The Infiltration

The protagonist must get "inside" a bad-guy organization and pass as a bad guy to accomplish a goal.

This is not just when they have to disguise themselves temporarily, but spend time among the villains and the Mooks themselves. Spending so long can cause a Not So Different moment or, in a more severe case, lead to Becoming the Mask.

When a team must infiltrate, the story often bears resemblances to The Caper or The Con. Girls Behind Bars is usually a case of infiltration.

A common twist is to make the protagonist kill or do something to his old friends. The Hero will fail here, usually, but the Anti-Hero will often pass. Spy work is also crucial, because Only the Knowledgable May Pass often comes into play.

When infiltration is unnecessary, the heroes may decide to "slip by Right Under Their Noses" anyhow.

Contrast The Mole. See also Dressing as the Enemy. Sometimes involves becoming a Fake Defector. One subtrope is Impersonation Gambit, where the hero steals the identity of a real person the bad guys have never seen. Flock of Wolves is a comedy trope where everyone else turns out to be "infiltrators" as well.

Examples of The Infiltration include:

Comics

X-Men comics: Cyclops goes undercover as Eric the Red, redirecting his Eye Beams to appear that he has energy weapons in his armor's hands. (Both the Eric the Red and Red X identities were used later by actual villains, and the identities are now associated with them, not the original disguised heroes.)
In the third episode of Tale Spin's pilot series, Plunder & Lightning, Kit Cloudkicker pretends to betray Baloo, Molly and Rebecca in the Iron Vulture to his former mentor Don Karnage, to allow them to escape. The fake deception is so convincing and surprising that Baloo believes himself betrayed, and angrily leaves Higher For Hire with the SeaDuck to Louie's to party his cares away, until he hears Kit desperately radio for help in the fourth episode.
This was The Unknown Soldier's whole career. Impersonate someone, get inside the target area, terminate the target (officer, secret weapon, intelligence gatherer, Etc). Sometimes he could get the target's protectors to terminate the target for him.
Brubaker's Sleeper is one of these with the added twist of his handler falling into a coma and leaving him trapped behind enemy lines with no one to report to.
In Tiger and Bunny, Ivan is tasked with infiltrating Ouroboros after the terrorist organization in question decides to take the city hostage. He's detected by the faction's leader, Jake, but he still manages to escape with his life and pass on information vital for taking back the city.

Film

The Departed
- Leonardo Di Caprio's character plays the trope straight.
- Inverted i.e. bad guy infiltrates good guy organization with Matt Damon's character.
Serenity has Simon Tam infiltrating an Alliance-operated hospital to free little sister River from continued Super Soldier experimentation and Mind Rape.
Infernal Affairs, played by Tony Leung Chiu-Wai.
Reservoir Dogs has the main characters trying to figure out which one of them is an undercover cop. Sure they can figure it out, if the right guy lends them an ear.
White Heat has an undercover agent posing as a prison inmate and subsequently joining Cody Jarrett's gang.
Diamonds Are Forever has James Bond infiltrating a diamond-smuggling operation.
Donnie Brasco, in which an FBI agent infiltrates a Mafia family. This one was Truth in Television.

Literature

In Russia and probably all other post-Soviet countries, this trope is literally synonymous with the name of Stirlitz, the main character of a spy novel series and an incredibly popular television series based on it. He's basically a Soviet spy who is skilfully pretending to be a SS-Standartenführer.
Richard Adams' Watership Down. Bigwig uses this technique as part of Hazel's plan to free some does from Efrafa.
In Poul Anderson and Gordon R. Dickson's Hoka stories, Alex Jones inflitrates the Hoka Pirates to prevent actual fighting from breaking out.
The murder Sherlock Holmes investigates in The Valley of Fear centers around a Pinkerton agent who infiltrated a criminal gang in the United States by posing as a murderer and counterfeiter, before turning on his supposed allies and helping the police break up their operations. It's Truth in Television: Sir Arthur Conan Doyle based this story on a real-life Pinkerton agent (an agency of private detectives often used in the days before the government created the FBI) who infiltrated and then broke up a gang of militant miners known as the Molly Maguires in the 1870s.
In Brian Jacques' Martin the Warrior, Brome gets into Marshank by pretending to be a sea rat.
In Sandy Mitchell's Warhammer 40,000 novel Scourge the Heretic, Keira poses as a noblewoman to infiltrate a Chaos cult. Meanwhile, Kyrlock and Elyra attempt to infiltrate a smuggling operation: Kyrlock by pretending he deserted and Elyra posing as a servant running away from a mistress whose husband she had slept with and whom she had robbed.
Many times in the X Wing Series. The Rogues pass as Imperial civilians to get on Coruscant. The Wraiths pass a warlord's subjects, then as stormtroopers, then later as pirates that the warlord wants to recruit. The Rogues set themselves up as members of one Imperial faction.
In G. K. Chesterton's The Man Who Was Thursday, Syme is taken to an anarchist meeting and, being a policeman, sets out to infiltrate.
Done twice in the Age of Fire Series. AuRon infiltrates the Circle of Man's main base to end their enslavement of dragons and to protect his friend's nation. In the next book, Wistala does the same to the Wheel of Fire Dwarves, this time to get revenge on those who slaughtered her family.
Septimus Heap does this in Darke by disguising in Darkenesse to get into the Darke Halls and rescue Alther Mella.

Live Action TV

Used by both the good and bad guys on 24. So much so that you start to wonder if anybody on that show ever heard of a background check....
Sayid infiltrates a terrorist cell in the flashbacks of the Lost episode "The Greater Good."
"Mirror, Mirror", one of the most popular Original Trek episodes, featured the good guys from the Enterprise having to spend some time among their evil universe counterparts.
The entire premise of Wiseguy.
Vladimitr Sharapov does this in The Meeting Place Cannot Be Changed.
Janis Hawk in FlashForward.
Happens often in Burn Notice, although Michael occasionally takes the identity of a potential business associate of that episode's villain rather than a member of their group.
Callen of NCIS Los Angeles makes his careers, plural, out of this trope, and undercover work is a specialty of the L.A. team.
Chuck has Mary Bartowski in the backstory and Sarah in season 4 undertake these by pretending to do Face Heel Turns.
The Hardy Boys Nancy Drew Mysteries: "Game Plan", in Season 3, has Frank Hardy joining a criminal organization by pretending to be a drifter looking for work. At one point, he seems to have gone totally over & sold out the Feds, to the point of pulling a gun on his brother Joe.

Video Games

The modus operandi of the Metal Gear series.
In Betrayal at Krondor, James and Locklear pretend to be Quegan mercenaries to infiltrate the Big Bad's army in order to deactivate the Rift machine through which more of that army is arriving each minute.
Dragon Age: Origins: After the protagonist gets captured (avoidable, if you can win one of the game's toughest fights), you are given two options: Break out on your own, or select two companions to control while they do this. Their different bluffing attempts are some of the funniest moments in the game, like Sten and Oghren's circus act.
Several Prototype missions. Even in non-mission military consumptions, there's a huge EP bonus for acquiring a skill and leaving without alerting the troops.
This is whole premise of Splinter Cell: Double Agent.
In the Thief: The Dark Project mission "Undercover", Garrett infiltrates the Hammerites by passing as a novice.

Web Comics

Western Animation

In Avatar: The Last Airbender "The Boiling Rock", Sokka and Zuko dress up as prison guards to get back Hakoda (Sokka's father).
The Legend of Korra "The Revelation." Mako and Korra disguise themselves and sneak into an Equalist rally.
Spoofed in a short on OH Yeah! Cartoons, in which a crime-solving doughnut infiltrates a criminal organization under the guise of a new recruit to save his fellow officer. As the doughnut unties him, the officer says "I thought for sure you were in that box of doughnuts!". The doughnut responds, "Huh...never thought of that."
Teen Titans does it three times: Cyborg enters the HIVE Academy under the guise of "Stone" to find out what secrets they're planning next. Later, in a mission against the HIVE with the Titans, he is beset by the HIVE's top agent, Bumblebee, only to find that she is a spy (though she's more of a Fake Defector, as she has not donned a new identity for the mission.) Also, Robin goes undercover in Slade's organization as Red X, but Slade sees through the deception. Bumblebee in HIVE gets this trope lampshaded when Brother Blood learns she was an infiltrator and screams rhetorically "Did anyone come here to actually learn?" (or words to that effect.)
The entire concept of Punch/Counterpunch of Transformers, an Autobot spy who has the ability to adopt a Decepticon robot mode. In the Japanese Transformers Headmasters continuity, he had even managed to become firmly entrenched in the Decepticon ranks as Scorponok's closely-trusted informant.

Tabletop Games

Everyone in Paranoia is trying to do this at all times, due to a combination of Gray and Grey Morality and City of Spies. Swapping sides is not uncommon.