Ysuran Auondril, an elven necromancer in Baldurs 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.
Rucks from Bastion spends the whole game trying to atone for helping to design the superweapon that caused the Calamity, by using the Bastion's Restoration function to go back in time and have another go at the whole situation. However, it's heavily implied that doing this just creates a "Groundhog Day" Loop where the Calamity keeps occurring, until the Kid finally refuses to activate it and instead takes the Bastion and leaves the wreckage of Caelondia.
In Bendy and the Ink Machine, Henry returns to a dilapidated animation studio where he used to work on request of his old friend, Joey Drew, who is in a wheelchair and cannot return himself to release the souls he trapped in ink, nor can he himself slay the soulless Ink Demon he created through his experiments. He does provide key information to Henry on how to slay Bendy. That is, Joey is this trope if the Henry we play as is a real person in-universe, and Joey's request wasn't just a ruse to trap Henry in a "Groundhog Day" Loop.
There are quite a few from the BioShock franchise:
Brigid Tenenbaum worked with the Nazis in World War II while she was imprisoned in one of their concentration camps as a young woman, 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 as she slowly began to see them for the young girls they were, culminating when she feels absolute, blinding hatred and fury when one of them sits on her lap, until she realizes that it's not the girls that she hates.
Booker DeWitt, the Player Character, did such terrible things at the "Battle" of Wounded Knee that he considers himself past salvation, acted so brutally that the Pinkerton Detectives kicked him out, and turned to drinking and gambling until he wound up in Columbia following the promise of "Bring us the girl and wipe away the debt." He makes it clear throughout the game that he deeply regrets all the terrible things he's done and is continuing to do, and eventually decides to give up on his Mysterious Backer and just keep the girl safe. Gets turned Up to Eleven once Elizabeth, with her newly untapped powers, takes him through his temporally-repressed memories and he remembers that he sold Elizabeth away as a baby to Comstock, and when he tried to go back on the deal and chases down Comstock and the Luteces to her back, she lost the tip of her pinky when it was sliced off by the dimension warp-hole.
Comstock is a subversion. He too was at Wounded Knee, but when a traveling preacher offered him baptism, Comstock perverted the meaning of the ritual - rather than considering it the first step on his path to redemption, he took the "cleansed of your sins" bit literally and treated it as the last step of his redemption, meaning he was no longer responsible for his crimes. As time wore on, he even decided that said crimes were actually virtues to be applauded.
The Lutece twins, despite spending most of their time being incomparably silly, are also an example. They (mostly Robert) blame themselves for most of Comstock's sins due to developing all of Columbia's technology (and especially for kidnapping Elizabeth when she was a baby), and are trying to make up for it by helping Booker in various ways throughout the game. Rosalind doesn't particularly care about it and is inclined to let things unfold as they may since she believes what's going to happen will happen whether they want it to or not, but Robert gave her an ultimatum that if she didn't help him try and set things right, he'd leave her forever.
BlazBlue's 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 an understatement.
In BoxxyQuest: The Gathering Storm, its clear that Cornelia feels this way about herself, having still not forgiven herself for the things she did while under Boxxyfans control in the prequel, and feeling unworthy of being friends with the same people she was created to kill. As for how the rest of the party feels, its pretty clear that they forgave her long ago, if they were ever angry at her to begin with.
In Camp Sunshine, a slasher-style survival horror game, The Shaman is an example. The game's ending reveals that he is actually the ghost of Jacob Illerman, the father of the game's supernatural serial killer, who feels great remorse for locking his son away to protect others and having ultimately had to kill him years ago. Helping the protagonist, Jez, is his way of both atoning and of saving his son's soul from the demons that had possessed him.
Dante from Dante's 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. After realizing just how many sins he committed in life, he gives up on his own redemption accepting that he deserves to be in Hell. All he wants is to save Beatrice. He gets his chance to atone anyway.
Angel Quijano, who has the redemption arc in the untold stories of Los Perdidos, tries to make up for failing in protecting the survivors that where infected in the safe houses by rescuing more survivors and killing as much corrupt soldiers as she could before dying
Adam Kane does this in the last part of his untold story of Los Perdidos, he hacked the city's communications and infected the survivors thinking this was the best thing to ensure the country's best interests, but it wasn't until he captured the president when he started to suspect if the government is protecting its people, then he lied about destroying the only piece of evidence about the government's crimes.
Brad Park also struggles with the moral ambiguity of the situation after he was given zombrex by Nick Ramos whom chastated Brad for being a government tool for destruction. After being told that, Brad looks for answers for what he meant of being a tool. Then in his journey he found out he was lied, betrayed and used by the government to cover the tracks of their lies and conspiracies. At the end, he tosses his ZDC badge in disgust.
The Deer God's player character is one, if he is good-aligned. Once a big game hunter, he was reborn into a fawn's body to atone for his crimes against nature.
If the Red Prince is played as a heroic character, he'll express deep regret for some of his actions before his exile, like owning slaves and coming up with the plan to use Deathfog on the Elven homeland, and promise to do his best to make up for them.
Sten 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, something he's still continuing 10 years later.
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.
Cullen sees joining the Inquisition as a chance to atone for not seeing and stopping Meredith's madness quickly enough and for his previous hatred of mages, which led him to overlook a number of the atrocities that were committed against many innocent ones in the Kirkwall Circle.
There's also Blackwall, a.k.a. Thom Rainier, who assumed the identity of the real Warden Blackwall in order to repent for having ordered the killing of a general and his family, then leaving his men to hang while he went into hiding.
Jiub, the Nerevarine's fellow prisoner aboard the Prison Ship at the beginning of Morrowind, only gets a few lines of dialogue and does not reappear in the game after you leave the ship. However, his short appearance was enough to make him extremely popular with fans and Bethesda took notice. Oblivion makes him Legendary in the Sequel, stating that he became St. Jiub, Eradiator of the Winged Menace, after driving all of Vvardenfell's much reviledCliff Racers to extinction. His spirit is encountered during Skyrim's Dawnguard DLC, where he offers a sidequest to help him finish his opus and ensure that his legend is remembered forever after. In his opus, he states that he set out to eradicate the Cliff Racers in atonement for his previous "sordid" life as a skooma addict and freelance assassin.
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.
Brunwulf 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.
Madena, Dawnstar's court wizard, and Runil, a priest of Arkay in Falkreath, who were both battlemages who fought in the Great War. Madena became a pacifist to atone for her actions and Runil became a Good Shepherd. Madena fought for the Empire, but Runil fought for the Aldmeri Dominion. Both of them are Shell Shocked Veterans.
As it turns out, Deacon from Fallout 4 was in his younger years a member of a Synth-hating gang who left after the group jumped off the slippery slope and lynched a suspected Synth. He attempted to start over, found a wife, and was trying for kids, until one day his old gang caught up with him - and killed his wife, who turned out to be a Synth. Deacon cut down most of the gangers, which eventually got the Railroad's attention, so he joined the Synth-advocacy movement as a way to atone for his past crimes.
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. If you pick the "Crush the White Legs" option by the end, you find him slipping again, and the ending you get depends on whether you rein him in or not.
If you get all four major expansions for the game and play an Evil character all the way to level 50, you can invoke the trope yourself with the Perk "Ain't Like That Now." Your Karma is reset to neutral and you become faster.
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 steal the Crystal of Water from Mysidia. After being tricked into destroying the Mist Village (a home of summoners), Cecil defects. 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. And in the sequel, Final Fantasy IV: The After Years, Golbez and Kain. Though it can turn into Redemption Equals Death for 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, 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.
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 Fire Emblem Fates, Nyx was once an Enfant Terrible thanks to having been driven mad with power as a child, but after she cast a spell which left too great a toll on her body she became unable to age. After a depressive episode this opened her eyes and now she seeks to atone for her sins.
In Fire Emblem: Three Houses, there is Gilbert, a member of the Knights of Seiros who seeks atonement for having failed in his duties years ago when the king of Faerghus was killed, leading him to abandon his family and even his name, Gustave and join the Church of Seiros to atone for his failings. Deconstructed, as many point out that all he is doing is making himself miserable in his attempts to attone. There is also Dimitri, who, after the timeskip, is initially blinded by revenge to the point of becoming He Who Fights Monsters, eventually coming around to seeing how self-destructive this was to him and his allies and vowing to make amends by ending the war and opening the way to a peaceful new world.
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.
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. Also happens in God of War III 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. By the time of God of War (PS4), Kratos has spent an unknown amount of time living in peace in the woods with his new family, and part of the game's major themes is Kratos finding the ability to forgive himself and truly atone for his past through his second chances with his son Atreus.
It is at least heavily hinted at that the insane doctor Faust used to be an even MORE insane serial killer, Doctor Baldhead. He wears a paper bag over his face clearly out of shame.
Another atoner is the main character Sol. He's the creator of the Gears, which caused rampage towards the world. To atone for that, he sets on a journey to destroy ALL of his creations.
Tarnum from Heroes of Might and MagicIII spin-off Chronicles series. In his first life he was a Barbarian who, in his bid to free his people from the Wizards of Bracada, became the brutal Barbarian Tyrant. When he perished in single combat against a heroic knight Rion Gryphonheart, his soul was deemed unworthy to enter the afterlife by the Ancestor spirits. They charged him to earn redemption as the Immortal Hero and sent him back to the land of the living. The various quests the Ancestors send him on not only help right great wrongs, they also force him to face the legacy of his own brutal past and grow as a person. Though he ultimately fails to save the world of Enroth in the last entry of the Chronicles series, he ultimately achieves his redemption in the fourth game by raising a young Barbarian named Waerjak to reunite the Barbarian Tribes on the new world of Axeoth without repeating Tarnum's past mistakes.
I Have No Mouth and I Must Scream: 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.
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.
Sagacious Zu was once a servant of the Empire known as a Lotus Assassin. He 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.
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.
In Kingdom Hearts III, Vexen, after awaking as Even accepts an offer from Saix, to become Vexen again, then becomes The Mole within the ranks of the real Organization XIII. He and Saix want to atone for their past actions and Vexen gets assistance from Demyx to help recover the extra vessels in his Replica Program, along with help from Ansem the Wise and Ienzo to help restore Roxas and Naminé.
Atton is a big example of this: he used to enjoy torturing Jedi to death/until they turned to the Dark Side.
The Jedi Exile was the only Jedi that returned to face punishment for following Revan during the Mandalorian Wars. The Exile willingly accepted exile to the Outer Rim and banishment from the order, as a means to atone for firing the superweapon that wiped out every single living thing on Malachor V, including their own troops.
The Legend of Zelda: The Wind Waker: The King of Red Lions aka: King Daphnes Nohansen Hyrule. In a similar case as Auron from Final Fantasy X above, he couldn't pass on to the afterlife due to his regrets. However, instead of becoming a physical ghost, he became a boat.
Matsu from the Mecha chapter of Live A Live looks out for Akira because not only did he used to be the leader of the Crusaders gang that terrorizes the city, but he's also the one who shot and killed Akira's father.
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, Chaos Vortex. 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.
In Lunar 2: Eternal Blue, Leo has sort of an atonement obsession. He doesn't know that Defeat Means Friendship. There's also the matter with Ghaleon. Being dead seems to have caused something of a change of heart in him.
Shepard 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.
Mass Effect 3: Both Miranda and Jacob become ones to a certain extent due to their past work with Cerberus. Miranda is also attempting to atone for considering putting a control chip in Shepard when bringing him/her back from the dead.
Zero 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.
Ciel from the same series can also qualify: part of her founding the Resistance is from the guilt she feels over constructing Copy X.
Also from 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.
In the Good End for Mermaid Swamp, the old man, a.k.a. Yukio Tschuida becomes this. The reason behind the main characters at the mansion is to bury the corpses of the "mermaids." He wanted to repent for his family's crimes, but he couldn't do himself because of his own disturbing fascination of the corpses. He is a bit of a Well-Intentioned Extremist with this, but he makes it up to Rin and her friends in the end.
Hanzo Shimadda has spent his entire life trying to atone for killing his younger brother, Genji. It's clear he regrets the action; however, upon finding out that Genji is not dead after all, he's a more downplayed version, as it's clear he isn't sure how to take the information, or if he believes it's really Genji at all.
Baptiste Augustine is another character in a redemption journey after he defected Talon. In his story, Baptiste explains that he became an orphan in the omnic war and he had to become a freedom fighting combat medic in order to survive. When he was offered a position in Talon, he thought he could get better supplied to protect people in need, until he learned the hard way he was nothing but a hired gun that did more harm than good
How the heroes' HeelFace Brainwashing on corrupt adults works: they lose the twisted desires that caused them to abuse others, but still remember what they've done, driving them to confess to their crimes and try to do everything they possibly can to repent.
The heroes themselves qualify, as many of them feel compelled to make up for various mistakes or failures, such as failing to stand up to corrupt adults. Ann in particular feels guilty for not doing more to help her best friend Shiho around the time that Shiho tried to kill herself, and her Confidant involves dealing with those feelings of guilt by trying to become a stronger person and better friend.
Sojiro Sakura eventually admits that a large part of the reason he took in his adoptive daughter, Futaba, was because he felt as though he failed to protect her mother, a good friend of his.
Sadayo Kawakami, the protagonist's homeroom teacher, once tutored a student who wasn't doing well at school due to having to work to pay off his guardians' debts, but had to stop the tutoring when people accused her of playing favorites. Shortly thereafter, the student was killed in an auto accident, and Kawakami, feeling responsible, paid the money that the guardians demanded from her, ending up having to secretly moonlight as a maid in violation of school rules. With the help of the protagonist, she comes to realize that a better way to atone would be for her to devote herself to being a better teacher, but the guardians of her dead student have other ideas, since they're greedy lowlifes who made their ward slave away just because they were jealous of his parents.
Yuuki Mishima becomes the heroes' main Knowledge Broker and PR guy to make up for doing abusive gym teacher Kamoshida's bidding. At the end of his Confidant, he becomes one again when he comes back to his senses after his little power trip from managing the Phansite, vowing to continue using the Phansite to help people as it was originally intended to.
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.
In Pokémon Black 2 and White 2, a portion of Team Plasma who truly do want to help Pokemon have split off from the main group and are doing their best to right the wrongs the organization has done. While they are still pro-Pokemon rights, they are no longer revolutionaries who want to separate Pokemon and Trainers, and in fact have been trying to return all the Pokemon Team Plamsa stole in the first game. They even help the player against Neo Team Plasma, who are hell-bent on taking over the region and enslaving Pokemon for themselves.
Probably the case with Wes in Pokémon Colosseum. At the start of the game, he is a member of the criminal group Team Snagem, but he quits, blowing up their headquarters and stealing the Snag Machine in the process, later giving the location of the place to the police. However, he never gives a reason for his change of heart. (Of course, he never says why he joined the group in the first place; but then, he really doesn't talk much at all.)
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.
In Raven's Cry, Marcus, Christopher Raven's Parental Substitute and Lancer, raised and looked after Raven all his life in an attempt to atone for having led Captain Neville to Christopher's father's home, resulting in the deaths of Christopher's entire family.
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. He does just that, gets his family back, and starts repairing his livelihood and relationship with his son. Unfortunately, out of the blue the government agent in charge brings the US Army to his ranch and guns him to death, though he's able to save his family in the act.
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 Sakura Wars (2019), Anastasia Palma eventually regrets her involvement in helping President G/Genan Sotetsu and Yasha's evil plan to resurrect the Demon Emperor. As such, she atones for it by helping the Flower Division kill Genan and Yasha for good.
Shadowverse has Erika. Her desire to atone for the atrocities she committed as an assassin drive her loyalty to the Princess, now serving as her guardian Samurai Maid.
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.
Siegfried Schtauffen, post-Soul Calibur II, is working to atone for the evil things he did as Nightmare by destroying Soul Edge.
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.
In one case, it's Subverted when the guy who wants to be The Atoner dies just after he is defeated.
Levi Tolar 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.
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.
Loni from the same game is also an atoner, though his initial guilt is mostly exaggerated in his own mind, and his character arc is mainly about him realizing he wasn't responsible for what he thought he was.
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.
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.
Festus from Telepath RPG changed careers to healing to make up for the suffering he caused doing unsavory things for the Shadowling army.
The Tiamat Sacrament: Many of the Saphirites were once Ry'jin's soldiers, who bought into his lies of a necessary coup, only to be disgusted by his indiscriminate slaughter against the castle residents and genocide of dragons. They rebel against him in order to atone for participating in his atrocities.
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. It turns out that he doesn't have any memories of his involvement in the attack because he wasn't involved in the attack.
Sarah in the white chamber is actually this, having murdered all of her crewmembers beforehand to take the Artefact and now being forced by Arthur to relive these events until she regrets her actions. Whether or not she succeeds is up to the player's actions.
In the Wrath of the Lich King expansion, 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. Many older Orcs who fought in the first and second war share this mentality - the Burning Legion turned them from a peaceful hunter-gatherer society into savage butchers, and now they are free the "Proud" part of Proud Warrior Race matters a lot to them. Case in point, the reason they settled in the harsh desert land of Durotar and ignored fertile lands to the west and north is because they want to experience hardship as a form of penance for their past actions; it helps that Durotar keeps them sharp.
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.
When the Ebon Blade created four new horsemen to lead the fight against the Burning Legion, Sally Whitemane is the only one who seeks atonement for her time as a fanatical member of the Scarlet Crusade. Nazgrim just wants a good fight, Thoras Trollbane wants to save Azeroth after failing to protect Stromgarde, and Darion Mograne just continues doing Death Knight stuff like he's always been doing.