Hartigan: Then there's thunder from behind me and lightning bolts punching holes through my chest. I guess I won't be having that steak I was looking forward to, after all. My last day on the job. Hell of a way to start my retirement. Bob: Damn it, Hartigan, I warned you. Hartigan: Hell of a way to end a partnership.
At one point in Death Note, L, who suspects Light of being Kira by then, says he would be disappointed if Light turned out to be Kira because Light's the best friend he's ever had. It's especially heartbreaking because the audience has known from the beginning that Light is indeed Kira. Word of God says that he was probably lying. However, Matsuda wasn't — in fact, in Matsuda's case it was arguably worse: Light had been deceiving him for five years straight by the time the finale comes up and he tries to have Matsuda murdered. It's next to no wonder that poor Matsuda snaps massively in the end... and shoots Light several times while screaming and crying.
Freesia from the second season of Jubei-chan was a very calculating Dark Magical Girl who had wormed her way into Jiyu's home (and bed). When Freesia finally reveals herself later in the series, she shatters Jiyu's mind, sends her wounded off a cliff, and turns her father against her.
This is actually most of the premise for Saint Seiya: The Lost Canvas. The main character's best friend, Alone, becomes the host of the evil god, Hades. As one of Athena's saints, our hero must fight against his best friend.
Alone means "Halo" in Italian (the setting of the story). The meaning in english is possibly intentional.
After Arachnophobia's arc in Soul Eater, it turns out that Justin Law had gone through the first phase of this, but afterwards... well, turns out that Law worships Asura, not Shinigami-sama, is an extreme misogynist, likes to be playing Ho Yay with his longtime apparent enemy, and more than likely helped set up Kid to be kidnapped by the arc's Big BadChessmaster. So, he subverted this while acting The Mole. He might still like Stein, though, because he did retreat before injuring him.
As of chapter 96, Chrona is stepping up to the role too.
In Code Geass, Lelouch and Suzaku, as Suzaku is in league with the Emperor himself for a while.
Youko's Poisonous Friend Yuka Sugimoto in The Twelve Kingdoms becomes her rival to become the Queen of Kei. Though unlike others, she gets better and relinquishes her claim, returning to Hourai/Japan.
In one story of Franken Fran, Fran's younger sister Veronica realizes that the only girl that had befriended with her in the private school where Fran has sent her is actually working for a criminal organization that is kidnapping students and selling them to pedophiles in foreign countries.
In Devilman, Akira's best friend Ryo Asuka, the guy who got him into the whole horrible mess, turns out to be Satan.
The third-to-last episode of Star Driver reveals that Sugata is the long-absent Emperor of Glittering Crux.
As of chapter 117 of Medaka Box, Zenkichi joins the Flask Plan to teach Medaka the value of failure.
In Kore wa Zombie desu ka?, Eucliwood Hellscythe considered the King of Night to be her friend still, despite him unleashing a lot of megalo (demons) into the city to harm people and her new friends. He wanted to die, since he became an immortal zombie to serve her, but she wouldn't do it.
In Season 2, Nene, implied to be the strongest fighter in the underworld, is seen eating and drinking with Chris, the current Big Bad, and implied to be the strongest magical girl, who had fought each other before in the past.
In a filler arc, Naruto learns that the old man he often ate with at the ramen shop is actually a ninja from a village that had been destroyed, who seeks revenge against the Leaf Village. Interestingly enough, his friendship with Naruto actually was genuine, and he replaced the deadly explosive tags across the village with harmless ones, intending it as a scavenger hunt similar to the games he played with his son.
In StrikerS Sound Stage X of Magical Girl Lyrical Nanoha, the culprit behind the Mariage killings turns out to be Teana's partner Runessa; Teana seemed to get along well with her, offering her a permanent partnership position at the end of the case, and Runessa, despite being the Detective Mole, was touched by the offer.
In Sword Art Online, Kirito eventually realizes that Heathcliff, head of the most successful guild in the game, is actually Kayaba Akihiko, the man who trapped them there in the first place.
Kirito: It always bugged me...something that any child knows. There's nothing more boring than watching someone else play an RPG.
All over the place in Attack on Titan. Eren learns that Annie Leonhart, the girl that taught him how to fight, is really the Female Titan responsible so slaughtering his squad mates. Not long after that, he learns that meek Bertolt Fubar and Team Dad Reiner Braun were the Colossal Titan and Armored Titan all along. And therefore, indirectly responsible for a good majority of the death in the series. To say he's lessthanthrilled is an understatement. For an extra twisting of the proverbial knife, all are presented as sympathetic and genuine in their attachment to the people they've betrayed.
Chisato Inoue from the Vampire Princess Miyu TV series turns out to be this. Subverted in that Chisato wasn't aware of it either until almost the end, when her once-sealed demonic powers starte coming to the surface and her brother Tokiya, a full-blooded Shinma, is killed. From then on, the at first oblivious Chisato embraces her position as the Apocalypse Maiden and faces Miyu head-on, wanting to avenge Tokiya's death...
This happens to Spider-Man with alarming regularly. His friends and co-workers are guaranteed to either die, go mad, or both.
Comics 101:[T]he Jackal was merely the latest in a long tradition in AMAZING SPIDER-MAN in which nearly everyone in Peter Parker's life either becomes a villain or is related to a villain in one way or another. Need examples? First girlfriend Betty Brant? She married Ned Leeds, who eventually became the Hobgoblin. Schoolmate Liz Allen? Her brother was the Molten Man. JJJ? His son becomes the Man-Wolf. Peter Parker's parents? Turns out they were killed by the Red Skull. The list goes on and on (and on). In a world like this, one of Peter's college professors becoming a supervillain makes perfect sense.
Grunnel in With Strings Attached. He genuinely likes the four and is fascinated by what they have to say about Earth. But when Brox comes up with a use for Paul that Grunnel knows Paul won't agree to, Grunnel quite readily backstabs the four to ensure Paul's participation in Brox's scheme. As he says to Ringo: � Brox is my friend. You are not my enemies. Do you understand the difference?� Yet he prevents Brox from killing George and Ringo because he likes them.
Drew in the Hannah Montana I Didn't Sign Up for This. She is quick to befriend Miley and dates Lilly but in the last chapter, she is revealed to be a murderous sociopath that cares about no one but herself.
In the side stories to MGLN Crisis, it turns out that Racquel Benna/Zettin, the fruit vendor Fate knows was actually a scientist who worked alongside Precia and Scaglietti, creating a clone of Clyde Harlaown who served to impregnate Precia with Alicia. Racquel said she moved near Fate hoping to tell Fate the truth one day.
The entire plot of the My Little Pony: Friendship Is Magic fanfic Inner Demons revolves around a prophecy that Twilight Sparkle will be consumed by her inner darkness and become Equestria's Evil Overlord. This happens within a matter of chapters, and the rest of the story is dedicated to her trying to kill the rest of the Mane 6, and them trying to fight and/or redeem her (until the climax, there's a bit of debate among them).
As another Twilight Sparkle-related example, Pages Of Harmony, Twilight is driven by a desire to extract the Elements from her friends by capturing and murdering them in various ways specific to their Elements. Though much like Light in Death Note, she appears to believe she's doing it for the greater good, and her friends try to get through to her and get her to come to her senses. She doesn't listen.
Another Twilight Sparkle-related example (these are popular, aren't they?). Death Note Equestria has her taking on the role of Light as Kira. She's so determined to defeat L and enforce her vision of justice on the world that she even goes so far as to engineer Rarity and Pinkie's death as part of her cover; she does have a few Villainous BSOD moments along the way, but that hasn't stopped her so far.
In the Medaka Box fanfic World As Myth, Hanhaba Shiranui fills this role towards the Broadcast Club in general, and Zenkichi Hitoyoshi in particular.
Films — Live-Action
Happened at least twice to Indiana Jones - Elsa Schneider, who was obsessed with the Holy Grail enough to help the Nazis in Last Crusade; and Mac working with Communists in Kingdom of the Crystal Skull:
Mac: I'm a capitalist. And they pay.
More than once to James Bond, though he ought to have expected it. The biggest example is Alec Trevelyan aka Janus from Golden Eye, who once was James's partner and best firend friend as well as Agent 006, but after faking his death becomes the Big Bad of the movie.
In Snake Eyes, the best friend of the detective protagonist sets his friend up to cover up the assassination of the Secretary of Defense at the stadium. He's a Well-Intentioned Extremist who cooperated with a group of military contractors because of a dispute about a military software system that might be dangerous, which the Secretary wanted to cancel.
The villain in Sneakers. "I cannot kill my friend." [hands gun to mook] "Kill my friend."
The Truman Show. Truman's "best friend" since childhood (who is really an actor) at one point appears to truly be listening to Truman's plight and confusion, almost seeming to really want to help his buddy understand the crap that's going on with his life. However, he allows himself to be instrumental in the biggest Mind Screw the studio pulls on Truman in bringing his "father" back from the grave. He later leads the hunt to capture Truman once he starts escaping. Earlier drafts and deleted scenes emphasized the actor being torn over doing such a thing to a man he had genuinely come to view as his best friend, and in these drafts he initially redeemed himself by intentionally looking the other way when locating Truman and allowing him to escape.
Hot Fuzz. Danny Butterman, the cop Nicolas befriends is actually in on what is going on, but tries to keep him out of trouble, even going so far as faking his death. Considering that when Nick tries to explain, Danny immediately enters an extreme state of denial and then sends him back to London, it's possible that he was aware on some level, but subconsciously never connected the dots for the sake of his own psyche. When Nicholas returns to stop the NWA, though, he chooses to join him.
Happened to Hartigan at the beginning of his segment in Sin City, when his partner shoots him in the back to keep him from killing the bad guy. But, you know, he really ought to have seen it coming, what with the partner being played by Michael Madsen.
Textbook example in the Samuel L. Jackson and Ed Harris film, Cleaner. Ed Harris is Sam's best friend that helps him but later betrays him.
Subverted in Talladega Nights: The Ballad of Ricky Bobby. Ricky Bobby is betrayed by his best friend Cal, who steals his glory, his house and his wife. Despite this, Cal continues to call Ricky on the phone to chat and ask advice (for instance, asking where things are stored in Ricky's house). Ricky, out of force of habit, chats with him until he remembers that he is mad at Cal.
As with most tropes in the film, both parodied and lampshaded. The Kid recognizes Practice as the man who "killed Mozart", F. Murray Abraham.
Street Kings. Detective Tom Ludlow's entire police unit is in on Washington's murder and have gone way too far in their corruption, keeping Ludlow in the dark because of his better morals. Capt. Wander (the prime mover in the whole operation) even admits at the end that despite ordering him killed, he loves Tom more than any of the other guys in their unit and unlike them he is irreplacable for him. They say goodbye as family before Ludlow shoot his friend.
In Motives the lead protagonist is set up for a fall by his best friend. Why? To steal the protagonist wife.
In Dark Blue, Jack Van Meter sets up Perry's murder, which fails when Bobby is killed instead.
In Another 48 Hours, Jack's fellow detective, Ben Kehoe, is revealed as a big time drug dealer. The character had been used for some exposition in the first film and it was somewhat given away by having him slick back his hair and wearing a suit in the second.
Elijah is the Big Bad of Unbreakable, which he reveals only when he and David are starting to become friends near the end. He sees life as the prototype of a story after becoming intrigued by the comics his mother gave him, so he killed hundreds of people in mass disasters over the years to find his antithesis, a real hero. He manipulates David over the course of the film to fill this archetype, not to save people, but to find meaning in his own life.
In R.I.P.D.Hayes turns out to be a dead-o, and organizing the dead's plan to reconstruct the Staff of Jericho.
In The Amazing Spiderman 2, Harry Osborn turns out to be this in the end, angered at Peter for refusing to give him his blood so that his disease could be cured. Electro can also count.
Senator Paine from Mr. Smith Goes to Washington admires Mr. Smith's idealism and doesn't want to see him ruined by the political machine that he ends up fighting, though not enough to come clean. Until the end, that is, when his conscience finally gets the better of him.
Long John Silver, Jim Hawkins's mentor figure and the local Magnificent Bastard, is probably the most famous example of this trope. So much that he manages to get away with it in the end.
In Agatha Christie's Ordeal by Innocence, the former nanny is this to Philip Durrant, warning him to stop prying into the murder of his mother-in-law, which she committed on behalf of the victim's delinquent son. She murders Philip to cover her tracks.
This being Kitiara, the surprise isn't that Soth is evil, but that he'd betray her. For his part, although he knows it's selfish, Soth does what he does purely out of love for Kitiara. It's a big bad dysfunctional family they've got going on.
Robert Harris' Fatherland, where Xavier's old friend Max Jaeger turns out to be the source of the SS's inside information.
Fidelias to Amara in the Codex Alera series. Not much of a spoiler, though, since his real allegiance is revealed within the first couple of chapters of the first book.
Red Seas Under Red Skies begins with a flash-forward scene where best friends Locke and Jean are in a standoff with two assassins, all four of them armed with crossbows. With some reluctance, Jean suddenly turns on Locke, claiming to be in league with the assassins' employer and demanding he hand over his weapon. Subverted, however: when we eventually get back to this scene in the main story, it is followed by Jean using both crossbows to shoot the assassins dead while their guard is down.
In Sergey Lukyanenko's Rough Draft, the main character has just killed a powerful Functional who was trying to kill him. He then meets his friend but quickly realizes that he's one of them. The friend initially tries to help him but then nearly kills him. It gets weirder in the sequel, Final Draft, where the friend returns, explaining he was just scared. At the end, though, he challenges the main character to a duel.
American Gods: One of Shadow's old friends, Low-Key Lyesmith from his stint in prison, is actually Mr. World/Loki. This becomes especially trying it involves Mr. Wednesday, he turned out to be working with Loki the entire time, working to manipulate both sides into a devastating war.
In Aristoi, Zhenling was part of the Big Bad's plan to crack Gabriel's encryptions all along.
In The Underland Chronicles, to all appearances, Henry's affection for his cousin and his offer to rule with her are sincere.
Gaheris Rhade from Andromeda. However, "The Unconquerable Man" put a twist on it. Gaheris actually won the fight originally, but got frozen in time like Hunt did in the pilot. He eventually gets rescued by Beka and company, just like in the pilot. In fact, he lives through much of the series plot, though it plays out far differently. He tries to rebuild the Commonwealth to make up for the fact that his people slaughtered everything that moved after the Andromeda was lost, and were ultimately nowhere near the Warrior Poets he had thought. Tyr is killed by Rhade for betrayal, Perseid gets annihilated, and the universe is about to be ripped to shreds when Trance tells him there's another chance to fix it all. Rhade eventually agrees, uses said universe shredding phenomena to travel back in time and kill his previous self moments before he begins his mutiny, takes his uniform, and throws the fight with Dylan Hunt at the beginning of the pilot episode. Chronologically, the main series then follows. Does anyone have anything for a headache?
In season 6 of Supernatural, the Big Bad of the season, to whom both Crowley and Eve played Disc One Final Boss, is revealed to be Castiel, who has decided that to defeat Rafael and put Heaven on the right track, anything is acceptable - in this case, taking on a million souls. The Winchester boys do their best to stop Castiel throughout the final episodes of the season, while he continues to plead for them to accept him and his reasons for evil.
In Luther, the antagonist of the first series' final two episodes is DCI Ian Reed, Luther's friend and confidant, who is actually a Dirty Cop.
Subverted in the episode The Great Game from Sherlock. When John appears to meet Sherlock at the pool, we (and Sherlock) assume that he's Moriarty. However, it's soon revealed that he is strapped to a bomb and the real Moriarty was just making him say lines that imply he is.
In Jekyll Peter Syme turns out to be working against Jackman. And makes the argument that after so long pretending to be a friend they really are friends, even after betraying him.
24 plays this straight with Nina Meyers and plays with it for Tony Almeida. While Nina was The Mole working for the first season's Big Bad, Tony through his own warped sense of justice is aiding the seventh season's Big Bad to get him to trust him so he can kill him in revenge for being the mastermind behind the plot that lead to the death of his family.
Since we rarely get much of an insight into the personal lives of the detectives and prosecutors who appear on the numerous Law & Order series, it's almost a certain bet that whenever an old friend of one of the characters shows up, it will turn out that they've become one of these.
This describes Lex Luthor for the first four seasons or so of Smallville, and intermittently afterward. Notable in that this isn't presented as a twist, but as a continuing theme throughout the series — he legitimately likes the protagonists, he just sees their demands that he stop digging up their secrets as a requirement to tell them he's stopped in the interest of courtesy (rather than a moral need to actually stop).
Dr.HannibalLecter to Will Graham (and to a lesser extent, Jack Crawford) in Hannibal. In a departure from the source material, where Graham never met Hannibal before exposing him as the "Chesapeake Ripper" and arresting him, Hannibal is here referred to Graham as his FBI-mandated psychiatrist. He becomes friends with Graham and Crawford and lends his medical and psychological expertise to the FBI's Behavioral Sciences unit, the group out to catch the Chesapeake Ripper, while Gaslighting Graham for his own amusement and other ends.
By the end of season one, Graham realises that Hannibal is this trope, but by then he's been manipulated into near-insanity and framed for a string of Hannibal's murders, destroying his credibility.
In the second BIONICLE movie, Turaga Dume starts out as a trusted friend and city leader to both Toa Lhikan and Toa Vakama, even if he DOES act a little strangely. Turns out he's the one who ordered the rest of Lhikan's team to be killed off years ago and for ex-Toa Nidhiki and Krekka to capture him as well, even managing to capture and imprison half of Vakama's team in the Coliseum and generally causing mass chaos and destruction all around. And then it turns out that Dume is not Dume at all, but rather Makutadisguised as Dume, who has been in stasis for years. Even better, before this, Makuta was a trusted guardian of their home island, meaning there are two examples of this trope in one movie.
During the summer of 1991 The Ultimate Warrior turned to his friend Jake "The Snake" Roberts for help in learning how to defeat The Undertaker. Roberts explained that after passing three tests, Warrior would have the "knowledge of the dark side" to defeat Undertaker. These tests included Warrior being locked inside a coffin and being buried alive in dirt. The final test was Warrior walking through a room full of live snakes to reach a chest containing "the answer". Warrior opened the chest, only to be immediately bitten by a King Cobra. As Warrior weakened from the effects of the snakebite, Roberts was joined by The Undertaker and Paul Bearer, revealing the three were working together all along. Jake Robert's last statement to The Ultimate Warrior was "Never trust a snake".
In Magic: The Gathering, the Big Bad for the Antiquities expansion is Urza's brother Mishra. But the true Big Bad, Yawgmoth, has been manipulating both brothers this whole time. Urza does not take this well.
Old school Japanese PC/NES adventure game Portopia Renzoku Satsujin Jiken (The Case of the Portopia Serial Killer) has this as The Reveal, as the titular killer turns out to be Yasuhiko "Yasu" Mano, who is not only the main character's partnerbut also the single most unlikely suspect as he is with you throughout the entire game, executing the commands of the unseen protagonist. The shock factor was so high that nowadays the phrase "Yasu is the culprit" is something of a meme amongst old fans.
Flipped around in Dragon Age: Origins: The villain Loghain thinks that his king and son in law is a Big Bad Friend who is selling out the kingdom to the same empire that his father and Loghain expelled from the country just one generation ago. Thinking the king has already made his Face-Heel Turn and become The Quisling, he betrays him and takes control of the kingdom himself.
Return to Ostagar reveals that the king was indeed planning to divorce Loghain's daughter Anora and marry the Empress of Orlais had he survived the battle, which if Loghain is a party member at the time has him both vindicated and furious that he was right all along.
Subverted again in Dragon Age II, where Cassandra is convinced that Varric's friend Hawke was the Big Bad responsible for everything and went to Kirkwall specifically to start the Mage-Templar War that is currently sweeping Thedas, when in reality, they were simply the Right Man in the Wrong Place and were swept up in events far outside of their control.
Played straight with Anders, when he destroys the Chantry to incite a Mage Rebellion, ultimately leading to said war.
We don't actually see the moment of revelation for Phoenix Wright, but Kristoph Gavin is the one who set him up to be disbarred and dishonored in Apollo Justice: Ace Attorney. He then spends seven years pretending to be his dearest friend until Phoenix finally takes him down.
And in Investigations Shi-Long Lang is shocked to discover that Byrne Faraday's killer and a key member of the smuggling ring is his assistant Shih-na.
Calisto Yew serves as one to Byrne Faraday and Tyrell Badd, her accomplices in the Yatagarasu, when she betrays and kills Byrne, due to being The Mole for the smuggling ring the Yatagarasu is fighting.
Implied by Apollo in the last case of Dual Destinies, when he states that Prosecutor Blackquill seems torn after The Reveal of Bobby Fulbright's true identity, as the two of them were partners. The previous cases also give the feeling that there was a strong, if unusual, friendship between them.
Special Agent Kato the third and final Big Bad in Shadow Hearts Covenant, doesn't let a little thing like wanting to destroy the world ruin the good friendship he has with Yuri. He even encourages the heroes to stop him if they truly believe they've got the right moral standpoint compared to his.
Joshua in The World Ends with You. You actually have him as a member of your party for 1/3 of the game, as well as a cutscene that starts out short but is slowly revealed (an attempt to confuse the player as to whether Neku's killer was him or the Reaper, Minamimoto). The game switches itself up on you: It intentionally makes you suspect that Joshua did it, then reveals it to be Minamimoto with some rather convincing evidence, even so far as to make you think that Minamimoto could be the final boss, especially after he revives himself. Then, the end of the game does a 180 and reveals that Joshua was not only the killer, but the Composer of the game as well: He killed Neku (who could use any pin) so that Neku could take his place in the Game that would determine Shibuya's fate.
The Boss in Metal Gear Solid 3, before defecting, was Naked Snake's mentor and one of his closest friends. She celebrates her Face-Heel Turn by beating him up and stealing his rescued hostage. It was a ruse to make Volgin trust her and Snake wasn't in on it.
The same goes for Naked Snake as Big Boss with the chronologically later Metal Gear as the commander of the young Solid Snake.
Vossler from Final Fantasy XII fights alongside you for a chunk of the game, but sells you out to the Archadian Empire afterwards on the belief that it would be better to surrender to stop the bloodshed instead of continuing a seemingly fruitless rebellion. He's immediately given the Straw Traitor treatment, fights you as a boss later on, and then dies dramatically on an exploding warship.
The Neverwinter Nights mod series The Bastard Of Kosigan has a couple. That group of mostly-nice witches you were helping out in the first module? Oops, they were manipulating you into helping them summon an ancient demon with which to wipe the world clean of civilization and start over with magic-users in control. Your lover in the second module? Whoops, she was the mastermind behind every assassination attempt on you or your family for the entire story so far. Both cases give you the chance to join them when their plots are revealed, which due to the story's Grey and Grey Morality, isn't that far off the 'good guys' plots.
In Dungeon Siege 2, the Azurite Scholar that has been helping you throughout the game turns out to be the Overmage of the Cinbri, who has been manipulating both you and the Big Bad in order to reshape Aranna in his image.
In EarthBound, Pokey claims that Ness is his best friend, and you can tell a cop that you're both friends, too... until he does a Face-Heel Turn. Though, that would make him The Dragon Friend... Until Mother 3. In that game, it shows that he really did consider Ness a friend; he cherishes the latter's weapon, the "Friend's Yo-Yo" and keeps a shrine to him in his headquarters.
In Fallout: New Vegas, Pacer is this to The King. While The King himself is a genuinely good man who does what he can to help out and protect Freeside, Pacer is a xenophobic jerkass who makes outsiders pay a toll in order to see The King (who will at least refund the player personally) and starts fights with the NCR.
He is mostly a Poisonous Friend... unless the Courier negotiates a peace agreement between the NCR and the Kings without using the King's favour. Then he tries to lead a coup to stop it.
In RosenkreuzStilette, Iris is considered like a kid sister to the rest of RKS, including Tia. What they don't know is that she's really the Big Bad who's making RKS fight against the Holy EmpireFor the Evulz. She eventually reveals to Tia who she really was and the real reasons for the war, and that she really did all that for both said reason and to become god of the world. That's where none of RKS trusts her anymore.
At the end of Beyond Divinity, its revealed that your only ally throughout the game, the unnamed Death Knight, is actually, Damian, the Big Bad of the Divinity series.
In Grand Theft Auto: Vice City, Lance Vance sells out Tommy Vercetti to Liberty City mafioso Sonny Forelli in the final mission out of opportunism because he felt he was being sidelined by Tommy in the Vercetti criminal empire.
In Grand Theft Auto: San Andreas, Big Smoke and Ryder betray the Johnsons to corrupt police officers Frank Tenpenny and Eddie Pulaski to get rich off the drug trade.
Billy Grey in Grand Theft Auto IV: The Lost and Damned. He ultimately decides to sell out the entire Lost MC for his freedom; however, Johnny Klebitz infiltrates the prison and personally executes Billy before he can testify.
Space Pirates and Zombies has Don who turns out was a zombie leader/commander all along, and was leading you to the core to unleash the zombies.
Pavel in Metro: Last Light is Artyom's travel companion for a major part of the game and the two end up saving each other's life several times before they finally make it back to a civilized station where they are safe to relax and stock up on supplies before they each make their way to their respective homes. Over a farewell meal, he tells Artyom that he's not just forced to be a soldier for the Communists, but actually believes in their principles. At that moment two communist officers appear behind him and it turns out that he's not just a simple scout, but a Major who was tasked to capture Artyom and just happened to end up in the same Nazi prison after his team was killed. And he just had been spiking your drinks.
Livia in Alpha Prime. At the end, it's revealed that they're not just The Mole, but were the Company's agent that orchestrated the plot in the first place. This also leads into the bad guys winning.
In Sluggy Freelance Torg believes Riff is one of these following the "Hereti-Corp freelancer" revelation, though it's more a case of "unwitting stooge." Played straight with Sam during the "Vampires" Story Arc.
Defied in Perfect Kirby with Bill, the Big Bad of the first installment. Kirby considers Bill an annoyance, and while he is surprised by Bill being the Xbox smuggler, he rejects Bill's claim that they're friends.
Kirby: Bill, we've only known each other since you moved in, two weeks ago! Bill: When did this happen, three weeks ago?
Todd Ianuzzi from Beavis And Butthead is a variation of this trope. Most of the time is associated or pretends to be a friend of Beavis and Butt-Head, but he is really an Ungrateful Bastard and a bully who enjoys committing crimes. However, Beavis and Butt-Head think he is "cool".
In Avatar The Last Airbender, fire lord Sozin was best friends with Avatar Roku. the two became distant due to Roku's duties as the Avatar and Sozin's plans for conquest, and Sozin betrayed him as soon as he had the chance.
Sequel series The Legend of Korra has Varrick for Bolin. He did betray him and his friends, intended to use Unalaq's plan for his own selfish benefit, but Bolin still respected him and was still willing to accept his help against their real enemies.
In "The Mystery of the Urinal Deuce", we find out that it was Stan Marsh who put the dookie in the urinal. Though it was terrorists who caused 9/11. The "9/11 Truth" movement is a Government Conspiracy in order to keep the "retarded one fourth of America" in line through fear.
In several other episodes, Eric Cartman. Though something of a parody, because his friends know he's not to be trusted—-it's just that somehow, he usually winds up convincing one or more of them to believe him anyway, just to stab them in the back. Further parodied/lampshaded in the Wal-Mart episode, where Kyle Broflovski keeps pointing this out, though Cartman still seems to think they all believe him.