Most of the remaining humans in the Vortex World in Shin Megami Tensei III: Nocturne once the true stakes are revealed. Hikawa was evil to begin with, then Isamu sacrifices Hijiri to summon Noah and Chiaki sics her angelic army on the Manikin city of Mifunashiro to summon Baal Avatar.
In Persona 4Golden, the protagonist himself can go through one if he makes friends with Tohru Adachi before realizing he's the killer, confronts him (instead of keeping his thoughts to himself and then aids Adachi via destroying crucial evidence. This unlocks the "Accomplice ending": it has Adachi becoming a Karma Houdini for the murders and even taunting the protagonist before he (the MC) leaves Inaba. Doing so actually gives a decent reward for a New Game+. At the very least, it's much more cost effetive than what you get in the true ending.
The supposed Face-Heel Turn of Ralgha "Hobbes" nar Hhallas in Wing Commander III didn't work for many fans of that series who have only played the PC version (the console versions used bigger CDs than computers of the time, and could thus fit the explanation cutscene into the game; the novelization also covers the explanation). In this case, he was an (unwitting) mole.
Sorbet in Magical Starsign fakes one as part of an elaborate plan to trick the Big Bad, and it's so convincing that even your party falls for it...unfortunately, you waltz in just as her plan is about to come to fruition.
Fortunately, it wasn't the best thought out plan anyway...
Queen Ashlelei in Malicious, the once great and respectable ruler turned into a ravaging war demoness after a series of traumatic events, her two chilren being killed by her husband, King Eldrake their father, in front of her is one of these events to name.
The player's wingman Solo-Wing Pixy does this in Ace Combat Zero after witnessing the horrors of war, including the enemy dropping seven nuclear bombs on their own soil.
The PSP game Crisis Core (where you play as Zack, the guy Cloud absorbed the personality of) portrays this moment at the end. You even get to see Sephiroth before he went batshit. There's quite a few of the villains that do a Heel-Face Turn.
Vincent Godfrey is interesting in the fact that he Face Heel Turns twice without ever commiting a Heel-Face Turn. When you first start the Worgen starting experience he's a loyal Gilnean citizen and is seemingly important in helping cure your character of the Worgen curse. He then Face Heel Turns against you when he finds out that King Greymane is a Worgen and attempts to ransom him to the Forsaken until rescued by the player character. After killing himself, he is risen as a Forsaken and helps the Forsaken players in helping fight Gilnean Rebels in Pyrewood Village before he the betrays the Forsaken and sets up shop in Shadowfang Keep.
The Zandalari trolls have turned hostile after their homeland on Zandalar Isle is destroyed in the Cataclysm, and by the time of Mists of Pandaria, they have allied with the malevolent Thunder King.
In Starcraft you have Sarah Kerrigan, who go from being the protagonists girlfriend to becoming the queen of blades, then you have Arcturus Mengsk who seems like a nice guy then turns into a genocidal dictator. Followed by Samir Duran who first joins up with the United Earth Directory to bring down Arcturus Mengsk, and then betrays them to the Zerg, then he betrays the Zerg to some unknown higher power.
Not to mention the Wanderer from Diablo II who is heavily implied to be the protagonist from the first game. In fact Blizzard (who makes Warcraft Starcraft and Diablo) is so fond of this trope that it has become known as the Blizzard Principle when in a video game you have to take on lasts games protagonist (or other good guy) who have gone mad.
Both Big Boss and Zero certainly qualify with regard to the Metal Gear series. One became the leader who of a mercenary nation who start war and is the antagonist for the first two game, while Zero and his Patriots are the antagonist behind the other numbered games. All because the Boss died.
Sigma from Mega Man X was originally the leader of the Maverick Hunters before he caught (and soon after became) The Virus from Zero and decided to go evil and declare war against mankind. Zero, in turn, does a Heel-Face Turn, caused by said virus transfer via a punch to the forehead.
Gradius ReBirth retcons Venom into an example of this—he starts off as James's CO, but becomes a heel after you complete the game's third loop. He goes on to become the Big Bad of Nemesis 2 and 3, two lesser-known installments released on the MSX over 20 years before.
Kazuya from Tekken. He was originally a Ryu-esque cookie-cutter hero but eventually let the devil consume him and became (arguable) one of the bad guys. By the beginning of the sixth game, he had plans for world domination.
And there's also Kazuya's son with Jun, Jin Kazama. He was The Hero for about three games, then at the beginning of the sixth game, takes over the mega corporation and uses it to start World War III and try to Take Over the World, which prompts Kazuya to speed up his plan for world domination.
To be fair though, it's heavilly implied that Jin is doing this just so that he can kill off his own bloodline by any means necessary, bringing both Kazuya and Heihachi out for him to fight up front. Though no one is aware of Lars, Heihachi's illegitimate son. Though quite villainous and menacing still, this does make Jin more of an Anti-Hero, or an Anti-Villain maybe.
The entire Mishima Zaibatsu, by 'Tekken 6, are caught in an endless Heel-Face Revolving Door. It would be boring to watch this over and over again, and the more interesting characters seem on the periphery by now, but alas, Namco takes the position that Elites Are More Glamorous.
In Neverwinter Nights 2, Neeshka, Sand and Qara will betray you at the end of the game if their influence is too low. And if you manage to keep Sand, Qara will automatically betray you and vice versa. The Sand-Qara conflict is explained by deleted content though.
And Bishop does so even earlier. He never was much of a Face to begin with. Though he can be persuaded to back out of the final fight.
In the backstory for Star Fox 64, Pigma Dengar betrayed James McCloud to Andross. Later in the series, Andross's grandson Dash Bowman undergoes one of these in two alternate endings for Star Fox: Command.
In a rare example of the player doing this, the original Streets of Rage has, near the end of Round 8, Mr. X asking you if you want to join him. In a 2-player game, if one player answers "yes" while the other answers "no," they will fight to the death, with the winner being asked again if they want to join. If the winner says no, and defeats Mr. X, the winner gets an alternate ending in which he or she becomes the new syndicate leader.
Soul Calibur: someone is doing one of these every five minutes. We have Siegfried, who did a Face to Heel (before the series even started) to Face to Heel to Face to Well-Intentioned Extremist Heel...and then back to Face again. Then there's Yun-Seong, who isn't all the way there yet, but he's getting there. Raphael, who did a Face Heel turn from 2 to 3, and did a Heel/Worse Heel turn from 3 to 4. Sophitia has done this in 4: arguably she has a good reason, but as she has been infused with the power of Soul Edge, there's nothing saying that she might not like this state of affairs later on. Then you've got Pyrrha, who went from Face to Heel (somewhat against her will) and then back to Face, and then BACK to Heel, before finally settling on Face.
In the fifth game the holy sword Soul Calibur itself somehow manages to turn heel whilst remaining determined to destroy the evil Soul Edge.
At the end of the Fallout 3 dlc Operation: Anchorage, an Outcast defender named Sibley gets disgusted that his superior is sharing the spoils with a "local" (you) and attempts to kill him unless you stop him.
Also, in the main game, Anna Holt is the one who tells the enclave about the project purity activation code, after she's captured, and later shows up as a scientist working for them in their base. Oddly enough, you still get bad karma for killing her.
In the Halo series, your buddy friend, 343 Guilty Spark does this on two occasions. In the first Halo, he helps you to activate the ring until Cortana stops him, saying that doing so will kill everyone. 343 Guilty Spark sees this as breaking protocol and then tries to kill you. This also happens in Halo 3, where you go to destroy the ark. 343 starts going off at you again and then kills Seargent Johnson. You quickly kill 343 Guilty Spark with Johnson's spartan laser.
In Call of Duty: Modern Warfare 2, Gen. Shepherd has one near the end of the game and kills Roach and Ghost.
Possible in Spider-Man: Web of Shadows if you choose to let the Symbiote have its way. In the end of an all villain story, Spider-Man becomes the emperor of the Symbiotes and rules over New York City.
In Guild Wars, Vizier Khilbron, who appears about halfway through the Prophecies campaign, provides indispensable assistance to the players on several occasions in fighting the White Mantle and their Mursaat allies, and turns out to be the Big Bad who has been manipulating the player all along to set up the proper conditions for his Titans to assault Tyria so he can take it over.
The leaders of the White Mantle, and the White Mantle as a whole. The Bonus Mission Pack shows White Mantle founder Saul D'Alessio as a pretty swell guy, fearlessly defending his homeland from the Charr in an epic battle with help from the Mursaat. What did he get for his trouble? The Mursaat kidnap him and take him away forever as payment for their help. The remaining survivors, who felt understandably betrayed and ripped off, decided fighting for justice isn't all it's cracked up to be, and instead started a campaign to take over Kryta and secure absolute power for themselves.
Shiro Tagachi. Granted he was manipulated into becoming corrupt and evil, but it's strongly implied that he used to be quite a fearsome defender of the innocent in his younger days.
Torin, a rather unimportant Ascalon Guardsman in the beginning of the Prophecies campaign, becomes a bandit after the apocalyptic Searing event. A quest directs you to find him and his bandit comrades outside Fort Ranik and kill him. The reason for his face heel turn is never explained. Then again, he was the minor-est of minor characters to begin with, so it's probably not important to the storyline.
More Ascalon Guards turn heel after the Searing: Footman Tate and Footman Quinn stole a priceless artifact from a temple and ran off with it. Their reasons are never explained, though it's probably simple greed. A quest has you hunting down the traitors. Footman Tate surrenders after a short dialogue, but Footman Quinn is hiding far from any civilized settlement and will attack you on sight without a word.
Markis, the Shining Blade councilman from Prophecies. He initially appears as a high ranking Shining Blade officer with the group's best interests at heart. After a few conspicuous absences, it's later revealed that he's a White Mantle infiltrator. Late in the campaign, he taunts you about Saidra's death and your stupidity at falling for his ruse. It ends with the player's group getting a very well-deserved Roaring Rampage of Revenge on him.
Elonbel from the Nightfall campaign. A local guardsman on Istan who cuts a deal with a local bandit group. When the player discovers his treason, he sides with the bandits and you're forced to kill them all. He's actually pretty tough, being a relatively high level enemy in a starting area of the game.
In the wii flight game Innocent Aces Orishima does this after a mock battle with the player because she had so much fun that she wanted a rematch.
Something similar to Sophitia above happened in BlazBlue: Continuum Shift. By the end of the series, Litchi Faye-Ling is forced to join the bad guys' side, since the bad guys kept the lover she's been trying to cure (Arakune) as a hostage and they had the cure she badly wanted, and she has to join if she wants both the cure and that lover. Throughout the series, she's usually one of the genuinely good characters.
Jan Kurtas/Medusa in Odium was a victim of Viral Transformation that turned him into a monster, but - unlike all other townspeople - he did not become an insane killing machine. Unless you blunder into the (entirely avoidable) scripted sequence where he finally succumbs and attacks you. (You can get an Optional Party Member as a replacement afterwards.)
Nathan Hale in Resistance 2 in the ending. Though only briefly.
You don't even go that fair. Just let one of the Martins escape during the final sequence and kick back and watch the fun. You get the same ending either way.
Septerra Core. Selina, when she saw Doskias almost getting killed by one of the good guys. Actually, she goes back and forth a few times throughout the game.
Marty "Monk" Malone is a loyal Corleone enforcer and a good friend of the protagonist in the video game adaptation of The Godfather. When his sister is murdered late in the game to get at the protagonist, Monk becomes embittered and eventually turns traitor, forcing the player to kill him.
Subverted in Pokemon Mystery Dungeon Explorers, when your partner seemingly sides with Darkrai, only for the hero to immediately deduce that they've been trapped in a nightmare due to knowing they'd never give up so easily, and snap themselves back to reality by attacking the latter of the two.
Clyde in Vigilante 8 goes from a member of the Vigilantes opposing OMAR and their thugs to the CEO of OMAR who stole a time machine to kill his former leader and ensure the submission of the US in the sequel thanks to finding Houston's mind control bracelets in a service station bathroom.
In the second to last route of Duel Savior DestinySelbium Volt turns on Taiga due to first blaming him for Mia's 'death' and when that turns out not to be the case he still blames him for ...something or other and gets even more antagonistic. And despite Taiga attempting to show him mercy, he tries to stab him in the back after the Duel Boss fight and gets killed for his trouble.
This isn't a trope that Starscream in Transformers: War for Cybertron would go down as he's more related to The Star Scream, but he starts out as an Autobot Scientist at the beginning of the Decepticon campaign. After Megatron bests his defenses, Starscream switches from the Autobots to the Decepticons. He later pulls his own trope off.
Mortal Kombat Deception sees Kabal actually reverting to his bad guy ways and running with it. After being rescued from death by the Chaos cleric Havik, Kabal is convinced to resurrect the criminal Black Dragon clan. He then finds Mavado (the Red Dragon thug who put him at Death's door), pays him back double, steals back his hookswords (which "feels good" for him to hold again) and then hires young, methodical killers to transform the Black Dragon from a band of pirates into a nihilistic organization determined to overthrow civilization. And Heaven help you if you don't fit Kabal's criteria of what a Black Dragon should be.
In Sly Cooper: Thieves In Time, the villainous Black Knight terrorizing Medieval England is revealed to be Penelope, a supporting character and ally in the previous game and love interest of Bentley. She has gotten tired of Bentley "wasting" his brain power with the Cooper Gang, and gives her boyfriend's time machine plans to the Big Bad in order to gain profit, kickstarting the entire plot of the game.
Oddly enough, her change from quirky Love Interest to evil Mad Scientist was probably the strangest part of the story. Since there wasn't any Fore Shadowing in the previous game that would lead to her becoming evil, it came off as clumsily executed. This is forgiven, however, because after all, if she didn't suddenly change sides, then we wouldn't have a game.
Happens to Salem in the 3rd game Army of Two: The Devil's Cartel, and he is also the final boss in the game.
In Final Fantasy Tactics A2 there's a pair of paladins who were known for the superb swordsmanship and skills in combat. However, one of the paladins, Frimelda, is superior to her other paladin friend, Luc Sardac, in battle skills. Luc Sardac tries his best to match his skills with Frimelda's, but he could never get any better. Rather than accepting his limitations, Luc Sardac decides to kill Frimelda so that he would be the superior paladin. It didn't stick due to Frimelda's sheer force of will keeping her alive, but as a zombie. When the zombified Frimelda and your party confront Luc Sardac over what happened, he decides to attack you.
In Kid Icarus: Uprising, Pyrron is just your everyday, Large Ham, fire happy sun god. He's just about the only guy who knows what the Auron are all about, and while he's mostly an idiot, he certainly knows how to make them hurt. Until you reach the Auron brain, and in the middle of the boss fight he dives right in and completely takes over the alien hive mind.
Pyrron: "I've leveled up! I'm a Level Infinity Epic Super God...PLUS!"
In A Witchs Tale, Loue seems to undergo this temporarily when you fight him for his doll.
In the New Game+, Anne grows up to become the Eld Witch.