Witness Protection is a function of the U.S. Department of Justice, in which a person who has given significant information about someone who is wanted for crimes, is given a new identity in a new location. It may be used in the case of an innocent party who testified against, say, a member of the mafia, but is often used to protect a member of organized crime who has done a Heel-Face Turn and testified for the government in court. To keep said witness from becoming either part of the concrete used to construct Exit 74 on the next Turnpike or the main ingredient in Bark-O Dog Food, the Federal government provides them with a new place to live and a new identity.
This operation will be very expensive, and the party who has been granted relocation will be subject to significant restrictions. Usually, they will not be allowed contact with anyone from their past, may be required to change occupations, or have to do other things to protect their new identity from discovery by those who might harm them. If they cause their cover to be broken, it is extremely likely they will not receive a new one.
Once the person goes in, it's basically a one-way black hole; there is no connection between them and their previous life. If they are wanted for crimes or leave behind debts prior to going into the program, they will not be reachable. The Justice Department has even told the IRS to get lost for the collection of unpaid taxes by someone who went into the program. So far, not a single person who has entered the US Federal Witness Protection program and followed all the rules properly has ever been killed (although the same cannot be said for people who don't follow the rules).
This idea can be used in fiction in a number of ways:
If the protagonist goes into witness protection, expect focus on the hardships of the program. Frequently they were an innocent who has had to turn their life upside down because of someone else who is a threat to them; often they lost a loved one to the people they had to run away from (which may be why they were testifying in the first place).
If it's someone the protagonist knows, it's a convenient way to have them Put on a Bus and lose all contact with the rest of the cast without actually killing them. Similarly, you can expect copious Angst about losing someone they cared about to witness protection (like a boyfriend or girlfriend losing their lover who follows his or her family into the program).
It can also be approached from the other end: the protagonists start digging into someone's background, discover that it looks suspiciously fabricated and dig deeper under the assumption that they're a bad egg, and find themselves on the wrong end of a "back off" lecture from a US Marshal.
The protectee might just blow the whole thing off and Ditch the Bodyguards, leading to exactly the kind of dangerous escapades everyone was trying to avoid in the first place.
Some states provide a similar (but less comprehensive, obviously) program for witnesses to state crimes. Other countries also have similar programs.
If someone starts over themselves, without government assistance, they are Starting A New Life.
A number of films have used the premise of witness protection, either as a story Ripped from the Headlines, a True Story or total fiction. The trope can be used dramatically, or for comedy:
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Anime and Manga
FBI agent Jodie Starling in Detective Conan grew up in Witness Protection. She offered it to Ai Haibara as well, but was turned down.
Film - Animated
A similar program re-locates super heroes who reveal themselves in The Incredibles.
Hide In Plain Sight - A man is attempting to find his daughter, who went with her mother and step-father after his ex-wife's new husband leaves organized crime and goes into Witness Protection.
Film/Breaking Point - a man who goes into Witness Protection decides to respond when criminals murder the boyfriend his daughter had to leave behind.
Goodfellas - organized crime member goes into Witness Protection after testifying against his former associates. The last lines are him whining about how it's such a comedown, never mind all the disgusting things he did as a wiseguy. Ironically, the wiseguy the movie was based on (Henry Hill) invalidated his Witness Protection because he couldn't resist bragging about being the guy in the movie.
Lethal Weapon 2 - Cops have to watch and protect a guy who ripped millions off from the mob before he testifies, then gets to disappear into Witness Protection with the money he swiped.
Sister Act - After witnessing a mob hit, a singer is placed in witness protection in a convent.
Eraser. Arnold Schwarzenegger is the titular US Marshal whose job it is to make those in the federal Witness Protection Program disappear, as far as the world of the witness is concerned.
There's a Mary-Kate and Ashley movie with this as the premise. Basically, Mary Kate and Ashley witness a bank robbery taking place; the bank robbers threaten them, or MK&A/the government has reason to believe that they'll come back to try and remove the witnesses to their crime. So MK&A and their family go into Witness Protection and eventually end up in Australia, running a bed and breakfast. (They stop at several states along the way, including Utah, and accidentally blow their cover rather spectacularly each time. In Utah, though, it's deliberate; they're under cover as Amish, and the girls just look at each other and then shout to everyone in hearing distance "We're in the Witness Protection Program!" Then they get told that this is the last chance they have, and are moved to Australia.) The rest of the movie is about the girls trying to assimilate into Australian culture, adopting a baby kangaroo, and trying to evade the bank robbers when they finally show up in Australia. At the end of the movie, the bank robbers are apprehended, and the girls are given the option to return to the life they used to know; they prefer to stay, but admit their real identities to their new friends, now that the danger's over.
Bullitt starts off with the titular cop being assigned to one of these. It's his team's failure to keep the "witness" from getting killed that drives the plot for the rest of the film.
Snakes on a Plane - The Hawaiian mob boss puts said snakes on said plane to kill a witness, because he'd "Tried everything else!"
in the film Mobsters And Mormons a family of three( with mob/mafia connections) is relocated to Utah. Hilarity ensues as they try to fit in, and deal with the overly friendly neighbors.
Donnie Brasco went into this after the events detailed in the movie. Al Pacino's character in Real Life was very surprised and very, very pissed when "Donnie" walked into the courtroom to testify as an FBI agent. Eventually the agent was able to return to his normal life after the Fed's managed to get the Mob to call off the hit on him.
Did You Hear About The Morgans? a film with Sarah Jessica Parker and Hugh Grant is about a Manhattan couple who witness a murder, and are sent to Wyoming for witness protection.
In the end of We're the Millers the protagonists end up in witness protection, still posing as a family.
The premise of both I Am the Cheese and Zach's Lie. The former's protagonist learns about it as a young teenager and the bad guys manage to kill his parents anyways, causing him to go crazy and have a hallucinatory Vision Quest that comprises about half of the book, while the latter's enters the program at about the same age.
Although done under the CIA instead of the DoJ, in the Jack Ryan novels, several Soviet defectors are given new identities.
The captain of the Red October, for example, goes from "Marko Ramius" to "Mark Ramsey", with Ryan internally reasoning that the names are similar so Ramius is more likely to remember his cover identity.
Also happens in Without Remorse, to the man who would become John Clark. He gets to keep a love interest.
Hush by Jacqueline Woodson is about Toswiah Green, a girl who ends up in witness protection after her father testifies against a criminal and his life is in danger.
One Tim Dorsey novel featured a man in Witness Protection who reported a possible lead to a kidnapping and was promptly lionized by the press against his wishes when it played out. The people he was hiding from recognized him in the news and came after him and his son.
In The Truth, Lord Vetinari mentions having to arrange witness protection for a parrot, currently living under a false identity as a large budgerigar.
Live Action TV
In Smallville, Chloe goes into witness protection and to a safe house as she is going to testify against Lionel Luthor. She is promptly blown into a million pieces upon arrival.note Not really.
In the television show Cape Wrath, the protagonists are moved to a town seemingly inhabited solely by those in witness protection, and the secrets they all hold serve to be an important plot device.
The TV show In Plain Sight features U.S. Marshals involved in this program and the various plights of their charges.
Darnell "Crabman" Turner is in this, and as soon as he gets spotted on TV by the entire country, he gets lifted with his family and vanishes.
In a case of artistic license, Joy manipulates the system by blowing her family's cover numerous times until she gets to live the life she's always wanted (a trophy wife in a gated community). She soon finds it to be a case of Be Careful What You Wish For, because with her trailer trash past, she has a tough time fitting in with the other women.
In The Sopranos, while looking at colleges with his daughter, Tony Soprano comes across a former member of the Mob who'd turned State's Evidence and gone into the witness protection program. Needless to say, the informer doesn't survive the experience.
Used in Bones, Brennan's parents went into it, as did the man that killed her mother.
The man that killed Christian was in Witness Protection, but kicked out after the murder was revealed. The Brennan family wasn't in Witness Protection. They went on the run after Max and Christina found evidence of FBI agents killing an honest agent and framing a Civil Rights Activist during a bank robbery. One of the corrupt agents later became Booth's boss's boss. He used that position to track Bones and Booth's attempts to find Max, murder the man that murdered Christina (so he couldn't rat out the corrupt agents), and threaten Russ and Bones. Max killed him, but was later found not guilty
Wiseguy. Undercover cop John Henry Raglin advises a participant in the Garment Industry case to go into the Witness Protection Program. When she asks Raglin (who's posing as a mob enforcer) how come he knows so much about it, Raglin jokes, "Half my relatives are in it."
One of the victims of the week in an early House episode is a mobster who is being prepped for this. It's this revelation that enable's that episode's Eureka Moment.
In 24, Jonas Hodges is supposed to be sent into witness protection - but an assassin gets to him first.
The Wire - the complete and total failure of Baltimore's local witness protection program is a major, recurring plot point. In fact, Carcetti uses the bad press from a witness murder to win the Mayoral election. The kicker: The guy was actually killed by a ricochet from dumbass drunks shooting bottles. In Season 1, a kid agrees to testify against his gang, but the best that Baltimore can do is drop him off at his Grandmother's house in the country. He gets bored, wanders back into the city to hang out with his friends, and is murdered.
An episode of Criminal Minds had it turn out that one of the victims was in witness protection, along with her father, an ex-mob enforcer. Who goes on a Roaring Rampage of Revenge once he discovers where his daughter is being held.
One episode of Flashpoint had a little girl and her parents go into the Witness Protection after the girl had seen a group of men murdering her friend's family (including her friend) when she was at a sleepover. However despite remaining hidden for months, the killers (themselves dirty cops) managed to find them because they bribed a cop into telling their location.
In Warehouse 13, it's eventually revealed that Claudia's on-again, off-again boyfriend Todd is in witness protection; between this and the Masquerade surrounding the Warehouse, they each spend most of an episode being incredibly suspicious of the other until they simultaneously confront each other and realize that neither one actually knows anything about the other's secrets.
In the season 1 finale of Castle, the victim is a plastic surgeon who did a face alteration on a mob witness going into protection. Castle and Beckett have to convince the FBI to let them have access to the witness, and they eventually end up effectively using the witness as bait to catch the killer.
There's a Veronica Mars episode where Keith is hired to track someone down; he eventually figures out that his target is in witness protection and his clients are Russian mobsters.
In the Monk episode, "Mr. Monk Gets Cabin Fever", Monk witnesses a Chinese gangland murder and enters protective custody in the worst of places (for Monk)...nature!
Starsky & Hutch: In "Targets Without A Badge", Starsky finds a woman who crosses his path oddly familiar; it develops that she's a friend from childhood, supposedly dead in a car crash, who had actually gone into witness protection with her parents.
On Sons of Anarchy, the gang is forced to intimidate a young girl in Witness Protection to keep her from testifying against the gang. One group of bikers wants to kill her outright, the other considers that too much, and it nearly ends in a shootout.
The Mentalist: In "Red Sauce", the CBI's murder investigation gets a lot more complicated when the victim, who worked at a local video arcade, turns out to be a mob informant in witness protection.
An old boyfriend of Juliet's is in the program in the Psych episode "A Very Juliet Episode".
The victim in the Rizzoli & Isles episode "Don't Stop Dancing, Girl" was in witness protection, but someone from her past hunted her down.
Macgyver helped get someone into witness protection. Two episodes deal with this character, "The Eraser" and "Back from the Dead".
Gary goes into witness protection in the Early Edition episode "In Gary We Trust".
Ellen, an old friend of Neal's is revealed to be in witness protection in the season three finale of White Collar.
Then in the fourth season, it's revealed that Neal himself grew up in Witness Protection, along with his mother and Ellen.
A witness to a crime doesn't want to testify because they are in witness protection in an episode of JAG.
A suspect in a murder investigation is about to enter witness protection in the NCIS episode "Nine Lives".
The Hardy Boys Nancy Drew Mysteries episode, "Creatures Who Came On Sunday", revolves around a secret installation of the Federal Witness Protection Program. The Hardys soon blow all that out of the water, endangering quite a few people, and barely get off with a lecture at the end — though in the course of the episode, they get three "back-off" speeches, including one from the Big Bad trying to track a witness down.
Flack has to work with a witness he earlier had put into witness protection in one CSI NY episode, and prevent the scenario from going down the tubes completely.
Rose's recurring boyfriend in The Golden Girls was in witness protection. He thought he was free when it was announced that the guy who was after him was dead, but he turned up alive and Miles had to leave to take a new identity. Later, he returned because he was desperate to see Rose again, and in the process, the other guy is arrested, freeing him for real.
Witness Protection was a made-for-TV cable film that dramatized the program.
The Dukes of Hazzard: One episode featured a newcomer whose land Boss Hogg wanted to buy. The problem was that the newcomer was under the trope.
Delocated is a parody Reality Show about a man who is in the witness protection program. He wears a ski mask and voice harmonizer at all times to hide his identity, despite having his entire life filmed for television. The Russian mob is also still targeting him the entire time.
Barney Miller had to deal with a serial reoffender in the program that being held by the officers. His federal minder showed up and got him off (it was relatively minor offenses), and delivered a powerful threat to him.
One more time, and we're transferring you to Kansas. You know what's in Kansas? Wheat.
Shortland Street had Justine Jones faking her death and going off to witness protection in Sydney so she could testify against dodgy pharmaceutical company Scott Spear. Her status ends up blown by Brooke Freeman, but it's of no matter as the Whitetails end up giving themselves away
When The Simpsons became the Thompsons, complete with large-lettered shirts reading "WITNESS PROTECTION PROGRAM".
An early episode of Family Guy had Chris witness a robbery, which gets the family sent to a particularly horrible example of The Deep South.
In Futurama Bender goes into witness protection after witnessing the robot mafia beat up Calculon for money owed. The crew appear to find him living as a hick farmer on the moon, whom the mob then murders. Only for the real Bender to appear in a pizzeria across the street, but he can return home now that the Donbot thinks he's dead.