller is not held responsible for his collaboration with William Allen Hillman Fitzclarence because of weak evidence. Later he becomes the leader of the political opposition and any accusation against him would only allow Mueller to accuse the Grayson government of a political vendetta.
- After it is revealed that Havenite agents assassinated Roger III Winton, Elizabeth Adrienne Samantha Annette Winton is forced to cover up the assassination since a trial would result in massive witch-hunts, an anti-Haven “Red Scare” or a declaration of war. One of the conspirators has standards and confesses her role. She participated out of well-intentioned idealism; she is not a traitor to the state.
- At the end of Dan Abnett's Warhammer 40000 Gaunt's Ghosts novel Blood Pact, Gaunt is assured that Rime's death at Rawne's hands is being passed off as an honorable death in battle. He's glad not to have the Inquisition breathing down his neck for killing an Inquisitor.
- The final fate of the Camerlengo in Angels and Demons.
- In Star Trek: Mere Anarchy, the Capital City of planet Mestiko is named vosTraal in honour of a native leader, Traal. According to the history books, Traal sacrificed himself to save the planet. What those books leave out is that this was in fact a Heel Face Turn and he was originally a traitor, allied with the Klingons. Only when he realized that the Klingons cared nothing for his people and would gladly sacrifice his tribe did he turn on them. In order to keep the troubled planet united, this is obscured from history in favour of an entirely heroic portrait.
- Twisted a bit in the Elenium. The person who's been blackmailed into trying to murder Sparhawk for half a book takes poison before confessing, and expects to be outed as a traitor. Instead, Sparhawk and Kurik arrange matters so everyone will think one of the besieging army shot him.
- Sea Quest DSV
- “Games”: Rubin Zellar says he was sentenced to a remote prison since none of his clients wanted to be exposed for collaborating with him. It is later discovered that at least 91% of the evidence against him was destroyed; the remaining was labeled top-secret.
- “Good Soldiers”: the SeaQuest is sent to destroy evidence of illegal medical experiments conducted by the  United Earth Oceans Organization. In addition to the fact that the enemies of the UEO would gain a propaganda victory; the people involved in the illegal experiments are seen as heroes and or have become high ranking members of the organization.
- Star Trek
- Section 31 is able to remain hidden since those in the United Federation of Planets either: do not believe Section 31 exists, lack evidence, are working for them, or realize that exposure will undermine the government. Those that do oppose them, such as the Kirk cabal, lack the power and evidence to do anything useful. 
- The  Tezwa incident and  Min Zife’s involvement are covered up to avoid war.
- In Star Trek the Next Generation, Worf's father is made a scapegoat for treason actually committed by Duras' father, because the Klingon government does not dare offend Duras' powerful family.
- Babylon 5
- Jha’dur states she will escape a trial since none of the major intergalactic nation-states wants her to expose their collaboration with the Dilgar or they want her immortality drug. , 
- In several episodes, the Drazi government refuses to help since they do not want to be humiliated or lose an advantage. , , 
- Space: Above and Beyond: The Chig War starts due to political-industrial deceptions. Nevertheless, there is no proof other than rumors.
- In the Firefly episode "Ariel," Jayne, about to be Thrown Out the Airlock by Mal for betraying Simon and River to the Alliance, pleads with Mal -- not for his life (he already tried that and failed), but for Mal to make up a story to conceal his guilt. This convinced Mal to give him another chance.
Jayne: What are you gonna tell the others?
Mal: About what?
Jayne: About why I'm dead.
Mal: Haven't much thought about that.
Jayne: Make something up. Don't tell 'em what I did.
- Unfortunately for Jayne, the cover-up itself doesn't last long, at least in regards to the ones he betrayed. Those darned Psychic Powers....
- Life On Mars. In one episode a drug dealer dies after rough handling by a CID officer, and even the victim's mother doesn't want an inquiry. Sam Tyler uncovers a tape of the incident and gives it to apparently by-the-book Superintendent Rathbone, only to see Rathbone destroy the tape in front of him as "the matter has been handled internally" (with the guilty officer's demotion) and he's not going to bring the police department "crashing down" over this matter. Tyler says bitterly that men like Rathbone should be "surgically removed" -- of course, coming from 2006, Tyler knows all too well that corruption can't be eliminated without destroying public faith in the police.
- In Doctor Who, when Time Lord Presidential candidate Chancellor Goth was revealed to have assassinated the President to further the Master's scheme, Borusa ordered that his You Have Failed Me death be explained as dying heroically fighting the Master.
- Percy from the 2010 show Nikita uses this to his advantage. The reason Government officials have not shut down Percy and Division long ago is that Percy has numerous "black boxes" (black portable hard drives) that contain all of the government's dirty secrets on them, hidden, and they can be activated to be shown to the public if Percy so chooses, and if he is killed, which is why he is untouchable and is the reason why Nikita can't just easily infiltrate and kill him
- In Fringe, John Scott's betrayal is covered up to prevent scandal touching the FBI. Which is rather a good thing as it later transpires that he wasn't a traitor at all, but deep undercover.
- Team Castle agrees to cover up Captain Montgomery's shameful past because of his years spent as The Atoner. Plus, he's dead.
- On Sons of Anarchy SAMCRO does this all the time. They need to present an unified front to both their allies and enemies so all disputes and betrayals are handled internally and a cover story is presented to the outside world. From the beginning a major plot element is the fact that if the truth about John Teller's death ever came out, it would be impossible to cover up and it would destroy the club.
- In the show's backstory, the Sons were once involved in a bloody gang war with the Mayans. One of their associates betrayed them and was killed for it. He was buried in an unmarked grave with some dead Mayans and his family was told that he was abducted and murdered by the Mayans. The truth only comes out when the bodies are discovered years later.
- When two prominent members of the Belfast chapter betray SAMCRO to the IRA, they are both killed. One of them is publicly denounced as a traitor but the other is given a hero's funeral and his part in the betrayal covered up.
- The Horus Heresy of Warhammer 40000 is unknown to the vast majority of the Imperium's population-including the fact that fully half of the Adeptus Astartes Legions went rogue and joined Chaos.
- That depends on the edition and writer, mind.
- Additionally, one particular Legion is keeping further the secret that half their number turned right after the Heresy.
- And it's not made certain which half...
- Happens in Suikoden I; Sanchez is exposed at a vital point for the rebellion, and the game's strategist orders that his treachery be concealed (with the rest of the cast forcing him to play his role) because the knowledge of a high-ranking traitor would undermine confidence. Even after the game's end, he is eventually secretly 'pardoned' (but exiled to a single city and never genuinely forgiven) because the revelation that one of the heroes of the revolution was a traitor would be dangerous for the stability of the new republic. However, the fact that he's a high ranking character with no Star of Destiny who constantly offers the main character alcohol should have been a give away if you were paying attention from the beginning.
- Happens at one part during Metal Gear Solid 3 Snake Eater, and staying true to the series premise, is much more twisted than usual: (extra big spoiler) to get a spy close to Big Bad Volgin, the Boss is given the mission to pose as a defector and gaining Volgins trust by bringing him two "stolen" nuclear bombs as a gift. But apparently nobody had thought that Volgin would use them against a KGB facility. To cover up that the US government practically gave the nukes to Volgin, Naked Snake is given the mission to kill her, so that nobody will ever suspect that her defection was fake. Being loyal to her country to the end, she accepts death by the hands of her former pupil and best friend. Snake learns about it only after he had killed her.
- In Tales of Symphonia Dawn of the New World, the heroes of the first game keep the truth about Mithos, Martel, and the Church secret, because frankly, the world doesn't need that kind of disillusionment.
- In the original game, Lloyd and the party remain quiet about Governor General Dorr collaborating with the Desians by enabling the people of Palmacosta to be taken to the ranch so that he can get his wife turned back to normal, so that the city can get through the crisis while trusting its leadership. Lloyd gets a significant across-the-board drop in the party's Relationship Values if you decide to say that you're not OK with this. Palmacosta ultimately gets destroyed at the end of Disc One.
- In Sacrifice, if you side with James, the hero covers up the fact that the prophet Mithras was the omnicidical demon Marduk in another form..
- Happens a lot in the Resident Evil universe post destruction of raccoon city. Mostly due to goverments and "big pharma" covering their asses after the umbrella disaster.
- In The Order of the Stick, the circumstances of Lord Shojo's death at Miko's hands are concealed from the people of Azure City in order to prevent morale from being more seriously damaged than it already is. This may well contribute to the We ARE Struggling Together! situation leter on.
- Donovan Deegan hid from his wife the fact that their friend Karnak had tried to Murder the Hypotenuse (namely, him) just before his Heroic Sacrifice.
- Inverted very early on in Girl Genius. Silas Merlot, in a fit of temper, reveals that Dr. Beetle has been hiding a Hive Engine (a piece of poorly-understood technology containing highly dangerous organisms which can turn their victims into The Renfield) for his own research, which Baron Wulfenbach has expressly forbidden, because of the danger. Fearing the Baron's harsh punishments, Beetle panics and tries to bomb the Baron, but the gambit backfires and obliterates Beetle instead. Merlot gets about halfway through the first sentence of trying to conspire with the Baron to hide Beetle's death when the Baron declares his undying hatred for traitors, and he holds Merlot and his theatrics directly responsible for what just happened. He then declares that Merlot's punishment is that he is now in charge of Beetleburg...after the much-beloved Dr. Beetle is given a hero's funeral and the full details of his death, Merlot's involvement included, have been released to the public.
- Done in The Simpsons concerning Jebidiah Springfield (posthumously).
- The United State military refused to admit that the M16 was malfunctioning until Congress overrode them and ordered improvements to the rifle. , , , , ,
- When the Nazis suspected Erwin Rommel knew about a plot to assassinate Hitler, they offered to ignore it if he would commit suicide, or according to other sources, be shot privately. This was because he was such a hero the Nazis feared public accusations would be harmful to morale. Faced with the potential consequences for his family, he agreed, either killing himself by poison or being quietly shot by the SS.
- Anthony Blunt, one of the Cambridge Five (a group of KGB moles in Britain's intelligence services) wasn't charged after he agreed a plea bargain and named agents he'd recruited. He was in charge of the Queen's portraits and got a knighthood. Subverted as he was then outed in 1979 and stripped of said knighthood.