In Alien in a Small Town, the alien calling himself Paul was responsible years ago for wiping out a small human colony on Jupiter's tiny moon of Adrastea. While it was, arguably, an honest albeit very stupid mistake born from his inexperience (he honestly did think they were about to attack his ship), the guilt for his actions and his need to atone for them have become the driving force of his life.
Cyan's mother, Belinda, becomes this at the end of The Amy Virus. She admits that her husband scared her into promoting a sham diet and emotionally and financially abusing their daughter, and that she's never been brave enough to stand up to him until Cyan runs away. Afterwards, she decides to divorce him and take full custody of their daughter so he can't hurt her ever again. Then after finding Cyan in Portland and reconciling with her, Belinda promises to expose the truth about the sham diet, stop claiming Cyan's autism is in remission, and make amends to the people she has hurt.
Ancillary Justice: Breq, after having killed lots of people because she was ordered to do so and didn't dare refuse, and to a lesser extent, Seivarden, who has some regrets after being a useless drug addict and stealing and selling Breq's ship to buy new drugs.
In The Reveal at the end of The Annals of the Chosen, Farash confesses he wished to atone for the sins he committed as the Chosen Leader. He never genuinely wanted to hurt anyone, but he used countless people, made a town his personal harem, and shirked his duty. Once he lost his power, he began to realize how horrible of a person he truly was and desired a way to make amends. So when he was offered the role as the Chosen Traitor, he accepted.
Artemis Fowl in the seventh book The Atlantis Complex is one of these. The guilt he has felt over his dealings with the Fairy people has caused a split personality. Artemis, who is cracking up, and Orion, his innocent alter ego, who's a moron. Artemis spends most of his parts of the book trying to make up for all the harm he's done, especially to Holly.
John Morgan Wilson's Benjamin Justice is atoning times two. To begin with, he's atoning for writing a series of articles about a man dying from AIDS that won a Pulitzer...and then turned out to be fake, which wrecked not just his career, but also that of his editor. As it turns out, those articles were themselves an attempt to atone for his own failure to be at his partner's side when he died of AIDS.
The Bible is full of this one (it's Older Than Feudalism). Examples include Joseph (atoning for pride), Moses (atoning for murder and later for disobeying God's orders), David (sent a man to die so he could have the guy's wife), Solomon (mainly legends, such as when he lets Ashmodai the demon king trick him), Judas (mostly in legend, for betraying Jesus), Paul (for persecuting Jesus' followers), and more saints than you can shake a stick at.
In Border Songs, Madeline Rousseau is a drug-runner and heavy drinker for most of the story, but cleans up at the end.
The Breaking the Wall trilogy: When a character who essentially committed Suicide By Romantic Rival gets a chance to redeem himself after death, he takes it and becomes a steadfast ally of the protagonists and a viewpoint character in the third book.
In Sandy Mitchell's Ciaphas Cainnote HERO OF THE IMPERIUM novel Duty Calls, the Battle Sisters realized that they had sheltered a renegade Inquisitor, and conclude their own zeal had misguided them; they sacrifice their lives for the escape of the people who brought them the truth, and regard it as the only possible atonement.
St. Augustine of Hippo considered himself one. It's pretty starkly apparent when you read his Confessions.
The Dresden Files: Sanya, a tall, muscular, black Russian. In his youth, being dark-skinned in Russia led him to be an outcast. He became seduced by the power of the Denarian, a coin that contains a Fallen Angel within, and his handler Rosana. He did many evil things under her influence and the coin's power. However, when he learns she sees him nothing more than a puppet, he leaves, thinking, My God, What Have I Done?, and relinquishes the coin. His genuine guilt purges the demon from within. Shortly there after, Sanya runs into a Knight of the Cross who offers him a chance to do some good and the Archangel Michael came forth to give Sanya Esperacchius making him the Knight of Hope. He now seeks to help people where he can. He is also a devout atheist, suggesting to Dresden that the Lord, His Angels, and the Fallen might just be super advanced beings, or he might simply be insane, but neither possibility change he can still do good with this sword.
Xanth from The Edge Chronicles. In the beginning, he was a Guardian of the Night, then, befriended Rook, made a HeelFace Turn, but was called back to the Guardians, helped infiltrate them and came back to Rook and Magda's side, where he was generally regarded as evil and tried to atone.
Andrew "Ender" Wiggin, becomes this after realizing that he had killed off the entire species of the Buggers—and that the whole War was a huge misunderstanding. He becomes the "Speaker for the Dead", accepting the Demonization his brother Peter has placed on his name (as Ender the Xenocide) as more than reasonable, and in general spends the next three thousand years without much company hopping from world to world, trying to make up for what he did. This is genuine atonement because Ender is a genuinely nice guy who was originally tricked into doing the nasty thing he did, on account of how he was, like, 12 at the time.
The Buggers themselves are this in the original book. As most Buggers are unintelligent drones that Queens control, they didn't think that individual beings without some Hive Mind behind them were real people. When they finally realized just how many individuals they killed, they immediately ceased the invasions, and while they didn't appear to take actions common to the Atoner, they seemed to feel they deserved the extinction that Ender brought to them, given that they had accidentally killed more individual humans than there may have been individual Queens in their entire population.
Fingerprints series has a complex example with Steve Mercsepher; the things he does to "atone" for his past evil are generally a lot worse than the the stuff he's trying to atone for but since he may count as a Well-Intentioned Extremist, the intent is still there.
Severus Snape, revealed in The Deathly Hallows. He coveted friends and darkness, becoming seduced by the dark ideals of the Death Eaters in his youth. He ends up destroying the one genuine friendship and his information led to his friend's death. For added salt, he has loved Lily Evans since they were children. After that fateful night, he set out on a path to protect Harry Potter.
Albus Dumbledore coveted power in his youth and had great ambitions to change the world. His actions led to the tragic event of his mentally-damaged sister laying dead and he was possibly her murderer in a chaotic fight between Grindwald, his brother, and himself. After that, he resigned himself to being just a teacher who would be better suited giving help to young students rather than taking any political power.
Gellert Grindelwald led the Wizarding World into a great war. He caused a lot of death and destruction. And after his capture and imprisonment, he lies to Voldemort about ever having the Macguffin Voldemort covets himself, trying to keep the man from claiming a powerful and dangerous magical tool. This is averted in the movie.
Regulus Black. He loved the idea of the dark arts, but realizes soon it isn't for fun and games. So, he seeks to fight Voldemort with all he could and sacrifices his own life in hopes that his ally and house-elf Kreacher can destroy Voldemort's soul.
Percy Weasley (never a villain as such, but he is shown to regret his past behaviour).
Tam Lin in House of the Scorpion was a Scottish terrorist that attempted to kill the prime minister of an unnamed country (presumably the UK). his bomb ended up killing a bus full of school children, and he was forced to escape to Opium for asylum. He commits suicide mid-way through the book (although this isn't revealed until the end) after helping Matt escape.
In Chris Roberson's Imperial Fists novel Sons of Dorn, Captain Taelos wants to be one. His commanders, however, sends him to collect aspirants instead.
Erill in Kane novel The Dark Crusade is forced by cultists of Sataki to commit unspeakable evil. Throughout the rest of the novel she is trying to make up for it. Unfortunately, her first attempt at atonement is a disaster, which ends in more death and suffering for her and her friends.
This happens to Jean Valjean over the course of Les Misérables. Although Valjean's 'horrible acts' themselves comprised stealing a loaf of bread to feed his starving family, trying to escape his prison sentence and then a couple of petty thefts from a bishop and a young boy upon release, he is less focused on these than what his prison stay turned him into. While in prison he lost all faith in God, society and human nature, vowing to take his revenge upon society at large once released, and it is this state of mind that he feels he has to atone for. One of his first acts upon release is to contemplate cold-blooded murder of an innocent man who had sheltered and fed him, and it is this mindset that horrifies him after his redemption. He is often a bit excessive about how much he punishes himself, however.
A key example would be his adoption of Cosette. After discovering that he had failed to intervene in the chain of events leading to Fantine's terrible fate, he took it as his personal mission to give her daughter the good life that she never had. He nearly sacrificed his own life several times over merely to bring about her happiness.
Boromir: I tried to take the ring from Frodo. I have paid.
In Masques Wolf seems to consider his fight against the Big Bad this, as he is the son of said villain and committed countless atrocities before he was able to recognize the evil of such actions and ran away.
Jordan Kyle from The Mortal Instrumentsdoes seem to sincerely regret what he did to Maia, and only picked Simon as an assignment so he could get close to her.
Razor Eddie, Punk God of the Straight Razor, in the Nightside series. In his teens he was a gang member, serial murderer, and all-round psychopath, until he underwent an unspecified but apparently horrific forced Epiphany Therapy at the hands of an equally unspecified but horrific supernatural being. He still kills people, but now he goes after the people who think their power and privilege protect them from their crimes, so he operates on the side of good. As far as one can tell.
Invoked quite eloquently by Taylor, the narrator/hero of the series, in the first book.
"He's a killer," I said. "Razor Eddie. Punk God of the Straight Razor. These days he kills with good rather than bad intentions, but in the end all he is, is killing. And he wouldn't have it any other way. Hard to get close to a man like that. Someone who's gone much further into the dark than I ever have. But... he turned his life around, Joanna. Whatever epiphany he found on the Street of the Gods, he threw aside everything that had ever had power over him, in order to earn redemption. How can you not admire courage like that? If someone like him can change, there's hope for all of us.
In a weird example, John is an atoner for something that he didn't do yet—specifically, destroying the world in an alternative future.
John Brenton of the Paradox Trilogy is motivated by his guilt over the things he did in the past as a member of a Government Conspiracy charged with upholding Masquerade. Though he is sincere in his desire to redeem himself, he is introduced as an antagonist, both because of his willingness to go to extreme and morally dubious measures and because the protagonist is initially unknowingly working for The Men in Black.
Adam Kelno, in Leon Uris' Q.B. VII spends the years after World War II working at a free medical clinic in Borneo to atone for having collaborated with the Nazis in medical experiments conducted on as many as 15,000 concentration camp prisoners. The novel explores the libel suit he brings against the reporter who brings this information to light.
Captain John Armstrong Brannigin in Alastair Reynolds' Revelation Space. He tries to kill himself/itself several times, via a giant deathray shot at his own hull. One of his crimes mentioned is overwriting the mind of one of his crew members with a copy of his own.
Hotzenplotz in Robber Hotzenplots makes a HeelFace Turn for robbing people and tries to spend rest of the book to make up for it. First, people don't believe him.
The Scarlet Letter has Hester successfully atone (settling on the outskirts of the village, patiently wearing her letter, and nevertheless managing to earn a living and forgive herself for her sin). Her onetime lover Rev. Dimmesdaletries to atone privately, with tragic results.
Mr. Canis from The Sisters Grimm is the Big Bad Wolf of Fairy Tales, trying to make up for his crimes. When under control, he appears as an elderly man—albeit one much stronger than you'd expect for his age and tall, thin build—but turns into a proper wolf when his Superpowered Evil Side emerges.
Dillon Cole from the Star Shards Chronicles. After spending the first book spreading chaos, destruction, and death, he manages to purge the spirit parasites that corrupted him and spends the rest of the series attempting to undo his evil deeds.
Kyp Durron is a serious Karma Houdini in the Jedi Academy Trilogy, in which he is influenced by an ancient evil spirit and goes on to use a superweapon to destroy a planet with 25 million people on it, and after getting rid of the spirit and nearly dying getting rid of the superweapon, is allowed to rejoin the Jedi Academy. All subsequent novels featuring him have that action haunt him to some extent. Even when he's not dwelling on it, someone is reminding him.
Wraith Squadron's Tyria Sarkin hasn't really done anything, but that's just it—she's the last of the Antarian Rangers from her homeworld, the Rangers being sort of supplements and allies of the Jedi. She takes it sort of personally.
Tyria: I've failed at everything I wanted to do in life so far. I failed to keep my family alive. I failed to learn the traditions of the Force and uphold my family tradition. I failed to enter the fighter corps on my own merits. But I got in anyway, by way of a cheat I shouldn't have accepted. Now all I want to do is find some sort of grace, something that will make up for my failures. Just once before I die.
Garik "Face" Loran, also from Wraith Squadron, qualifies as well. He was a child star in Imperial holodramas, and feels guilty that his films were used to make the Empire look good and to up recruitment numbers. This is part of why he keeps the scar he received as a child during an Imperial/Rebel firefight at least, until Ton Phanan leaves him money in his will with the requirement that he get the scar removed and realize that he's more than made up for whatever he did unwittingly as a child.
Galaxy of Fear has Mammon Hoole, who accidentally helped cause the once-thriving planet Kiva to become a Ghost Planet. He tried to ignore and forget his crimes, tried to alleviate his guilt by helping the Alderaanian orphans, but eventually has to return to Kiva. When confronted by the furious spirits of the Kivans, rather than try to escape or defend himself he submits. It's not really his fault—he was told the experiments were completely safe—but he feels responsible. He only escapes when he learns that Gog, his partner in the experiment and the one who lied to him about the experiment's safety, is still alive, since another part of Hoole's atonement was pursuing Gog across the galaxy to stop him from creating more tragedies like Kiva.
In Star Wars: Kenobi, Annileen pegs Ben (Obi-Wan Kenobi) as being out in the Tatooine desert to atone for some past failure or misdeed. Privately, Ben admits that while his mission to safeguard young Luke Skywalker is paramount, if he finds redemption for his role in the loss of Anakin and the rise of the Empire in the act, so much the better.
The Star Wars Expanded UniverseShort Story "Rebel Bluff" features Ria Clarr, who is attempting to make up for discovering the rich mineral deposits that existed under Lothal's farmland and reporting about it to Grand Moff Tarkin, which resulted in the Empire evicting all the residents to Tarkintown. She does this by handing out the credits from the sabacc pot she stole from Lando and then inspiring them to stand up to the Empire.
The Stranger Beside Me: Ann Rule joins the crisis hotline in order to atone for failing to stop her brother's suicide.
The Sword of Truth series: post High-HeelFace Turn, Sister Nicci, who afterwards wishes to be known as "just Nicci". After changing sides, she becomes one of Richard Rahl's most trusted lieutenants, and heals him from a fatal injury at the beginning of Chainfire. She mentions off hand in one of the later books that there are some times when she feels almost suicidally guilty for her previous crimes and for not killing Jagang when she had the chance. In fact, she is such an atoner that her motive for joining the villains in the first place was because she believed it was the only moral cause to make up for her sins.
In Poul Anderson's Time Patrol — particularly, "Brave To Be A King", Harpagus, dying, confesses that he had forced a time traveler to become Cyrus because he had been sent to kill the true Cyrus, and he had done all of it to atone. When Manse figures out how to keep the true Cyrus alive, one thing he uses to motivate himself is Harpagus will no longer suffer from the terrible guilt, even though Manse will remember it.
Use of Weapons: Zakalwe is presented as Sociopathic Hero, but still a person who is somewhat admirable, and certainly cool in a James Bond kind of way. There are many hints to his dark past, and the revelation of his past ultimately puts him at the Moral Event Horizon, and it's very difficult to tell if he genuinely repented, or was just trying to run from his past and pretend to be a good guy. The title in part refers to how The Culture is willing to use less than admirable people and methods to fulfill their aim of spreading utopia. However, MAJOR SPOILER AHEAD: The Stinger in the novel Surface Detail reveals that Zakalwe was one of the hero in the book, and he's shown as having genuinely changed his worldview and become a better person. This novel is set about a millennium later and he had to essentially go through Hell first.
At the end of James Swallow's Warhammer 40,000Horus Heresy novel The Flight of the Eisenstein, Voyen tells Garro that the only way he can atone for belonging to the lodge is to leave the Space Marines and dedicate his life to discovering a way to cure the disease that tainted Decius.
Graham McNeill's Warhammer 40000Ultramarines novel Dead Sky Black Sun recounts Uriel's quest to redeem himself, bound by a death oath, after he diverged from the Codex in Warriors of Ultramar.
Niall from Wicked Lovely, after realizing the true nature of the dark court, and after he realized that he inadvertently caused the deaths of the mortals. He's been atoning for it for 1200 years by the time of Ink Exchange, and still feels guilty. Appropriately, he is also the series' official woobie.
In Wise Blood, Hazel Motes becomes this in the final chapters. He blinds himself, walks with rocks and glass in his shoes, and wears barbed wire under his shirt. Whether any of this truly redeemed him is a question the novel doesn't answer.
Twilight of the Red Tsar: America has a huge change in attitudes towards Jews after the revelation of the Soviet Holocaust, leading to anti-Semitic views being practically eradicated and all Americans taught extensively about Nazi and Soviet atrocities, as well as a Jewish cultural revival occurring in the USA.
Syndicalist Hungary also makes up for its anti-Semitism after its delegates are attacked during a visit to New York in 1969 by angry protesters and Jewish Hungarian exiles. Hungary promptly establishes strong relations with Israel, celebrates Jewish culture in education and museums, rebuilds demolished synagogues and eventually becomes one of Israel's closest allies.
The international community becomes one on the whole to the Soviet Jewish community in the aftermath of the Soviet Holocaust after the failure to protect Jews during the Holocaust and failing to provide aid during the Chinese Refugee Crisis. Foreign groups and civil rights groups, alongside philanthropists, artists and ordinary citizens, raise hundreds of thousands for the Soviet Jews. In a major Pet the Dog move for them both, military dictators Chiang Kai-shek and Park Chung-hee send hundreds of Chinese and Korean volunteers to aid Jews in the refugee camps. Heartwarmingly, there's no shortage of volunteers, as many were survivors of or had lost nearly everything in the Sino-Soviet War and Korean War. Eventually, thousands of UN soldiers arrive to help protect the camps in Siberia.
Tatsu tries to play on this to recruit Hitman with a HeartJohn Rain for his own plans to reform Japanese society, but Rain is too cynical to really take it on board, despite feeling guilt for his past actions.