Attack on Titan: The protagonist Eren Yeager after the 4-year time skip in season 4 has a major change of character after finding out the past & future events thanks to the activation of his Attack titan unique ability. As a result, he has disregards towards people's feelings & lives around him, even his own close friends. In the finale, he resorts to use the Rumbling to commit massive genocide towards every foreign nation, believing it's a necessarily evil to ensure his homeland Paradis's safety, as well as a form of vengeance for his deceased mom.
Avesta of Black and White: With its incredibly heavy focus on moral absolutes, this trope actually has its own name with it being referred to as Tentsui. It is something so rare that most think of it as a mere fairy-tale, but should it occur then it will change someone's very Avesta (i.e. alignment) from good to evil. Despite how rare it is it still doesn't stop some, like Magsarion, from slaughtering whole villages of good aligned people just to make sure it doesn't happen. It is eventually revealed that the cause of Tentsui is that someone violates their Commandment, a set of restrictions they have to abide by, and that it can happen to an entire universe should one side prove victorious, eternally perpetuating the war between good and evil.
We know that Griffith from Berserk is a bad guy at the start of the series, but most of us wouldn't know this from the idealistic mercenary leader that we meet at the start of the Golden Age arc, who is about as close to a Messianic Archetype as one can get in a series like Berserk. The Golden Age arc follows Griffth's rise as one of the greatest warriors of his age, but the big turning point comes when Guts leaves him due to wishing to pursue his own dream, a Tragic Mistake which leads to Griffith suffering a downward spiral, boinking Princess Charlotte, pissing off the King and getting put to the torture for a year, and by the time he is rescued by Guts, Casca and the rest of the Hawks, he has grown to hate Guts. This, among other contributing factors, ultimately leads Griffith over the Despair Event Horizon at the fatal moment that a certain Behelit he always carries returns to him, and during the ensuing events of the Eclipse, Griffith betrays everyone he's ever led, offering them all as sacrifice and condemning them to be eaten alive by demons in exchange for one last shot at his dream and ascension as the fifth member of the God Hand, Femto.
Heppokomaru/Gasser in the manga sequel of Bobobo-bo Bo-bobo. He comes around eventually, though. This fact is made more infuriating when everyone discovers that the reason he betrayed Bo-bobo and his group was in order to save his sister, who joined the empire of the Big Bad on her own, and is rather unpleasant in the personality department.
In Brave10, it turns out Anastasia is actually working for Hanzo as The Mole.
Code Geass has enough FaceHeel Turn and HeelFace Turn to drive one mad. By the end of the series everyone has switched to someplace at least once and some have done it two or three times do really screw your list over. Practically the only character never to change sides is C.C., who was on her own side from Day 1 and just followed Lelouch out of obligation.
There isn't much of an other way you can describe the Black Knights selling out Lelouch to Schneizel in exchange for Japan's freedom, since it involved them abandoning their obligation to fight against Britannia and later inadvertently aiding Schneizel in his own Totalitarian Utilitarian plans.
Destiny of the Shrine Maiden: Chikane switches to the bad guys' side towards the end of the series, but it's really a gambit so she will die instead of Himeko.
Vegeta from Dragon Ball Z, who was admittedly already a HeelFace Turn and technically just returning to his original alignment, went through yet another HeelFace Turn after the showdown of rivals. The whole arc also has the bonus of being a mid-life crisis as well as being a Not Brainwashed moment. Come to think of it, he is probably the one character in the entire series to do as many alignment changes as a pro wrestler.
It could be argued that he never switched sides at all, as he's always been on the same side: his own. Trusting him is the fault of the heroes.
Laxus in Fairy Tail, though how much of a Face he was to start with is debatable.
The entire reason Oración Seis seeks Nirvana is the ability to cause these at will in whoever they want.
Gray in the anime exclusive arc, though he's more of a Fake Defector. It turns out that Natsu forgot a promise to the villager that was sealed by Daphne and he kind of wanted him to destroy Daphne's artificial dragon.
Megumi in Gate Keepers, after her envy towards Ruriko reaches its peak.
Guilty Crown: Shu has one of these after Hare is killed, abandoning his faith in being a kind leader and becoming harsh and brutal to never let such a tragedy happen again. It´s later revealed to be a mask he puts on to help the efficiency of the trapped school, and he abandons it after most of the selfish students get murdered by Gai.
Debatably happens in Gunsmith Cats when Misty Brown chooses to give up on Rally and instead go and live happily ever after with Psycho Lesbian Goldie, aka the woman who earlier brainwashed and implicitly raped her. Debatably because we don't know if she is doing so voluntarily or due to still being brainwashed.
Hellsing: Walter C. Dornez, loyal aide to Integra Hellsing, first seems to do a FaceHeel Turn against his will after been brainwashed by the villains, but is later revealed to have been a willing traitor since WWII. However, he later did a HeelFace Turn by killing Doc, complete with Redemption Equals Death.
I'm Gonna Be an Angel!: Mikael does a Face Heel Turn in the last episodes of the series which ends in an epic breakdown. He gets better.
Kill la Kill: Ryuko is brainwashed by the Life Fibers into thinking that Ragyo was a loving parent, puts on Junketsu (then has it sewn onto her body so she can't take it off), and starts going after Satsuki. Luckily, the combined efforts of all the remaining good guys help her snap out of it.
In Magia Record: Puella Magi Madoka Magica Side Story, Felicia Mitsuki initially starts off as a magical girl mercenary who decides to work with Iroha's group upon first meeting her. But when the Wings of Magius tempt her with the offer to eradicate all wishes, as Felicia wants to destroy all witches due to a personal reason, she readily accepts... or so it seems. It's explained later that Yachiyo hired her to spy on them, but for a short while, Felicia actually stays with them because they offered her a better deal. She eventually comes back around to Iroha's side, though.
Tobi, member of the terrorist organization Akatsuki, is indirectly responsible for almost everything bad that happens to Naruto, including the death of his parents and turning Naruto into a jinchūriki. He was once Obito Uchiha, assumed to have died in the Third Shinobi World War... and was Kakashi's best friend.
Panty & Stocking with Garterbelt: In classic Gainax fashion, Stocking slices Panty up into 666 pieces and reveals that she is a demon about a minute before the end of the last episode (whether of the whole series or just the first season is yet to be known).
During chapter 4 of Pocket Monsters BW: The Heroes of Fire and Thunder, this is done by Alder, who seemingly reveals to Shin that he disappeared from the Elite Four as a decoy to take Reshiram for himself so that he can remain when N succeeds in his plans. This is subverted after Shins Emboar defeats Alders Volcarona, where Alder reveals that N knew that Shin was The Only One Allowed To Defeat Him, and thus sent Alder to make sure Reshiram accepts Shin as the Hero of Fire.
Sasame in Prétear later joins the Big Bad to become her servant because he was in love with her and couldn't bear to fight her. The Big Bad herself also face heel turned due to love. Later they both undo this with a HeelFace Turn to once again join the heroes.
In Puella Magi Madoka Magica, every witch apart from ex-familiars counts as this due to how magic works in the general universe, the most prominent in-series example being Sayaka becoming Oktavia Von Seckendorff after her Soul Gem darkened completely and turned into a Grief Seed.
While Witches can be given a pass in that they really have no say in whether they become evil or not, we get a straighter example in Rebellion, in which Homura friggin' Akemi pulls one, hijacking Madoka's powers to give her a normal life. While whether Madoka WANTS a normal life or not is debatable, what with her her losing her memories of the nightmare she had endured during the series and saying she DOES, the fact remains that Homura is now a self-proclaimed 'demon'.
Soul Eater: Kim and Jackie do an unwilling Face Heel Turn under the influence of Arachnaphobia's insanity manipulation machine. The actions of Justin Law, however, appear for the time being to be genuine: killing BJ and framing Stein for the murder (though Medusa almost certainly had a hand in it), trying to kill Maka Albarn as her soul perception might uncover Asura for Shinigami. He also seems to enjoy taunting the imprisoned Death the Kid, and listens in when Gopher is beating the boy up.
Death the Kid apparently cracked under all of the pressure and torture and pulled a FaceHeel Turn of his own. Thankfully it was a very brief one; he got better thanks to Black Star snapping him out of it.
Post-Time Skip Rossiu, previously a good guy, sets up Simon as a scapegoat for the problems caused by the Anti-Spirals and takes over the government - and his plan to survive the Anti-Spiral attacks involves leaving a large portion of the world's population to die.
The real FaceHeel Turn award doesn't go to Lord Genome, but to his daughter Nia, who was the unwilling messenger of the Anti-Spirals. The worst part? She had just gotten engaged to Simon.
X1999: An unavoidable fate of Kamui and Fuuma. If Kamui chooses either side (Dragons of Heaven or Dragons of Earth), one of them would immediately turn evil and kills Kotori. In every media, it's Fuuma who turns evil, but there are what-if scenarios that it Kamui would have turn out as bad as Fuuma did, while Fuuma would stay good.
Yu-Gi-Oh! 5D's: The Dark Signers, although whether Rudger - their leader - was ever on the side of good to begin with is questionable.
Yu-Gi-Oh! ZEXAL: Shark turns out to be Nasch, the leader of the Seven Barian Emperors, but was killed by Vector in his past life. After Durbe shows him his past memories, he transforms back into Nasch and opposes Yuma to protect Barian world.
Yu-Gi-Oh! VRAINS: GO Onizuka/The Gore, who invokes this trope and its inverse as part of his wrestling persona. When he plays Gouki Dark Mask he also declares he takes a heel turn, switching to a more brutal play style. By season 2 of the anime, he ends up playing this straight by joining the Bounty Hunters aligned against Playmaker. Season 3 has Ai become the Big Bad and vaguely stating that he intends to follow Lightning's will, but its actually for a differentagenda
Zatch Bell!: Wonrei joins the Faudo revival cult when his bookkeeper is placed under a curse that will kill her if Faudo is not revived. However, this Face Heel Turn is fairly temporary, as expected given the nature of the series.