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Maximum Ride: Ari. he becomes good after breaking the Flock out of The School in STWOES. Sadly, not long after this, he expires and dies. The Flock and Jeb hold a funeral for him. Later, there are many Ari clones, but they are all still evil.
Also, Maya/Max 2. she starts out as an evil clone and later becomes a part of Fang's Gang. Although many fans still viewed her as evil, as she was essentially Fang's replacement for Max and ruined all the shipping.
Michael Grant's Gone series: Caine does this at the end of Hunger, either because Diana was bleeding out and she needed Lana to live, or because he realized how bad the Gaiaphage is.
Charles Dickens' Oliver Twist: Sympathetic heel Nancy, a prostitute who by default was a villain for her relationship with brutal criminal Bill Sykes, and at first enjoys her life. Nancy begins to turn after forming a relationship with the title character, a young street orphan who is kidnapped to be part of a band of pickpockets in London. Eventually, due to her desire to see Oliver become a respectable person, she decides to try to return Oliver to his family, but Bill brutally kills her before she can do more than give a few hints as to his location.
Ebenezer Scrooge becoming reformed by his experiences is the plot of A Christmas Carol
Hans Ebert in Chung Kuo, after having lost everything, does some serious soul searching and changes his ways.
Dolokhov in War and Peace goes from being a Manipulative Bastard of a Humphrey, something of a minor antagonist, to the trusted lieutenant of Vaska Denisov as the Russians chase the retreating French. He is still the same amoral asshole as usual (witness his reaction to the death of the little Rostov) - he is just putting is evil badassery to a good use.
In Fred Saberhagen's trilogy Empire Of The East, Lord Chup served the evil Empire of the title faithfully ... until one of its warlords demanded: "You must be for once not brave, but cowardly.... It will be difficult only once. You must learn to cause pain, for the sake of nothing but causing pain. Only thus will you be bound to us entirely." Then he killed off a major demon, turning the tide of a critical battle. His Heel-Face Turn actually takes up the entire second book of the trilogy (The Black Mountains) and he goes on to become a major hero on the rebel side.
The Dresden Files: Harry Dresden refers this as the 'Vader Effect'. He is accused of it himself on several occasions, most notably when he joins the Wardens, the quasi-military magical police who have been on his back since his youth despite not actually changing sides. More specifically, the 'Vader Effect' is that feared enemies make great allies, because you know exactly how scary they are to the other guy. It's a natural extension of the expression "glad you're on our side".
A far more dramatic instance is when Lasciel's shadow image, or Lash, is convinced by Harry that she has free will of her own and "dies" saving Harry's life.
Angelina is the brilliant, beautiful, and psychopathic villainess of The Stainless Steel Rat. After she is captured and the psych-techs have worked on her, she marries the hero and becomes an agent of the Special Corp who doesn't enjoy killing. As much.
Mara Jade from the Star WarsExpanded Universe went from wanting to kill Luke to marrying him. That makes her Heel Face Turn queen.
A more minor example from the EU is Lara Notsil a.k.a. Gara Petothel of the X-Wing Series, who starts as The Mole. She ends up falling in love one of her "enemies" and growing affection for her squadron, causing her to turn on her Imperial commanders and greatly helping the Rebels defeat the Iron Fist.
Implied with the thief that was crucified next to Jesus according to the Gospel of Luke. He asked Jesus for forgiveness for his sins, and received it.
Acts of the Apostles: Saul who persecuted Christians until he had a vision from God and became one of the most influential Christians himself under the name of Paul the Apostle. Hence, in German, vom Saulus zum Paulus ("from Saul to Paul") is a common figure of speech for a Heel Face Turn, naming this very trope on the German language TV Tropes.
Subverted strangely in Montmorency. The titular character starts out as a liar, thief, almost a con-man, but by the end of the first book he's happily working for the British government, alongside Fox-Selwyn. However, he's also Scarper, who remains a problem.
In David Eddings's Malloreon, Zakath. Over the course of the third and fourth book of the series, he goes from being the brutal monster he is initially depicted as in the Belgariad, to a valued member of the group, and his friendship with Garion shows sign of bringing peace to the world finally. So long as they live long enough to do so.
Inspector Javert in Les MisÚrables, whose world view explodes with the sudden realization that Jean Valjean is simultaneously a criminal and a good guy. To let Valjean go free would be unlawful, while arresting him would be immoral. Javert removes the problem by removing himself from the problem. He drowns himself in the river Seine.
There are quite a number of turns in the Harry Potter series:
The Malfoy family make a rather big one towards the end of the series; Narcissa makes the biggest change when she lies to Voldemort that Harry is dead so she can go into the castle and see if her son is alive. By doing this she saves the battle for the good guys. Her husband Lucius has quite a similar turn although he is not as active in his turn as Narcissa. Draco Malfoy's turn happens gradually in the sixth book when he is given a mission by Voldemort to kill Albus Dumbledore. At first he's extremely full of himself but as the year goes on, he buckles under the pressure when he realises that failure means his death. Dumbledore offers him a chance to officially make the turn and he begins to before he is interrupted. He makes another Face Heel turn in the final book but is reunited with his family. In the epilogue he and Harry appear to have abandoned their differences for good, although Word of God says that they are "not friends".
Regulus Black, Sirius Black's brother, joined the Death Eaters willingly but after Voldemort almost kills his house elf, Regulus realises what Voldemort is capable of and begins to have second thoughts. He finally dies in an attempt to steal and destroy one of Voldemort's Horcruxes
Gellert Grindelwald has a small role but makes the turn anyway. As a child he had a friendship with Dumbledore but he eventually became an all powerful Dark Wizard until Dumbledore defeated him in a duel and he was imprisoned for the rest of his life. In the final book Voldemort attempts to get information from him about the whereabouts of the Elder Wand (he was the Wand's previous master) but he refuses to tell and is killed on the spot. Later Dumbledore remarks that some people said he felt remorse for what he had done.
To a lesser extent, so does Dumbledore himself. While in love with Grindelwald he enthusiastically accepts his pureblood supremacist views, and only rejects them when they fall out.
Garyl Shadowslayer from Shadowslayers pulled a heel-face turn at some point in his backstory, going from killing his mother and brother to risking his life to save the realm of Blackwood.
Wulfgar, in The Crystal Shard. The Reghedmen barbarians collectively attack the Ten Towns and are defeated by their militias led by Drizzt Do'Urden and Bruenor Battlehammer. Bruenor captures Wulfgar, barely more than a boy, and sets him to work in his forge. Ten years later, Wulfgar becomes the protagonist (of that book, at least).
Twice in The Stanley Family series. In The Famous Stanley Kidnapping Case, two of the kidnappers pull this and end up turning on their boss. In Janie's Private Eyes, former bully Pete Garvey, who is friends with the dog thieves, turns them into the police once he sees they're putting the Stanley family in danger.
Played with twice in Star Trek: Stargazer. In "Enigma", Obstructive Bureaucrat Admiral McAteer seems to defrost into a Jerk with a Heart of Gold. After a dangerous mission alongside Commander Gilaad ben Zoma, he appears to make a peace offering and reveal a more understanding side to his character. However, it transpires he was merely trying to manipulate ben Zoma. In Maker, murderous super-powered alien Brakmaktin also appears to be reconsidering his former conduct and having an epiphany. It turns out it was just him screwing with his captive.
In The Lion, the Witch, and the Wardrobe, Edmund Pevensie starts out as a self-centered brat who is easily manipulated to side with the White Witch against the Narnians and his own siblings. Later, when he is forced to see (and suffer) her cruelty, he takes the first opportunity to switch sides.
In Heather Tomlinson's The Swan Maiden, Doucette's sisters are cruel to her because she has no magic. When she discovers that she has magic, her sister Cecilia has one of these toward her, even though Doucette is now her rival.
This tends to happen in some Indonesian literature (Mostly KKPK, short for Kecil Kecil Punya Karya or 'Little Kids Who Creates') written by children. The thing that irritates is that in nearly every single one of the books that plays this trope straight, the rich, snobby Alpha Bitch (Always the Alpha Bitch, no exceptions) will turn good halfway through the story due to some event, and will instantly and melodramatically apologize to the hero, who instantly forgives her without any doubts whatsoever, despite the fact that they had been fighting since the first day of school. If not her, then it's her Girl Posse who will turn their backs at her because they haven't realized until today about how perfect, nice, religious, smart, etc the heroes are. Afterwards, the Alpha Bitches join the hero's group and have adventures like nothing has ever happened between them.
Author Jodi Picoult has featured several of her books in which many of her antagonists make a face turn, or at least we find out they were never as bad as they initially seem. There is also usually an unspoken promise between the main heel and main face: Josie in Nineteen Minutes she actually makes a few turns between face and heel, but the final turn she ends up shooting Matt, the main bully of herself and Peter Anna in My Sister's Keeper At first Anna comes across as the antagonist, setting the plot in motion that she is suing for medical emancipation and refuses to explain why. By the end of the story, we come to discover her face turn that Kate asked her to make the lawsuit. Shay Bourne in Change of Heart from the get-go, he is painted as a vile man sent to prison for murdering a police officer and his stepchild, he even says things throughout the book that make you just want to punch him in the face, but he makes his turn toward the end of the book when the truth is revealed that he didn't commit murder, that he was defending the girl from being molested by the police officer
In Fusion Fire, Tel Tellai slowly turns from blind adherence to Phoena Angelo and aristocratic Netaian ideas about who is worthy to live to a genuinely Nice Guy who wants to work to reform the moral failings in the Netaian system.
Kthonia did this pre-series but seeing her daughter killed in front of her by a man leads to a Face-Heel Turn.
Becoming Benji's auntie mellowed Zarracka out. Not only does she help in the fight against Kthonia without a devious agenda but she volunteers to go back to her cell when it's over.
The Wheel of Time: Ingtar, Asmodean, and Verin, amongst others. Fans have debated whether Asmodean's Heel-Face Turn was genuine because Rand and Lanfear left him with little other choice, but Word of God has confirmed that it was. Verin may not count because she only swore an oath to the Black Ajah to escape death and study them from the inside, and appears to have intended to be The Mole from the beginning. Ingtar's example is played straight.
In The Host Wanderer's joining the side of the humans. She is not alone in this; other souls like Sunny and Burns do the same.
Aftran does this in the Animorphs series, although she's actually an interesting example; we never saw her as a villain, she was just very supportive of Visser Three and the Yeerk Empire.
In Worm, Bonesaw, considered one of the worst villains and a creator of terrifyingBody Horror, undergoes one, though she's not remotely trusted, and in constant danger of backsliding even though she does want to change.
In the Rainbow Magic series, a goblin in Sophia the Snow Swan Fairy's book does this, and Lydia does this in the movie.
In the sequel to Those That Wake, Arielle Kliest is fine wit torturing Mal and threatening him to get what the Old Man wants—but when she sees the totality of his plan, which involves assimilating every mind on earth, she's horrified and betrays him.