Once, they were a major villain. They did every crime one could think of, and did it with a song in their heart and a skip in their step. Then something happened. The Atoner has realized the error of their ways, possibly wants to make amends, and have decided that they will do so via heroic deeds. Simply going to jail won't do, because this isn't always applicable to their "sin." Besides, they have all these amazing skills from being a villain that would be wasted, and they can do more good out there.
The problem is, they often have to wrestle with going back to their old self, along with the massive guilt built up over years of carefree evil. Also, said previous villain skills usually involve killing people in very messy ways, which can result in karmically harmful situations. Other times their evil side won't go down without a fight, and manifests itself as a Superpowered Evil Side. Ultimately, it comes down to the fact that no amount of babies saved will make up for killing people in the past. The Atoner usually realizes that "Redemption is the path, not the destination" and continues for the rest of their life.
Sometimes 'the rest of their life' is short because Redemption Equals Death. Generally the only Atoners who avoid this are main characters who are already in the atoning stage by the series' start. Atoners often end up as Knights in Sour Armor. Those who believe redemptioninherentlyequals death may well become Death Seekers.
A subtrope of this is "Assassin Wants To Quit." Stories involving them allow us to cheer on the assassin as they battle their former employers using the same murderous skills they honed during their previous career. Atoners sometimes go on a Redemption Quest in order to atone. If their deed of atonement is especially painful, it may overlap with The Penance.
Would-be Atoners who are not sincere are trying to Buy Them Off. Not to be confused with The Aloner, though they can both coincide if the character is trying to atone for killing off everyone else on the planet. The Atoner must be careful not to run into the Heel Face Door Slam.
Genuine atoners have a high chance of becoming The Woobie, especially if they were an Anti-Villain in the first place. See also, Be All My Sins Remembered, where they continue to suffer a guilt complex over their past misdeeds. Contrast with My Greatest Failure - instead of a formerly evil character turning from their past, a good character feels the need to atone for not preventing a bad outcome (regardless of whether they could have changed anything). The Atoner may have experienced Go and Sin No More.
Ken Ichijouji in the second half of Digimon Adventure 02. After the breakdown of his Digimon Emperor persona, he works hard to undo all the damage he caused and redeem himself. Even as late as the series finale, however, when the characters are each shown their fondest wish Ken's vision is of himself beaten to death by the Digimon he abused as the Digimon Emperor.
In Digimon Tamers, there's Impmon, who became Beelzemon through a Deal with the Devil. Upon discovering his inner goodness, he realizes that he had completely crushed the soul of the former comic relief by eating her Digimon in front of her, which resulted in her being susceptible to being kidnapped and psychically tortured for several days by a modern-day Eldritch Abomination. Originally, Beelzemon was going to be the main villain (and indeed, in overall Digimon mythology, he is one of the 7 Great Demon Lords). However, the guilt of what he'd done broke and remade him.
To a lesser degree of drama there's Yamaki, who begins the series as the main villain and sinister man in black who ruthlessly deletes Digimon he sees as alternately disruptions to the natural order or the advance guard of an invasion, and threatens to take the children's partners away (to be fair, he doesn't do so when given the chance). However, when Juggernaut, his attempt to purge all digital life from the real world, not only fails horribly but opens the way for the real invasion, he has a genuine What Have I Done moment and spends the rest of the series working with the reunited Monster Makers to aid the Tamers. He modifies both the Hypnos system and many of his old programs into highly useful tools, and Juggernaut even becomes the means by which the ultimate enemy is finally deleted.
In the appropriately-named "Atonement Chapter" (Tsumihoroboshi-hen) of Higurashi No Naku Koro Ni, Keiichi is briefly able to break through the Groundhog Day Loop and is allowed to clearly see his actions in the first arc, in which the Hate Plague drove him to isolate himself from his friends and murder Rena and Mion. He becomes The Atoner as a result and redoubles his efforts to try and save Rena, who is now in the same boat as he was. Also, before he moved to Hinamizawa, he was a nihilistic loner who got his kicks by shooting at little kids with a pellet gun. When he severely injures a little kid (as opposed to the bruises it usually caused) he realized how horrible his actions were and turned over a new leaf.
Abel Nightroad from Trinity Blood is a centuries old Crusnik (uber-vampire who feeds on normal vampires, has superior destructive powers and is invincible) who used to hate humans and took the vampire side of the conflict when war broke out. He was essentially a living weapon of mass destruction and supposedly killed seven million humans. Eventually it was the death of his lover, who had sided with the humans (after telling him how to defeat the vampires) and had been trying to influence him, that caused him to change his views. Nine hundred years later, he's a priest of the Vatican and tries to avoid and prevent killing whenever he can, and is wracked by guilt for his sins.
Vash the Stampede from Trigun constantly is wracked by guilt over his past and the extensive body count that he blames himself for, even though none of it is truly his fault. What he truly has remorse for is the fact that he couldn't prevent said things from happening in the first place.
In the original manga Vash killed everyone in July except for himself and Knives who was critically injured. Vash was friends with several people in July and is forever haunted by killing his own friends for revenge.
Quent in Wolf's Rain is something of a variation on this. He only comes to realize that wolves are not evil when Toboe, the wolf he has been pursuing most vigorously, makes a futile attempt to save him from the Big Bad Lord Darcia. It is only afterthey have both been mortally wounded, and Quent realizes that it was Toboe who saved him from freezing to death on an earlier occasion, that Quent is able to redeem himself in a small way by comforting the dying Toboe as his own life ebbs away. It's not much - but it's enough.
The Prince of Tennis has Kippei "The Kyushuu Lion" Tachibana. While not an evil person, his playing style was highly violent. Then, his best friend and rival Senri Chitose became one of his victims when Tachibana accidentally hit him in the eye and almost blinded him. Wrecked with guilt, Tachibana seriously thought he should just leave tennis as a whole, but then his family transferred to Tokyo. He enrolled in Fudomine Junior High and and witnessed how the local tennis clubs' rookies were bullied by the sempais and the ex-coach; Tachibana stood up for them and became their leader and captain.
After being a Smug Snake and almost becoming the Big Bad, Yuri Killian from Kaleido Star decides to go into a 10-Minute Retirement and study art in Paris, only to return as a sponsor and later directly try to atone for his deeds. And not only for those he committed against the Stage.
And before that, the reason why Yuri was able to completely seizing the Stage is because Kalos Eidos let him do so as atonement for believing himself to have caused the death of Yuri's father on-stage due to a very ill-timed talk with him. Kalos saw Yuri's rise as his revenge for the death of Aaron and his (Kalos's) own punishment, which is why he didn't retaliate until the last moment.
Franz Bonaparta from Monster is played up as being the creepy childrens book author responsible for the madness that created Johan Liebert. As it turns out, he actually had everyone involved in the eugenics experiment killed so he could save Johan's twin sister from a similar fate.
Balsa from Moribito: Guardian of the Spirit wants to save eight lives for the eight lives that were taken in her protection as a child. To do so, she realizes would only mean something if she doesn't kill others. It's not easy to spare and escape a force of elite warriors.
Fullmetal Alchemist lives off this trope, as almost every single heroic character has done something either very stupid or very villainous which he or she is attempting to atone for.
Dr. Marcoh, Roy Mustang, Riza Hawkeye, and Alex Louis Armstrong's motivations are to atone for all the Ishvalans they killed during the Ishval Massacre. ESPECIALLY Armstrong, Roy, and Hawkeye. I.e., Roy's long-term goal when he becomes Fuhrer? He wants to turn the country into a democracy, and eventually be tried for his war crimes.
Ed and Al's primary reason for finding the Philosopher's Stone is to redeem their bodies after attempting to transmute their mom. At tie same time, Ed's own primary reason is to bring Alphonse back. It's either "our bodies" or "Alphonse"; he blamed himself for years, afraid to even ask Al if he blamed him for what happened.
Scar, whose transition from being motivated by revenge to wanting to break its cycle actually occurs during the series.
Dr Knox like the rest of above mentioned in the Ishavalan war, but he isolated himself from his friends and family.
Shou Tucker is an aversion; he doesn't seem to see anything wrong with combining his daughter and dog to accelerate his research. And this is the second time—the first time was his wife.
The 2003 anime version, however, uses Tucker in a villainous example. Once he finds out about Nina's death, he spends the rest of the series trying to bring Nina back, which extends to mutating himself into a grotesque beast man and siding with the likes of Greed and Frank Archer. Unfortunately, his efforts are in vain.
Lordgenome from Tengen Toppa Gurren Lagann, after hundreds of years of suppressing humanity underground, during the fight with the Anti-Spiral, he sacrifices himself to absorb the Infinity Big Bang Storm and transfer it to Spiral Energy, which the Dai-Gurren Brigade uses to defeat the Anti-Spiral. He even has a bit of a final goodbye to his daughter.
Fruits Basket: Ayame feels guilty about his neglect of his younger brother Yuki, and is trying to be a better big brother. The rift between them, and Ayame's natural extravagant manner not appealing to Yuki, makes it difficult, but Ayame persists and ultimately succeeds.
In the Back Story, Kazuma took on the Parental Substitute role for Kyo Sohma/the cat of the Zodiac because of his guilt over how badly he treated the last cat, his grandfather, when he was a youngster.
The reason Kagura is so hung up over Kyo is because A.) she only played with him as a child because his terrible home life/curse made her feel better about her own situation, and B.) she ran away in fear after seeing Kyo's true form and felt guilty about how withdrawn he became afterwards. Hence why she asks/warns Tohru to only approach and love Kyo if she really loves him, and not due to pìty.
Akito gets some of this after a Heel Face Turn, having realized how deeply their actions hurt others.
It's implied Braiking Boss, the person who ordered Luna's murder, is of this trope as well. He goes so far as to bury every follower of his that died from the Ruin, reasoning that he wanted to etch into his heart the pain the Ruin had caused.
Shuffle: After discovering that it was not Rin's fault that her beloved mother died Kaede Fuyou makes her purpose in life "to serve Rin-kun" — so she can make up to him for all the tremendous abuse she piled up on him. (who willingly took the blame because Kaede was this close to just let herself die by despair) before the discovery.
In Full Metal Panic, it's revealed that Kalinin always felt horrible guilt and great regret that he did nothing to save Sousuke's mother (who ended up plunging to her death on the frozen and broken down airplane). As a result, he feels the great need to make it up to Sousuke, and always had the great desire to adopt him as his own son. Unfortunately, Sousuke is sent to an orphanage, and the next time Kalinin meets him, he's shocked to see that Sousuke turned into a cold blooded, uncaring killer. This causes him to feel even more guilt for having let Sousuke go and become like this, and in turn becomes even more dead set on making it up to him.
Subverted in Kino's Journey. A once-violent criminal has decided to atone for his acts by accompanying the widow of a man he killed while she Walks The Earth as her bodyguard. The next scene shows the atoner dying in a forest clearing, as the widow has just emptied her pistol into him. She was so hurt that she didn't think he deserved atonement.
In the Code GeassGrand FinaleSuzaku - a former Death Seeker who wanted to atone for killing his own father, yet has been Geassed to Live at any cost - becomes one of these when he takes on the role of Zero at Lelouch's request. After killing him.
More than that, Suzaku was The Atoner all along. Driven to kill his father in order to save the population of his entire country, with dubious results, he joins the army... and starts being the Death Seeker he was up until the above scene in the finale.
Jeremiah Gottwald AKA Orange blames himself for not being able to protect Lady Marianne and her children and everything he does is him trying to atone for their deaths. This fuels his Chronic Backstabbing Disorder as after he finds out that Lelouch is alive; he betrays Britannia, under the guise of loyalty, to join the man who had been trying to destroy them, and after Zero left the black knights he followed him back to Britannia.
Both played straight and subverted in Baccano!. The straight example is Ennis, a HomunculusBattle Butler who detests her inability to oppose her master out of fear and tries to invoke Redemption Equals Death to redeem herself (it almost happens, but Firo negates the "death" part). Isaac and Miria subvert it: they want to atone for their (rather silly and harmless) past sins...Robin Hood style, technically escalating their crime spree.
In Magical Girl Lyrical Nanoha, the Wolkenritter join the TSAB to make up for their crimes committed while filling the Book of Darkness. Signum is particularly focused on this, as she states that she plans to repent for her crimes except when she is with Hayate, but Nanoha suggests that rather than regret what she did, she should just focus on helping people. Hayate is similarly motivated by a desire to make up for the Book of Darkness incident, having been subject to most of the blame for it and feeling responsible for it.
Chrono from Chrono Crusade deeply regrets joining Aion's side and being responsible for Mary Magdalene's death, and spends the entire series trying to be kind to people and help others to make up for his past sins. Also, the manga epilogue shows that Joshua Christopher joined the Order, with another character guessing he did it with hopes of atoning himself.
Raoh in Hokuto No Ken, at his very last moments before his suicide.
In Corsair, Canale tries to atone for his years as a Sharq assassin and particularly for the murder of Sesaam Zaiyaun, whom he was in love with. He requests that Ayace kill him several times, lest he bring anymore danger to the people he loves.
In Gundam Wing, this is a facet of Heero Yuy that shows up in a couple of major ways.
The first version of the opening credits hints at something that's finally revealed in Endless Waltz: one of Heero's first covert assignments (destroying an OZ mobile suit factory) went catastrophically out of control and ended up killing a young girl and her dog that he'd met the day before. Heero has been haunted by guilt over that ever since.
Vegeta from Dragon Ball Z in the Buu saga. He thought if he killed himself it would make up for the loss of Gohan, Who actually wasn't dead. And all the people at the stadium he'd killed earlier.
In Mai-Otome Zwei, Nina becomes this, wanting to make up for her actions in the previous series by helping Nao investigate the ruins in Episode 3, and fighting alongside Arika in the final battle in Episode 4.
In Muhyo And Roji, Enchu, despite being imprisoned for life in the Arcanum, studies to one day become an Executor and atone for his crimes.
Franken Fran has a seemingly demon-possessed cardinal and the front-runner to be the next Pope who turns out to have been a former gangster. After being saved from being shot in the head, he devoted his life to the Church, and faked the possession to avoid having an ex-criminal be Pope.
Alan from Windaria, who spends the bulk of his life rebuilding the world after he helped ruin it.
Gajeel from Fairy Tail becomes this after joining the titular guild. Confirmed as of chapter 212.
Crime Sorciere Jellal, Urtear, Meredy become this after the Time Skip.
Used as the twist in the Tenrou Island arc. After building up Zeref, who the villains are trying to awaken, as the most evil and powerful mage in history we find out he was never sealed at all, his inactivity instead having been due to a Heel Realization hundreds of years ago and making the arc villains actions pointless all along. Zeref embodies a particularly cruel version of this trope, desperately wanting to diefor his sins but being unable to control his Life/Death magic means he can neither die nor be anywhere near others so he can atone.
At the near-end of Shakugan no ShanaYuuji, knowing how much pain he had caused for the sake of Xanadu's creation with the power of the God of Creation, attempts to become this by leaving for Xanadu alone, in order to work to encourage the Crimson Denizens to live in peace with, and befriend, the humans living there. The love that he and Shana shared trumped this, however, and they leave for the new world together.
Yamamoto of Bleach regrets his actions when he first founded the Divisons and exterminated the Qunicy. At that time they were little more than killers, and Yamamoto was the worst of the bunch. In his eyes, he nearly destroyed Soul Society; he kept a portrait of his younger self to remind himself. Eventually this left him weakened, as he refused to depend on others for aid and so never regained his destroyed arm.
An even better example would be Retsu or actually Yachiru Unohana - the oldest captain after Yamamoto, who used to be the "most diabolical villain Soul Society has and will ever know" before her recruitment into the first generation of Gotei 13. Afterwards she became the 1st Kenpachi and founded the 11th division. In contemporary times, she is apparently trying to atone for her bloodthirsty past by becoming a healer, and seemingly one of the gentlest and most compassionate Shinigami seen.
Jeremy from A Cruel God Reigns feels that he should not experience love or be worthy of love to compensate for killing his stepfather.
Xerxes Break of Pandora Hearts is this, though he claims otherwise. This is because he was once Kevin Regnard, a Failure Knight driven to make a Deal with the Devil that required him to murder as part of his bargain. He made it with the hopes of changing the past, in order to bring back the murdered family he served. Eventually, after sacrificing 116 people to his Chain, he was dragged into the Abyss and was able to convince the Will of the Abyss to grant his wish. Unfortunately, he later learned his wish resulted in the family being murdered four years later.....by the one child that had survived the slaughter in the original timeline. The horror and grief over his actions are his driving motivation, though he keeps it secret from others.
In The DCU, post-Parallax Green Lantern Hal Jordan. Then it seemed that that Hal Jordan wasn't really Parallax, that he was merely possessed by an evil creature named Parallax that did all of those bad things and therefore absolves him of all responsibly and exempts him from Character Development. And then we see that he still feels responsible for his actions when being possessed, just like Kyle when he was possessed during the Sinestro Corps War. Part of his interaction with the Corps is trying to rebuild the trust he lost when he killed his fellow Corps members and essentially destroyed the original Green Lantern Corps.
Also from DC Comics, Pariah in Crisis on Infinite Earths, whose attempt to explore the origin of the universe has resulted in the destruction of his parallel universe, and personally believes that he may also be responsible for the destruction of the other parallel universes until the Anti-Monitor reveals that he himself is personally responsible for the latter.
Spawn. Especially since it was revealed that he chose to come back as a monster because that's how he viewed himself in life.
Marvel's new spin on Speedball fits here, even if Speedball was always a hero. Now he's blamed for 612 people he didn't actually murder. But, hey, he can change his name to PenanceBleedball and design a costume with 612 points of constant pain.
It turns out that he didn't make the suit for himself - he made it for Nitro, the true murderer. He only wore it because he felt he had to atone somewhat for failing to save all those people.
Also on the Thunderbolts team, there was Songbird, who honestly saw the team as a chance to redeem herself. Too bad the Thunderbolts were reorganized to be little more than killers on a leash after Norman Osborne took over.
The Thunderbolts could be a subversion. Most of them are little more than super-powered serial killers who joined up so they could kill under the law. Take for example Mac Gargan, a.k.a. Scorpion a.k.a. Venom. Easily the worst person to wear the symbiote. Rather than just being a pair of spider-haters out for revenge, Venom is now a violent, rampaging cannibal. He can't even tell friend from foe on the battlefield. And he's not the worst guy on the team.
Deadpool of the Marvel Universe is trying to atone, but the fact that he's so bad at it, combined with his natural psychopathy, means that most people don't even notice.
Which actually leads to the occasional legitimate Tearjerker. Especially in the recent X-Men Origins: Deadpool comic which managed to turn freaking Deadpool into a tragic character.
Eel O'Brian, aka Plastic Man, right from the 40s to his current incarnation.
A Batman story did a variant of this: Issue #127 of his self-titled book showed an alternative origin if his parents didn't get killed. In this version, Batman was a criminal called the Blue Bat, and the costume was worn by someone else. This all changed with an encounter with Bruce Wayne, who defeated the crook, took the costume for himself, and became Batman, noting, "This costume that was once a symbol of crime will now become a symbol of justice!"
Detective Harvey Bullock, a member of Batman's supporting cast, was introduced as a corrupt cop, but he saw the error of his ways. Since then, he's been working hard at cleaning up both Gotham City and his reputation.
Another Batman-related example: Scientist Kirk Langstrom, alias the supervillain Man-Bat, is often portrayed as trying to make up for the damage his Superpowered Evil Side has caused.
Back in the Marvel Universe, after several attempts to take over the universe, Thanos of Titan may have become the Atoner. In the Atrocious "Marvel Universe: The End" he destroys himself or seems to to save the universe, and then in a self-titled series started wandering around atoning for his old deeds. No one trusted his motives and the series was canceled before it was truly clear how genuine his motives were.
Gambit is another Marvel Universe example of this trope. He joined the X-Men due to the whole unwittingly helping some major baddies commit genocide thing. Admittedly Gambit never intentionally took part in said genocide and continues to be a much loved thief with a heart of gold to fans, but still.
In the Sonic The Hedgehog comics, Knuckles was like this for a bit after his time as the new Enerjak.
Recently Heel Face Turned villain Dimitri also feels the need to atone for his previous deeds, and issue #221 has a touching moment between him, NICOLE and Espio, both of whom are also invoking this trope following their respectiveactions during the Iron Dominion arc.
Similar, Flash Thompson, Venom IV, in the new series. A former high school bully who tormented many students during his teens (of which including Peter Parker and Jessica Jones), he was inspired by Spider-Man to turn his life around by joining the army. When he lost his legs in Iraq, he then signed on to become a Government-sponsored secret superhero using the Venom Symbiote. A lot of his motivation comes from wanting to make up for being such a horrible person during his teens.
Following Avengers Vs X-Men, Scott Summers, who under the corruption of the Phoenix Force caused the death of Charles Xavier, was willing to spend the rest of his life in jail paying for that and any other crimes he committed under its control (for those who don't know, that basically amounts to him refusing to do what the Avengers told him to do), until he realized that the sudden burst of new mutants mean that a large number of people are going to be hunted down by anti-mutant extremists, so he decided to break out of prison to protect them. Now, still hunted by the government and his former teammates, he's formed a new Brotherhood of Mutants so he can track down new mutants who need protection, whatever it takes. Most, however, just assume he's off his rocker and trying to upstage humanity. Though, he probably doesn't help his case by calling it a 'mutant revolution', or with the fact that his powers are on the fritz, making him unintentionally far more dangerous than he intends to be.
At one point, Hawkeye of the Avengers. After being manipulated to villainy, he joined the Avengers as a way to both make up for what he did, and also to do what he originally intended to do with his skills: Help people.
The Dragon Ball ZFan FicHonor Trip has Perfect Cell as The Atoner in an alternate universe where Gohan doesn't kill him at the Cell Games, but instead scrambles his programming with a blow to the head.
The X-Men fic The Wraith Saga presents an alternate timeline in which Jean Grey survived the events of The Dark Phoenix Saga and spends most of the story trying to atone for the destruction that she caused as the Dark Phoenix. At one point, she even returns to the charred ruins of D'Bari, the planet that she destroyed, to contemplate her past sins.
In The Blue Dragon, Malefor feels guilty of the past actions he did in the past, and throughout the story, atones for them.
In the Mai Hime fanfic, The Sword of the Lord, Nao and Reito are driven by a desire to atone for their actions in the Hime carnival. Nao despises Shizuru for apparently not doing the same.
Christian Humber Reloaded: Surprisingly, Vash sometimes is this. He turns himself in, apparently out of regret, after killing his friend Soku and the rest of her family in revenge for her turning him in. After bursting out of the stomach of a rogue dragon, he undergoes a quest to defeat the demon dragon Le Hung Doe. Unfortunately, those aren't even his worst crimes, and he remains largely unrepentant for actions such as killing six million people at the Super Bowl.
In many My Little Pony: Friendship Is Magic fics, Princess Luna, formally Nightmare Moon, becomes this after turning back to good after being banished to the moon for a thousand years.
There's also the redeemed members of the Dark World versions of the Mane Cast, but especially Applejack, who's working hard to atone so that she can join her sister in Pony Heaven.
Recursive Fanfiction gives Dark World another, rather surprising, example in the Valeyard, the Doctor's evil self and Discord's Starscream. After being killed and sent to Pony Hell, he's tasked with helping the recently departed Pinkie Pie rescue the soul of one of her adopted foals. Along the way, he rediscovers that Good Feels Good and, task completed, he rejects an offer of a lighter sentence in order to help the souls condemned to pull Havoc's chariot find redemption, wondering if he might earn it himself one day.
Light is this in AURagnarok, even though he's never acted upon his impulses he realizes he very nearly went insane as a teenager and was "a future Serial Killer in the making" and works to make up for it every day.
Captain Mendoza in the film The Mission used to be a cold-blooded officer who ordered the slaughter of many Guaraní natives, until he killed his brother in a fencing duel. He then went as far as climbing up a waterfall with a huge bag filled with Spanish armor tied to his back. Then he joined Father Gabriel and the Jesuits.
In Outlander, Kainan reveals that he had helped hunt the Moorwens to the brink of extinction, and that he considers his family's death Karmic Retribution. He doesn't have any qualms about killing the Moorwen that got loose in Norway, but he decides afterward to sever ties with his homeworld and stay with the Vikings.
The titular character of Solomon Kane was once a savage and ruthless mercenary. After an encounter with a demon and learning of his potential damnation, he pursued first a path of pacifism to cleanse his soul and then a path of righteous battle to cleanse the world.
Ulfric in Black Death. As it is likely that he had been at the battle of Crecy, where their opponents had been slaughtered instead of being given a mercy strike. He does give one to the woman accused of being a witch.
Pterano from The Land Before Time VII: The Stone of Cold Fire becomes this at the climax when Ducky (who he and his minions had kidnapped earlier in the film) finds herself in grave danger—coincidentally, the same danger that got one of his believers killed during an earlier expedition for the Stone.
Tony Stark, Natasha Romanov, and Bruce Banner in the Marvel Cinematic Universe. Tony and Natasha have legitimate sins to make up for (he was a selfish weapons dealer who didn't care that the collateral damage from the military-industrial complex's freewheeling use of his weapons caused hundreds of civilian deaths; she was a cold-blooded Russian spy and assassin, presumably working for ex-KGB operatives, who also indiscriminately killed hundreds of people, including numerous civilians and, by implication, children). Bruce, however, involuntarily turns into a destructive, mindless monster when he gets angry due to an experiment gone wrong, and all the deaths he's caused happened when he wasn't in his right mind, but that doesn't stop him from blaming himself or even trying to kill himself to rid the world of the Hulk.
In a similar case to Banner, Clint Barton became one after being freed from Loki's Brainwashed and Crazy mind control. In his case it's particularly noteworthy considering the only reason Loki enslaved him was due to his skill (making him a valuable pawn) and because he had 'heart', yet he still feels responsible despite having no control over himself. His first request upon being freed was to know exactly who and how many innocent people he killed while under Loki's thumb.
In By The Sword, Suba is this by training himself back into Master Swordsman shape so that he can teach the helpless students, encourage good behaviors in them, and correct the Maestro's, Villard, behavior before he becomes just like him.
In the Amazing Spider Man, Peter originally interprets Uncle Ben's death as something he needs to atone for, ruthlessly hunting down the criminal responsible for killing him. Its not until he saves a bunch of people from falling to their deaths, specifically a small child, and realizes that the Lizard was Doctor Connors, that he shifts to acting more like an actual hero.
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.
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.
Older Than Feudalism: The Bible is full of this one. 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.
A subversion in the Fingerprints series 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. May count as a Well-Intentioned Extremist.
Xanth from The Edge Chronicles. In the beginning, he was a Guardian of the Night, then, befriended Rook, made a Heel Face 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.
In Sandy Mitchell's Ciaphas Cain 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.
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.
At the end of James Swallow's Warhammer 40000Horus 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.
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
Kyp Durron is a serious Karma Houdini in the Jedi Academy Trilogy, when he got influenced by an ancient evil spirit and went 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 was 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.
"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.
Averted with NatasiDaala, though. The author who dredged her up for Legacy of the Force seems to have confused her with the highly effective and not-really-evil Grand Admiral Thrawn, who might conceivably be unanimously elected to the head of the new government. Might. Even with Thrawn, those people doing the electing who were part of the New Republic during his last campaign wouldn't remember him fondly, and he didn't subject a defenseless New Republic colony to orbital bombardment for kicks.
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.
Zakalwe, the protagonist of Use of Weapons comes across as a deconstruction of this trope. He's 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 newest novel Surface Detail reveals that Zakalwe was one of the protagonists in the book, and he's shown as having genuinely changed his worldview and become a better person. Granted, this novel is set about a millennium later and he had to essentially go through Hell first.
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.
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.
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.
The Sword of Truth series: post High Heel Face 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 Chris Roberson's Imperial Fists novel Sons of Dorn, Captain Taelos wants to be one. His commanders, however, sends him to collect aspirants instead.
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.
St. Augustine of Hippo considered himself one. It's pretty starkly apparent when you read his Confessions.
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.
Hotzenplotz in Robber Hotzenplots makes a Heel Face Turn for robbing people and tries to spend rest of the book to make up for it. First, people don't believe him.
Artemis Fowl in his 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.
Andrew "Ender" Wiggin, of Ender's Game, 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 with not much company hopping from world to world, trying to make up for what he did. Something of a subversion, as Ender is actually a 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.
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.
In Border Songs, Madeline Rousseau is a drug-runner and heavy drinker for most of the story, but cleans up at the end.
In a weird example, John of Nightside is an atoner for something that he didn't do yet - specifically, destroying the world in an alternative future.
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.
When a character who essentially committed Suicide By Romantic Rival gets a chance to redeem himself after death in the Breaking The Wall trilogy, he takes it and becomes a steadfast ally of the protagonists and a viewpoint character in the third book.
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.
In Poul Anderson's "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.
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.
Doctor Who, 9th-11th Doctors. After genocidally ending the Time War, the Doctor becomes an intermittent pacifist who won't let anyone else commit genocide. The 9th Doctor arguably has it the most, since it was either him personally or his immediate predecessor who committed the double genocide.
Rory, after apparently killing his own fiancee.
Dalek Caan. Made much better because Daleks were designed specifically to be unable to repent and seek to atone.
As the page quote indicates, this figures in the plotline of "A Town Called Mercy", as Jex, a scientist who turned members of his race into cyborg warriors, became a country doctor during the 1880s to make up for his crimes. The Doctor called him out on it. The Doctor is often cast as the Atoner as well, especially after it was revealed that he destroyed his own people to end the Time War after they had become genocidal. Oddly enough, in "A Town Called Mercy", his own Atoner tendencies came into question by Amy:
The Doctor: No, today I honor the victims first. His, The Master's, the Daleks'. All the people that died because of my mercy! Amy: See this is what happens when you travel alone for too long.
He doesn't really fall into this category until Season 7, as until then he didn't care at all about any suffering or death he caused. Even in Season 7, he doesn't make much of an effort to atone for his deeds.
Angel too, particularly the season 3 episode "Amends."
Andrew tries to become this in Season 7, after his attempt to play Goodfellas with Warren and Jonathan and take over Sunnydale went horribly, horribly wrong and the first evil forces him to kill Jonathan. He means well, but has some trouble fitting in with the good guys due to his general social awkwardness.
Angel: Angel, Faith, and Spike. Fittingly, this is a show that's all about a quest for redemption.
Seeley Booth of Bones is looking to save around 50 lives to make up for the 50 he took as a Sniper.
Nick Knight from Forever Knight. And really, heroic vampires in general.
But avoided in Moonlight, where Mick St. John was never evil.
The eponymous character on My Name Is Earl is atoning for a lifetime of petty crime, carelessness and Jerkassery, though he's sometimes comically inept, or has unconventional means of going about it. He states that his goal is to become a better person- it's an interesting question whether he's just going it to get good Karma, or if he's truly changed.
Michael from Prison Break is a double example. He embarks on his quest to free Linc from Fox River to atone for not appreciating the sacrifices Linc made for him and for thinking he was guilty. Later in the series he attempts to atone for all the deaths his actions have indirectly caused.
In Babylon 5, Delenn is the Minbari ambassador to the humans and completely devoted to improving the relationship between the two races and always the first to defend humans against criticism. In one episode it is revealed that when the first contact resulted in a misunderstanding that made the humans open fire and got the Minbari Supreme Leader killed, she was the one who gave the order to Kill All Humans! in response.
Some of the blame belongs to her colleagues though. Anybody should have known better than to give such a decision to a distraught young woman cradling the dead body of her mentor and first love.
Maybe they did know better: maybe the Warrior Caste wanted to increase it's prestige and knew it was a chance to Manipulate her.
She was the deciding vote on the otherwise split council. Essentially, picture the US Vice President. She was obligated to cast the vote that decided what would be done. The fact that she loved Dukhat was irrelevant.
Londo is this toward the end.
Or not. By that time he seems to have given up on his own atonement and was instead working to save his people believing he was damned whatever happened. Which is in its own way rather a heroic if gloomy thought but not quite the same thing.
The tie-in novel covering Londo's ultimate fate (official canon) does state that Londo achieved redemption in the eyes of his people, if not his own.
G'Kar also receives redemption, but has the (mis)fortune to achieve it in his own lifetime and among his own people, becoming revered almost as a living god as a result.
Sebastian Stark from the TV series Shark was a ruthless defence attorney until a client killed his wife shortly after Stark got him acquitted of spousal abuse charges. He turned around and joined the District Attorney's office, using his underhanded legal tactics to put away the types of criminals he used to get off.
In one episode, Lieutenant Columbo claims to have joined the police department as a way to atone for his rowdy past. Apparently, when he was younger he and his friends would stick potatoes in other people's exhaust vents so the cars wouldn't start.
While never explicitly stated in the show, it is hinted that Shepherd Book in Firefly is an Atoner.
Caprica Six of the new Battlestar Galactica fits this trope to a T: after seducing Gaius Baltar and conducting the bit of cybernetic sabotage required to render the Colonial Fleet so much space junk and led to the deaths of all but 50,000 of 50 billion people, her visions of Baltar (whom she decides she had loved) make her want to make up for the crap she had done to the humans. Her success is... variable.
LOST: Several characters. Subverted with Mr. Eko, who, as a former child soldier and later drug trafficker and ruthless killer, seems to be a clear-cut Atoner - until he is finally revealed to be utterly unrepentant, considering his past actions necessary first to save his brother and then to survive the bloody lifestyle he willingly took upon himself in doing so. Then he gets killed by a giant black smoke-tentacle.
Richard Alpert started as Atoner, which was his reason for gaining immortality from Jacob. After he accidentally killed a doctor for not giving medicine to his dying wife, a priest told him during confession that he will never gain redemption for his sin. Upon meeting Jacob, Richard was offered a job and a gift: while Jacob could not resurrect his wife or absolve him from all his sins, he granted him immortality so that he atone for his actions.
Ben finally became an Atoner by the end of the series, experiencing a personal breakthrough, helping Hugo to watch over the island in life, and staying behind in the flash sideways feeling he was not yet ready to move on.
In Stargate SG-1, Teal'c wants very much to atone for his actions as the servant of the Big Bad. This is especially true when he is put on trial for a killing he did as a Mook. Even though the trial is completely unfair, Teal'c refuses to escape and is determined to take the punishment as a way of making it up to one of his victims somehow. Fortunately, the Goa'uld attack the proceeding and Teal'c defends the innocents so wholeheartedly and that his accuser forgives him.
Daniel Jackson, in defending Teal'c at the trial, practically has to pull teeth just to get Teal'c to admit ANYTHING in his own defense, such as why he chose an old crippled man when he was order to kill one of the crowd as an example (in later raids, that group of refugees would be able to move faster and escape into their safety tunnels like the others).
Tomin gets like this in The Ark of Truth, after realizing how the Priors are twisting the religion of Origin to excuse genocide. Teal'c gives him some advice on how to live with himself despite the things he's done in the past: he should concentrate on helping other people, fighting so that others can be saved. While he may never achieve personal redemption, "that is the least you can do".
Mr. Finch from Person of Interest. He created a software program that predicts grand terrorist incidents as well as "smaller" crimes (namely murder), but made it to where the program dumped all of the data on those "smaller" crimes every 24 hours. After a series of incidents where he was made cognizant of how bad an idea that was, he began to seek out someone who could help him prevent one of those "smaller" crimes from happening each day. When he found Reese, he knew he found his man.
Reese is also trying to atone for his years spent as a government assassin. His work caused him to abandon his girlfriend and later prevented him from saving her from her abusive husband.
In Have Gun — Will Travel, Paladin's backstory makes him this along with an interesting spin on Redeeming Replacement. He was hired to challenge a man named Smoke who he believed to be a villain terrorizing a town. Smoke sarcastically referred to him as a paladin during their gunfight, and the future Paladin fatally wounded him, learning too late that Smoke was defending the town and the villain was his employer. Thus, he decided to don Smoke's costume and do good in that guise (starting with killing his treacherous employer).
On Downton Abbey there is Bates. Carson is also, slightly, but it's played for a laugh at his expense and own melodrama.
Sebastian Smythe, the main Big Bad for the first half of Glee's third season, shows signs of becoming this as of "On My Way," after Karofsky's attempted suicide.
Deconstructed with Mitchell from Being Human. He ended up slipping too much due to his Horror Hunger, resulting in murdering 20 people on a tube carriage. After trying to atone during the most of the next season, he realises he never will be able to overcome his blood addiction and his best friend George stakes him to prevent him being used as an "attack dog" by the Old Ones in an extremely tearjerking moment
Also applies to Hal, once an even worse vampire than Mitchell, who has managed to not kill anyone for 55 years, and manages his Horror Hunger by withdrawing from society and obsessively sticking to routine. The Big Bad of the season revealed that this is a cyclical thing for Hal where he becomes The Atoner for a few decades, ends up going Off the Wagon for some time and then tries to find a new way to atone. Whether he will really succeed this time remains to be seen.
Tess Mercer's character arc for the tenth season of Smallville is basically this. After a Heel Face Turn at the end of season nine, she spends the beginning of season ten mostly staying out of the way, and the rest of the season as the new Watchtower, helping the good guys while clearly hoping that she can at least try to make up for the things she'd done before. By the end of the season it also seems at times like she's trying to atone for her surprise Luthor bloodline.
Revolution: Miles did some pretty brutal stuff and was probably more brutal than Monroe at first. He executes two men who he believed murdered some travelers despite Monroe's objections. He seems to regret some of his actions which led to his leaving the Republic and him assisting the rebels.
Scandal: Olivia wants to do right by her clients, but especially the ones who are women caught in infidelity scandals. Those hit a little close to home for her.
Stefan from The Vampire Diaries. He has been a Ripper on and off for his entire immortal life, but has always realized the errors of his ways and therefore, always tries to atone for his dark past.
I've stoked the fire, seen more pain than you can know/The tears of the broken have washed away my soul/Pushed by desire to change the way my stream will flow/Now I've awoken, and I'm taking back control
In The Gamers Alliance, Omaroch becomes this after he breaks free from the dark god Mardük's control. He sees it as his fault that his sons ended up on a dark path, and he was partially responsible for the birth of the Godslayer who shattered the world's continents. He wants to atone for his past actions and hopes to be able to set things right again even if it means sacrificing himself to achieve that goal.
Sinestro is this in the World of Heroes roleplay, with interesting consequences.
Amanda Remous used to be a ruthless assassin and mercenary who was nearly borderline terrorist. After reuniting with her brother, she began to regret the things she did and joined Dino Attack Team, striving to redeem herself of the crimes she committed.
General George Ogel used to be the ruthless general to Evil Ogel's Skeleton Done armies. However, when he reunited with Talia Kaahs, he had a Heel Realization and decided to make it his goal to redeem himself.
George Brown was a young man who got caught in the wrong side of the realist-idealist feud, and later provided information on Cam O'Cozy and volunteered for a campaign in the hopes of redeeming himself.
Blaire Darkling tried to do this, leaving behind his life as the dangerous criminal Matthew Vherestorm and tried to redeem himself by working for Paradox, an organization devoted to researching the Maelstrom to help Nexus Force defeat it. Unfortunately, it didn't quite work out, as this ultimately landed him in another organization, XERRD, which went on to create the Dino Attack apocalypse.
A recurring character in Warhammer 40000 is Cypher, a fallen Space Marine who seems to be seeking redemption, and may or may not be the key to the salvation of the Dark Angels chapter and their successors, if not the Imperium as a whole. The setting being what it is, Cypher is fired upon by the Dark Angels at every opportunity and hounded by the Inquisition.
The Dark Angels themselves quietly style themselves as this, and refer to themselves the Unforgiven - all because ten thousand years ago, a few of their number turned on their brothers out of pride or confusion. This being 40K, Redemption Equals Other People's Deaths - the Chapter is obsessed with hunting down their traitorous kin, who have been scattered across space and time, and helping them find "redemption," usually after days or weeks of torture.
Though it is hinted in the lore that it is in fact the Dark Angels and their Primarch who were the traitors but who turned their cloak AGAIN after hearing Horus had lost, and the Fallen Angels are the remnants of the loyalist force that fought them, who know that truth.
Also, inquisitors can have witches that are atoning for their crimes as part of their retinue, but this being Warhammer 40000, they probably had to undergo painful torture beforehand. Also, they are regarded as little more than psychic lightning rods, with game rules letting them take a psychic attack instead of it hitting the Inquisitor.
This is also an inherent trope with the gas-masked Death Korps of Krieg, thanks to an attempted rebellion that threw Krieg into 500 years of civil war — and a self-inflicted atomic cleansing of their entire surface — before the loyalists retook control. The Death Korps, seeking to atone for this failure, regularly commit their regiments to the biggest stalemates, the bloodiest sieges, and the biggest meat grinders in the galaxy.
The Craftworld Eldar have this as well. They live extremely regimented and spartan lives intentionally because their past depravity and barbarism created Slaanesh. It happens on an individual level with their evil kin, the Dark Eldar as well: some of them have a Heel Realization and leave Commorragh, seeking new lives in Exodite societies, Harlequin troupes, or simply as hermits, mercenaries and corsairs. Doesn't sound like much, but considering what kind of stuff the Dark Eldar do, it's a really big improvement.
Here's a canonical tale from Pathfinder: Some years before the setting's current time, a fourteen-year-old Street Urchin named Seelah stole a paladin's helm, intending to pawn it for food money. Later, the paladin died of a blow to the head. Seelah, consumed with guilt, returned the helm with the intent to commit suicide on the paladin's funeral pyre. Instead, she was taken in by the order and became the iconic paladin.
In the world of In Nomine (an ongoing War between Heaven and Hell), it is possible for a demon to redeem and join the ranks of the angels, fighting to undo the evil they once supported. Just remember that old habits can be hard to break ...
One of the two main paths for Abyssal Exalted is to become this, make up for their dark deeds in the service of the Void and work their asses off to avoid spontaneously combusting from Resonance. If they can pull it off, they become Solars, without the Great Curse that messed up so very much of the First Age. The potential impact of this remains to be seen.
In BIONICLE, Brutaka is treated as one: sent to the highest security prison in this verse, sent to a suicide mission as probation, then welcomed back in the Hero Secret Service. The big surprise is that his best friend Axonn, who had to stop him when he betrayed, is another, according to the Atlas.
Dante from Dantes Inferno spends the game as one of these in Hell in order to redeem himself after slaughtering hundreds and commiting adultery in the Third Crusade. He frequently has animated flashbacks detailing his previous life.
Zero from the Mega Man X & Zero series attempts to atone for the damage he did as a Maverick, yet ultimately does not redeem himself until his true death in Zero 4, where he saves the last free colony of humans on Earth from destruction by sacrificing himself. Later on in Mega Man ZX, it's revealed that this action resulted in an unprecedented era of peace and harmony between humanity and machines.
Hee. Consider that it was Dr. Light's creations that were fighting for everlasting peace and whatnot, and it was Dr. Wily's greatest creation that ended up becoming the one who achieves it.
Ciel from the same series can also qualify: part of her founding the Resistance is from the guilt she feels over constructing Copy X.
Zero is also an odd case in that it's never made entirely clear how aware he is of his role in the problem. As far as he knows (at least until the very end of X5), Dr. Wily is just a mysterious figure who haunts his nightmares. By X8, however, Sigma is openly referencing catching The Virus from him. He only finds out the truth about Omega seconds before the confrontation. Also worth noting is that none of these developed from any conscious decision Zero himself made - the former resulted from a mind-controlling virus implanted in him and the latter a case of Grand Theft Me.
Zero is aware of his connection to The Virus. The ending of X6 (confirmed canon by Word Of God) states that Zero was sealing himself to remove a dangerous "component" in his body. When he re-emerges during the Elf Wars, Zero learns of his connection to Omega during their confrontation. By the end of it, Zero even realizes how much more damage he has inflicted, and decided to seal himself for a second time, this time permanently (at least until Zero begins, that is). That's twoHeroic Sacrifices in a row.
Also from Mega Man X: Dr. Cain. What did he do? Reverse-engineer the title character's design, resulting in the creation of the Reploid race. Sadly, he never got around to issuing "ethics testing" on all of his creations, resulting in the Maverick uprisings. He tried to make up for this by founding the Maverick Hunters, but most of his other attempts to improve the Maverick Hunters' effort only turned the situations for the worse: Repliforce, Dr. Doppler, and especially Sigma, his masterpiece.
Super Robot Wars: Original Generation has a few of these. In one case, it's averted when the guy who wants to be The Atoner dies just after he is defeated. Played straight with Levi Tolar, who was killed but later found resurrected by nanotechnology, lacking her memory. At first, they hid her true identity from her out of fear that she'd go back to being the Big Bad, but when she found out, she was determined to protect her "sister" and her sister's friends at all costs.
Levi plays it to a T in her native Super Robot Wars Alpha timeline, where never lost her memory but joins the heroes anyway, and ends up fighting her old masters in the final game.
Also Gilliam Yager, provided that you played Hero Senki
Super Robot Wars Judgment has Al-Van Lunks during the end of the game. After helping the heroes defeat Gu-Landon, he attempts to sacrifice himself to keep the energy released after the defeat of the Fury's mothership from killing all of the sleeping Fury. He feels that it's the only way he can atone for all of the horrible things he did. After a -lot- of convincing otherwise from the protagonist and the other two sub-pilots arriving in a repaired Raftclans that had been picked up earlier "just in case" which can do just what Al-Van himself was prepared to sacrifice himself for him to choose to live instead. By the end of the game, he's helping the Fury migrate to Earth, and has come to accept what he did.
Atton of Knights of the Old Republic II is a big example of this: he used to enjoy torturing Jedi to death/until they turned to the Dark Side. I mean come on! Attonement?
In Kotor II, it's the Jedi Exile, who's still trying to get over blowing up thousands of her own troops in addition to the enemy soldiers at the battle of Malachor V.
The Force Unleashed has Galen Marek/Starkiller. After hunting Jedi for Darth Vader, and gathering the enemies of the empire, he decides to save the rebel leaders and challenge the Sith. Unfortunately, since Redemption Equals Death, he must sacrifice his life to prevent the Emperor from killing the rebels and buying them time to escape.
The games aren't quite clear on the Redemption Equals Death part. We don't have Word Of God to confirm it either, so Starkiller in TFU II may possibly (though unlikely) be Galen Marek from the original TFU. Considering that the second game ended on a Sequel Hook, TFU III may clear it up.
If you convince the spirit of Aribeth that Tyr will accept her back in Neverwinter Nights Hordes of the Underdark, she becomes one. Nathyrra has been one from the beginning.
Sagacious Zu in Jade Empire. He was once a servant of the Empire known as a Lotus Assassin. Subverted as far as Zu feels no guilt over most of his actions as an Assassin, but his last mission — to kill an innocent woman and a child in an act of punitive revenge against the husband/father — pushed him over the brink and made him betray the assassins.
Death's Hand may become this as well, under certain circumstances. You can bind him to yourself, forcing him to serve you, and if you pursue the Open Palm ending and release the Water Dragon, his epilogue states that he spends the rest of his existence trying to atone for the crimes he committed.
Regal Bryant of Tales Of Symphonia has all the hallmarks of The Atoner cranked up to eleven, going so far as to voluntarily shackle his own hands and swearing to never use them for destructive means again after being forced to kill his mutated and brain-washed fiance — who was trying to resist killing him — to free her from the suffering she was undergoing.. At the time the party encounters him, he is serving a lengthy prison sentence for his 'sin'; however, only escaping and joining up after the party turns out to be his best (well, only) prospect for redemption - as well as revenge on those truly responsible.
Regal is actually preceded by Judas from Tales Of Destiny 2, who is the epitome of Atoner, though not shown quite so obviously. He's actually the dead traitor Leon Magnus, revived from the dead, but refused to work with a grander scheme of evil, and ends up helping the son of the man he betrayed.
Lloyd and Genis of Tales Of Symphonia are driven to atone for their attempt to help Marble resulting in their village being attacked and Marble herself being turned into a monster and forced to sacrifice herself to protect them. This is especially evident in their desire to save her granddaughter Chocolat.
There's also The Good Incarnation, the first of the Nameless One's incarnations, who became immortal in the first place to make a last-ditch attempt at redeeming himself from a life of evil. He failed because of flaws in the ritual that granted him immortality.
Finally, there's Morte, who remembers nothing of his mortal life besides an uneasy certainty that he somehow wronged the Nameless One and so remains his loyal follower through centuries of abuse, believing that he must deserve it. Although as petitioners can never, ever actually remember their lives, it might just as easily be Practical's manipulation striking again.
Siegfried Schtauffen, post-Soul Calibur II, is working to atone for the evil things he did as Nightmare by destroying Soul Edge.
Brigid Tenenbaum from BioShock. She worked with the Nazis in World War II, she marketed ADAM even though she was fully aware of the side effects, and she developed the Little Sisters, orphans who have been transformed into twisted corruptions of little girls whose vomit is harvested for ADAM. That last one sparked the contrition. They weren't even always orphans beforehand.
Riku. The remorse of his little "deal with the darkness" was so great, he needed over one year and help by his best friend Sora (who was surprisingly forgiving) to forgive himself.
Ansem the Wise at the end of Kingdom Hearts II. As he stated in the ending for Kingdom Hearts Birth By Sleep, "I tried to take revenge and did some terrible things to that boy and his friends." Yet by the climax of II he's truly sorry for everything.
Dark Knight Cecil from Final Fantasy IV becomes an Atoner after he is stripped of his command by the King of Baron for questioning his orders to destroy the Mist Village (a home of summoners) and stealing the Crystal of Water from Mysidia. His journey eventually leads him back to Mysidia, where the village elder reminds him that he has to go to Mt. Ordeals to become a Paladin to complete the change.
Later, Dragoon Kain seeks atonement for his service to Golbez.
Celes Chere, from Final Fantasy VI, a former General of the Empire that joins the Returners, then becomes the first hope in defeating Kefka after the Apocolypse.
While never a completely evil character, she did commit some atrocities like burning Maranda.
And was complicit in Terra's enslavement, although the game doesn't really touch on this much, apart from her recognizing Terra when they meet again in Narshe.
Shadow could also be interpreted as this trope, as he either dies in the world of ruin protecting the party from Kefka, or stays around to help the group (And watch over Relm). Shadow seems to hate himself both for leaving his friend to die, as well as for abandoning Relm and her mother. In the end, Redemption Equals Death, as Shadow remains in Kefka's tower to die while telling his dead friend that he's done running.
Rufus Shinra of Final Fantasy VII after he survives the events in the game. Although never directly mentioned again, he is vaguely referenced to be donating to respectable causes for restoring the planet...after nearly destroying it.
Reeve Tuseti also qualifies, although he was not nearly as villainous as the rest of Shinra Electric Company's ensemble cast; he's largely just feeling guilty that he had been part of the group, and that things happened on his watch.
Not exactly the trope per se, but Cloud Strife also tries to atone for the deaths of Zack and Aerith during the events of Advent Children despite not being a villain.
Same can be said for Vincent Valentine and what happened with the whole incident involving Lucretia, Grimoire, and Hojo.
Auron from Final Fantasy X might possibly fit this trope. His "sin"? Helpless to see his two friends, Braska and Jecht, sacrifice their life and humanity, respectively, to (temporarily) defeat Sin and aiding this cause by his deeds, even if he opposed the idea all the way up to the bitter end.
Reddas in Final Fantasy XII dedicates his life to preventing the use of Nethicite after he destroyed the city of Nabudis using the Midlight Shard during his career as a Judge Magister
In the World of Warcraft expansion Wrath of the Lich King, this seems to be part of the motivation behind the Knights of the Ebon Blade, the Player Character Death Knight faction. Seeking atonement through either the destruction of the Lich King, or die trying. The player starts off as initially serving the Lich King under the command of Darion Mograine, son of the former Highlord Mograne (both of whom are Fallen Heroes) though after Darion is convinced by Tirion Fordring to atone, they split off to become good Death Knights. On the other hand, more than a few Knights of the Ebon Blade are only The Atoner in the sense that they want revenge on the Lich King by any means necessary and still enjoy using the most evil powers the Lich King granted them against anyone who would dare stand in their way. Also, both Atoners and still-evil-vengeance-seekers were all Brainwashed and Crazy under the Lich King. Tirion didn't so much "convince" as "allow" Darion to switch sides. There seems to be a grand total of one Death Knight, Thassarian, who is well-adjusted about this.
Ormus the Penitent stands out in that he put out his own eyes, unable to bear everything he did as a Death Knight. While he is unable to wield the Light, he instead works to forge Saronite, and hands out the Ashen Verdict reputation rings.
There are also elements of the Horde that feel this way. Varok Saurfang's memories of having butchered innocents still haunt him, and who is determined to even put himself and his son in danger to prove that honor and valor are the true future of the Horde.
The number of 'good' death knights interested in being The Atoner can be counted on one hand. On average, they're the Token Evil Teammate, roleplaying player characters notwithstanding.
Every single protagonist save Ellen in I Have No Mouth and I Must Scream. Arguably, the one with the most to atone for is Nimdok, a Nazi scientist responsible for the deaths of thousands of Jews- including his own parents.
Gorrister is an odd example. He blames himself for the death of his wife, but he didn't actually cause that to happen. If the player does everything correctly, he eventually comes to realize this.
Kratos of God Of War was initially this, wishing to atone for his murder of his wife and daughter in order to free himself from the nightmares. However the Gods chose to forgive him but not take away his nightmares. This proceeds to make him more pissed off at them than he already was.
It's also arguably a subversion. The whole reason Kratos sought redemption from the gods in the first place was because he wanted to be rid of the nightmares. He has absolutely no qualms about slaughtering every living thing he comes across, and doesn't even care about being forgiven for his sins. He just wants to be able to sleep at night without being reminded of how much of a murderous dick he is. By the beginning of the second game, he's given up the idea of redemption entirely, and just goes back to helping the Spartans conquer the world.
And then plays it straight in God Of War 3 when he starts to accept the consequences of his actions and eventually sacrifices himself to release Hope back into the world, to the heart of humans.
Sten of Dragon Age: Origins wants to atone for murdering eight people in a berserk panic after losing his sword. This is a little less extreme than it sounds: in Qunari culture, a warrior's sword is his soul, and his life is forfeit without it, so that he cannot hope to return to his homeland if his sword is gone. In addition to that, the killing of those eight people dishonors him and shames him to his people, so even if he gets back his sword, he still has to atone for his actions.
Also, Loghain becomes one if you conscript him instead of executing him at the Landsmeet. At first, he fails to understand that you want to give him a second chance out of kindness and keeps insisting that he should be the one to do through with the suicide mission of killing the Archdemon, since in his eyes death will be his only way to atone. However, if you deny him this, he'll become a loyal subject of Grey Wardens and is dedicated to help in rebuilding the order as his atonement work.
Another major Atoner character is Leliana, an ex-spy and assassin who found religion and devoted her life to good works.
Anders in Dragon Age II, following the destruction of the Chantry in Kirkwall, can potentially become this if you have him at high rivarly and try to convince him that his merging with Justice was wrong and that there are other ways for mages to win their freedom, so that he will join Hawke's team when they side with the templars. If you side with the mages, Merrill will still invoke this when you ask the team if Anders should live or die.
Merrill: He should come with us. Do what he can to put things right.
Anders: Thank you for my life. I'll try not to make such a mess of it this time.
Hakumen. What's he atoning for? In the past, he was Jin Kisaragi, a complete Jerkass and evil man who was obsessed with his brother and had his share of depravities. To say that Hakumen is disgusted at his past is a frikkin' understatement.
The Legend of Zelda: The Wind Waker: The King of Red Lions aka: King Daphnes Nohansen Hyrule. In a simmilar case as Auron from Final Fantasy X above, he couldn't pass on to afterlife due to his regrets. However, instead of becoming a physical ghost, he became a boat. (He is a boat, motherf***!)
Mass Effect 2 has two main examples: Thane Krios, an assassin who's attempting to spend his last days trying to repent for his killings and trying to make a world a better place and Mordin Solus, a doctor who was a former Special Forces agent and upgraded the Depopulation Bomb affecting the Krogans after he learned that they were adapting to the original strain.
Shepard his/herself can be played as this if you choose the Ruthless background then play as a Paragon.
Or alternatively if you have the Earthborn background and War Hero reputation.
Both Miranda and Jacob become ones to a certain extent in Mass Effect 3 due to their past work with Cerberus.
John Marston, the main protagonist and player character of Red Dead Redemption fits this trope to a 'T'. He was once a murderous and thieving outlaw who rode with a gang who left him for dead after a botched robbery. He started a family and got started on a farm, but after only a couple years the government took his family and told him if he didn't capture or kill his former gang his family would be killed. Unforunately, he does just that, gets his family back and starts repairing his livelihood and relationship with his son when out of the blue the government agent in charge brings the US Army to his ranch and guns him to death.
Fenkenstrain in Runescape start to spend rest of his life in Harmony Island, helping local monks after killing a family, its servants and doing numerous experiments.
In the Spyro the Dragon reboot trilogy, Cynder is the main villain of the first game, turned into an evil adult dragon against her will. Spyro finally manages to save her and return her to her normal child age and kind personality. She spends the next two games trying to make up for what she did, even wearing the jewelry she wore as an adult to help her face what happened.
Gordon Halloway from The Longest Journey is another example, since his motivation in accepting the role of the Thirteenth Guardian was to atone for the evil he did as both Halloway in Stark and as his Arcadian alter ego, Black Chaos. Which is impressive, given that he had been forcibly split into two as a Vanguard experiment and never had a chance to develop humanity or a conscience before he was made whole by April.
Ysuran Auondril, an elven necromancer in Baldur's Gate: Dark Alliance 2, begins the game with nothing but a spellbook, a bad case of amnesia, and a strange desire to help everyone he comes across. If you investigate his past, he remembers being a member of the Eldreth Veluuthra, an elven terrorist faction that wants genocide against humans, and swears to make penance for his crimes.
In Professor Layton and the Unwound Future, Dmitri tries to atone for a time travel experiment that Bill Hawks pushed through before it was ready, resulting in the deaths of Claire and several other people by completing said time travel machine to save Claire, which Layton describes as "a twisted form of atonement". The Big Bad resolves to become one in the ending.
Mamiya Shinzo in Kara no Shoujo.He went insane and turned his lover int a model for a fresco by cutting off all her limbs and putting her into a large black egg. When he was sane agaiu, he absolutely repented and felt the fresco was a horrible horrible thing, but by then it was too late and worse, there was no real way to atone for it.
Fallout New Vegas has Joshua Graham, The Burned Man. The co-founder and former Legate of Caesar's Legion, after surviving his execution (or as he calls it, his "baptism by fire") he returned to his home of New Canaan to become a Mormon Missionary once again. In Honest Hearts he's now protecting a peaceful tribe from an evil tribe aligned with the Legion. However, the game also shows that despite his genuine desire to atone for everything he's done he still possesses the same brutality that he had as Legate Graham, only now rather than a General Ripper, he's a Knight TemplarBadass Preacher.
Paarthurnax, master of the Greybeards and younger brother and lieutenant of Alduin having realized the evil of the actions of his kin, helped the ancient Nords to learn Shouts and to fight dragons back. He waits on top of the Throat of the World, meditating and trying to come to terms with his actions, but also struggling at every moment between his will to make amends and his dragon instincts. His atonement extends to help the Dragonborn in his quest by helping him/her to obtain an Elder Scroll so the player can find and learn Dragonrend. He goes as far as fight Alduin to buy the Dragonborn some time to defeat him. It is possible to kill him and gain the help of the Blades by doing so, but the Greybeards will chew you for doing so. It pays off in the end as the dragons hail him as their new leader after Alduin's death as he swears he'll try his best to make them change their ways.
Brunhulf Free-Winter, the new jarl of Windhelm if you defeat Ulfric, wants to do anything he can to make people forget about the Stormcloak rebellion by rebuilding Windhelm's image and ending the Fantastic Racism Ulfric enforced. He wasn't a Stormcloak of a supporter of the rebellion, but he feels obligated to do so as a true Nord.
Erandur, the priest of Mara. Formerly a priest of Vaermina, Daedric Prince of Nightmares, he abandoned his former life after leaving his fellow daedra worshipers in a miasma-induced coma within the temple. Afterwards, he chose to devote himself to Mara and will help the player deal with the nightmares plaguing Dawnstar.
Merveille feels guilty for Creating Life without thought to how the lives she created would actually live, especially once their purpose was fulfilled. She and Béluga work together to undermine Bruno, wanting to learn to permanently seal Lares rather than helping him control it.
Elh, the Paladin who originally had the Lares medalion, feels guilty for betraying Red and attempting to kill him in the Rite of Forfeit. When he is forced in to Trance by The Order and nearly strangles her, she even says that it would be okay if he killed her in revenge for what she did. Luckily, it turns out that Redemption Equals Death is not in play; instead, Redemption Equals Red Telling Her To Stop Saying Nonsense.
Trauma Team has CR-S01, a surgeon sentenced to 250 years in prison for his involvement in a biological terrorist attack at Cumberland College. He doesn't have any memory of doing it, but this only drives him further to redeem himself by saving lives. In a subversion, however, it turns out that he doesn't have any memories of his involvement in the attack because he wasn't involved in the attack.
In Immortal Souls, John Turner used to be a champion street racer until a race gone wrong resulted in him accidentally hitting a man and sending him into a coma. He then becomes obsessed with trying to earn the forgiveness of the victim's sister and make it up to her, including falling in love with her along the way, though he can't bring himself actually admit he's the one responsible.
Karel from Fire Emblem Elibe. In the prequel, Rekka no Ken, he was a massive Blood Knight known as the Devil Sword who rediscovered a part of his humanity through his supports. In Fuuin no Tsurugi, his Older and Wiser self is the famed Saint of Swords, and acts much more mature.
Also, Harken blames himself heavily for being the Sole Survivor of Lord Elbert's crew and, if you recruit him, he'll fight to the end and his own to atone.
Other examples from that continuity include Horace and Katarina.
Little Busters: Mio holds a huge guilt complex for forgetting Midori, her imaginary friend turned real from childhood, after her parents sent her to therapy and gave her medication. Her route even involves her giving up her entire existence so that Midori can live instead of her. It's even sadder in that in the real world, Midori doesn't actually exist - she only appears in the game because that's part of the world Mio had the boys create.
In Hatoful Boyfriend Sakazaki Yuuya is midway between this point and My Greatest Failure. When he was very young someone killed his father to marry his mother, and would have killed his unhatched brother. Yuuya hung on to it and switched it with his new half-brother's egg so his brother would survive, then smashed the new egg. This action weighs heavily on him years later and is something he's unable to ever forget, though he's fully accepted it and what it means, and so he tries endlessly to do good and save people.
General Protection Fault's Trudy fits this trope to a T. She goes from relentlessly controlling others to her own ends, even seducing a man to run over romantic rival Ki's father, and almost taking over the world, to relatively normal worker for GPF.
An example of "Assassin Wants To Quit" is Marilith. And she wants to quit with her former hostage.
Rumisiel in Misfile. He wasn't a Big Bad, but it was his screw up and chronic drug/alcohol addiction that caused Ash and Emily's problems. Started off somewhat half heartedly, but has begun to get serious about his role.
Vash is a much more serious example.
In City Of Reality, it's revealed that the Manumitor, who made it his mission to undo the transformations made by the psychotic magical supervillain Hinto Ama, is actually Hinto Ama herself, attempting to undo the damage she has done. Until someone she cares about gets hurt, she absolutely refuses to use her powers, relying on technology instead, and tries to kill one of the heroes who is stuck in a transformed state, feeling that death is better than being trapped in such a form.
El Goonish Shive: Abraham tried to kill based on his overly broad criteria for an abomination. He relented after Nanase talked him out of it. He has since reconsidered his response to beings created by the Dewitchery Diamond. Now he provides the page image, but he's still obviously incorrigibly dramatic.
MSF High: After causing a giant war and nearly taking over the galaxy, the Legion surrendered, apologized, and became these. Exactly why has not yet been explored.
Subverted with Miko Miyazaki in The Order of the Stick. After destroying the gate, she's visited by the spirit of Soon Kim, believing she's officially redeemed herself. Soon however tells her that while she technically protected her goal by destroying it, the fact that she was unable to accept that she was ever wrong meant that she did not redeem herself, even in death. However, she does die in peace, knowing that at least she'll be able to visit her horse in the afterlife, if not become a paladin again.
Jack. Becoming The Atoner is an option for souls imprisoned in Hell and is actually a valid way to eventually escape the confinement and reincarnate on Earth. Even one of the Greater Demons—the titular Jack—is inclined this way. As a punishment for obliterating the human race he was made the Grim Reaper and forced to encounter every death thenceforth. Although, as an additional punishment, he was denied the memory of his sins, he still tries his best to give whatever comfort possible to the unfortunate hellbound souls.
After his attempts at global domination in ancient Egypt fell apart in a battle against Suras(/Zeus) in Wayward Sons, Kronos escaped, and wound up alone in ancient China, where he was taken in by a family of simple farmers. He would later use his powers to protect them from bandits, and all looked set to begin again... But Kronos had learned from his past failures, and vowed to create an empire of peace this time around.
Huang: What you did to those men... You must be a god! Kronos: Once I might have let you believe that... But I've learned my lesson. I'm not a god. But I am your friend!
"Iratu and I went on to live in Hell. Darius trusted us to take care of our little brother, but we just threw Buwaro away. If you are reading this and I am no longer around, then I've gotten what I deserved.
William Griffin of KateModern performed frequent dangerous medical experiments on unwitting girls on behalf of the Order, but then decides to try to bring the Order down.
In the Let's Play of Princess Maker 2, after Lizzie ends up dying in a fight with the God of War, Gendo Ikari (who plays the role of the girl's father), in a fit of Heroic BSOD decides to try and reconcile with his other kid... by playing a Shinji-raising Sim game.
Some agents in the Protectors of the Plot Continuum are former badfic authors hoping to undo the damage they've done to the multiverse, or ex-DIS who returned to the PPC when given the chance.
Yanagi in Canvas 2 after stealing the main character's painting five years ago.
In Marvels RPG, Ant-Man created Ultron, Iron Cross is a former Nazi-Super Soldier and Synch accidentally burned down his school when his powers first manifested. All are trying to atone for their pasts to some degree.
In Batman Beyond, Terry McGinnis is a mild atoner. He was something of a juvenile delinquent before meeting the now-retired Bruce Wayne, and sees being the new Batman as a way to make up for that.
Zeta, star of the spinoff The Zeta Project, has elements of this- a former assassin robot who gained free will and doesn't want to kill anymore. When he finds other robots of his type, he tries to stop them.
Subverted in an episode of The Simpsons. Mr. Burns, after losing his fortune and learning about ecology from Lisa, is determined to turn his life around and rebuild his fortune doing good works. Unfortunately, Mr. Burn's idea of "doing good" involves raping and pillaging the environment in an even worse way than he had as the CEO of a pollution-causing nuclear power plant. (Lisa then is forced to admit that Mr. Burns is just naturally evil—and when he tries to be good, his twisted sense of morality makes him even more evil.)
Princess Luna in My Little Pony: Friendship Is Magic is definitely one, trying to live down her 1000 year legacy as Big Bad Nightmare Moon. Mind you, her public relations need a lot of coaching from Twilight Sparkle, but she makes a real breakthrough.
DuckTales has Fenton Crackshell / Gizmoduck. Whenever he screws up, he will frantically do whatever it takes to set things right, although he often makes it worse until he ultimately succeeds.
The Avengers: Earth's Mightiest Heroes: Following the Skrull Invasion, Captain America, who was one of the first to be replaced and his image was used to try and convince humanity to surrender, became something of this as he tried to regain the trust he lost. Kind of an unusual example, being that he had nothing to do with the event he's atoning for and he's just as much a victim as any other Skrull victims.
Alfred Nobel set up the Nobel Peace Prize because he felt guilty about making a fortune selling weapons and inventing dynamite. It's believed that after his death was falsely reported by a newspaper and he read his own obituary, which referred to him as "the merchant of death" (but in French), he decided to leave a better legacy.
It's worth noting that Nobel had intended dynamite to be a mining tool when he designed it - he had a major case of My God, What Have I Done? when people weaponised it instead.
Many developers of nuclear weapons ended up this way, with the most prominent examples being:
J. Robert Oppenheimer, who had headed up the Manhattan Project during World War II, devoted his energies as chief scientific adviser to the United States Atomic Energy Commission after the war to advocate against nuclear proliferation.
Andrei Sakharov, the Soviet physicist who designed the two-stage thermonuclear hydrogen bomb independently of Edward Teller and Stanislaw Ulam (the design is known as the Teller-Ulam design in the West and Sakharov's Third Idea in the old Soviet bloc), and was involved in the "Tsar Bomba" project to design the world's biggest nuke (they succeeded, at 50 megatons). Sakharov developed a case of conscience, and became a leading opponent of nuclear proliferation, for which he won the 1975 Nobel Peace Prize. He then moved on to more general human-rights campaigning, calling for freedom and real democracy in the Soviet Union; he died in 1989, having just been elected to the first democratic Soviet legislature since the Red October.
D.W. Griffith was apparently too clueless and poorly informed to realize how incredibly racist Birth Of A Nation was, and was shocked when people were offended by it. He spent the rest of his career trying to apologize for it with anti-racist movies like Intolerance and Broken Blossoms, the first film to portray an interracial relationship. It's worth noting, though, that neither of these films actually attack racism against black people (the former is split between Babylonian sects, Jewish sects, Catholics and Protestants, and American political factions, the latter focusing on a relationship between a Chinese man and a white woman).
Mike Tyson, who's served his time for rape as well as numerous drug charges and biting Evander Holyfield's ear off... has devoted himself wholly to nonviolence and charitable work, going so far as to become vegan.
Adolfo Scilingo. A pilot during the Argentine military dictatorship, Scilingo's job was to dump the tranquilised (but still living) victims of the dictatorship out of a plane and into the ocean. Tortured by PTSD and guilt, Scilingo eventually became the first soldier to break silence, leading to the arrests of many low-level participants (the leaders had already been convicted). Believing that nothing he does will ever be enough, Scilingo went so far as to deliberatly go to Spain to testify in the war crimes trials, knowing he would be arrested by the Spanish government, and convinced that he needed to be.
Kurt Gerstein, an SS officer who was responsible for the development of Zyklon B as a method of "pest control". After witnessing the chemical being put to its true, gruesome use in the extermination camps, Gerstein was horrifed, and began desperately attempting to inform the international community of the massacres. He even risked his life by sabotaging shipments of the gas he had helped to produce. After the war he turned himself in to the Allies and compiled the "Gerstein Report", his eyewitness account of the Holocaust which was used as evidence in the Nuremberg Trials, before committing suicideout of guilt.
Robert McNamara, Secretary of Defense to JFK and LBJ, spent much of his later career admitting the Vietnam War was terribly wrong and trying to explain how he and his fellow politicians could have seen otherwise, like in the Oscar-winning documentary The Fog Of War. Despite this, and his anti-nuclear weapon and anti-Iraq activism, his obituaries almost uniformly painted him as a warmonger anyway. Overlaps with Modern Major General - the trope - he wasn't a military man at all but an auto-industry executive whose greatest legacy otherwise would have been the Ford Falcon.
Frank Abagnale, the con artist whose life was dramatized in Catch Me If You Can is this who has created a major anti-fraud company. Among the things he did with his money was pay back all of the companies he defrauded. In addition he also has worked for free for the FBI as well as other law enforcement and to this day he has never taken a penny from any law enforcement agency as reimbursement for his time as he considers it a public service to make up for what he did.
Cyber-example: Kevin Mitnick. He started out as a notorious cyber-criminal; today he is a successful IT security consultant. Ironically, in July 2009, his websites were defaced by, guess what, a cyber-criminal.
He's not alone in that regard. Lots of corporations will pay good money to people who will help them improve their cyber-security. Who better to understand it than people who commit those kinds of crimes? It turns out that IT security can be a good bit more lucrative than cracking.
The United Kingdom's Department for International Development (DFID) is one of the foremost international development agencies and the UK has one of the world's highest aid budgets, as well as being one of the few countries that gives aid gratis (without tying it to aiding British interests). It has been suggested by some that this is due to Britain's colonial legacy.
For that matter, all the former colonial powers of Europe qualify, to varying extents.
Former WhiteSupremacists. One of the links even go as far as having his tattoos painfully removed.
Now-deceased Senator Robert Byrd of West Virginia was very stridently anti-integration and was a high-ranking member of the Ku Klux Klan, but later in his life, after the sudden death of his grandson, realized that such intolerance was wrong, and came to become highly supportive of civil rights, as well as a high-profile supporter of Barack Obama. He would deeply regret his involvement with the KKK and his vote against the 1964 Civil Rights Act for the rest of his life.
Similarly, Byrd's longtime GOP rival Strom Thurmond had a similar change of heart in the 1970s, being one of the first Congressmen to openly appoint African-Americans to serve as his chief of staff. Unlike Byrd, however, Thurmond was never allowed to live his past down.