In the rogue zanpakuto filler arc of Bleach, Ichigo is tricked into breaking Yamamoto-Genryusai's barrier, allowing Muramasa to find out the location of his master, Kouga. Ichigo, upon learning his mistake, determines that he must go stop Muramasa so that he can fix his mistake.
More specifically, this is Ed's way of thinking. Al wants things to be alright again, and he knows they did wrong, but Ed has a whole The Atoner mindset and his primary goal is always to fix Al, whose predicament he feels is his fault. Some of this of course is Big Brother Instinct at work.
Roy Mustang is even more The Atoner, and his entire life revolves around achieving enough power to fully make amends for his participation in the massacre at Ishval.
Scar has a bit of this with his survivor's guilt.
Hohenheim is also like this about his role in the destruction of Xerxes and the birth of the Big Bad. Also survivor's guilt and I Am a Monster. (this is his Catch Phrase for a while.) This is why he left the family — he had to deal with his eldest son.
Izumi possesses shades of this vis-a-vis her miscarriage and subsequent attempt at human transmutation. Arakawa likes this trope.
What Nina Einstein tries to do in Code Geass R2, after the bomb she built under Schneizel's orders completely obliterates a good part of Tokyo.
In Higurashi no Naku Koro ni when Shion Sonozaki kills Satoko Hojo in the underground torture chamber, she believes at first that she's helping her essentially dead boyfriend Satoshi Hojo. Then she tries to talk to his shadow that has appeared on the wall (she's gone nuts at this point), when she realizes the last words of him were: Take care of my little sister [Satako] for me. She literally pisses in her pants at the realization, but realizes she's already crossed the Moral Event Horizon and goes off to brutally murder more people.
Ken Ichijoji, in Digimon Adventure 02, after discovering that the Digital world is not just an artificial construct in which he can play out his anger and issues concerning his brother's death. This method essentially turns him from the Big Bad to The Woobie.
In the first 02 movie, Willis had one of his Digimon go rogue; he had been chasing the corrupted Kokomon (now a Wendigomon) all over the US in an attempt to fix it. Even after the rest of the main kids show up, he is initially insistent that because it is his Digimon, he needs to make it right, himself.
Beelzemon of Digimon Tamers takes the cake, though. Since it's his fault Jeri's trapped by D-Reaper because it likes feeding off the despair she has for her dead partner, who he killed, he practically went insane trying to set things right, screaming "I'll save you if it's the last thing I do!"...and it almost was.
To elaborate on this: he's trying to break her out of an energy bubble, and gets it open. She freaks out because it's the guy who killed her partner, increasing his guilt. By the time she snaps out of it, the hole is closed and he starts trying to punch it open. He's so focused on saving her that he's shot in the back by about six razor disks in a truly disturbing was-this-really-for-kids scene and plummets to the sea of deletion goo below, trailing data in lieu of blood. And only got saved at the last possible second. And nearly died of his injuries afterwards. Good God.
In the Trigun manga, part of The Reveal in the flashback arc is that Rem was complicit in the testing to destruction of Tesla, the girl born from the bulbs before Vash and Knives were. Her mothering of the twins is an attempt to make amends for not doing anything to save Tesla. When they are found out by another researcher, he turns out to feel the same way.
Of course, Knives does not much care about that part, concludes with justification that Humans Are Bastards, goes Axe Crazy and makes a good shot at a Kill All Humans plan. And Vash spends the next several decades feeling he has to make amends for that, somehow, until Knives uses him to blow up a fucking city, and then he feels the need to make up for that. Then Knives does it again, although Vash managed to evacuate that one first.
A major villain successfully pulls this off as the punch line to one of Naruto's more spectacular Wham Arcs.
In Tsukigasa, Azuma feels incredibly guilty about cutting off Kuroe's arm, but doesn't know how to make amends. Eventually he gives Kuroe a blade and tells him to do whatever he likes to even the score but it's only when they finally are completely honest about everything that it gets resolved and Azuma can let go of some of the guilt.
In World Embryo, this is become Riku's motive, recently. His habit of lying had made many victims, including his friends and loved ones, and he intends to repair that.
In The DCU, we had Hal Jordan completely lose his sanity and decide to fix his failure to save Coast City... by killing the Green Lantern Corps, killing Sinestro, and then killing the universe... so he could remake reality "right". Fittingly, after all this nonsense, He went on to try and make all of that right, and ended up sacrificing himself to save the world (of course, he got better). Then a few years later, Geoff Johnsretconned the whole thing to Jordan being possessed by a killer space bug made out of fear, but...
Batman does this on Nightwing's behalf toward the tail end of The Joker's "Last Laugh" storyline: Batman doesn't want Nightwing to think of himself as a murderer.
This happens to Magneto. He's always been opposed by the X-Men, so by now he often attacks them at full power (which is a lot) instinctively. Sadly, the X-Men are mutants... some of the people Magneto wants to protect. Even worse, the one he accidentally hurts is the newest recruit, a 13-year-old (mutant) girl. "My God, What Have I Done?" is the short version of his monologue, when he realizes what he has done. Follow his Villainous BSOD and his firstHeel-Face Turn as The Atoner.
Aladdin said something to this effect in the first movie of the trilogy; "I've got to go back and set things right." He's referring to leaving behind the genie lamp, Iago grabbing it and giving it to Jafar, then Jafar using it to wish himself to be sultan and the world's most powerful sorcerer, in turn banishing Aladdin.
Atlantis The Lost Empire has this with Audrey, Sweet, Mole, Vinny, Cookie and Ms. Packard after witnessing Rourke punching Milo in the face and breaking the photo of his grandfather in front of him.
Specifically, Sara makes a very dumb wish which is then granted, and spends the rest of the movie trying to undo the mistake by winning her (half) brother back, since Jareth doesn't allow takebacks on wishing.
In The Empire Strikes Back, Lando does his best to get Leia, Chewie, Threepio, and Han out of Vader's power, though he was not entirely successful.
Vader goes through something like this near the end of "Return of the Jedi".
Legend. Lily touches one of the unicorns, making it vulnerable to attack and leading to its death. She tracks down the other unicorn and finds Brown Tom guarding it.
Brown Tom: You! You're the cause of all our sorrow. Lily: I'm — I'm so sorry. I didn't know. Please, please forgive me. Brown Tom: I'm not the one you should be askin'. Lily: Try and understand. I'm only trying to make things right. Darkness has sent the goblins back for the mare. It's not safe to stay here. You'll have to hurry! Leave now! Go!
John Woo's The Killer is about the Ah Jong, the title character, and his attempt to fix a tragic mistake that he made, which resulted in Jenny, the singer at the night club, being blinded by the muzzle-flash of his gun. The last hit that he goes on is an attempt to raise the money to have her eyes fixed, but unfortunately for him, Wong Hoi, his boss, has other ideas. It does not end well for him in the end, though then again, it takes the triad boss himself to finally kill him.
It probably also makes the single weirdest case of Moral Dissonance in film history.
This is also the plot to the classic film Magnificent Obsession. The life of wealthy asshole Merrick is saved at the expense of a brilliant, beloved and selfless elderly doctor's. The doctor's widow blames Merrick, he responds by stalking her and ends up causing a car wreck that blinds her. Merrick becomes a doctor himself so he can operate on the widow and fix her eyes.
In Theres Something About Mary, Pat Healy is visiting Mary Jensen's house and accidentally kills her dog. And his reaction to this is to, quite literally, attempt to resuscitate the dog.
In Iron Man, Tony Stark realizes what enormous damage his company's hyper-effective, super-powerful weapons (which he designed himself) are doing to the world, and is subsequently so horrified he shuts down the weapons department of Stark Industries and becomes a superhero to do damage control, also becoming The Atoner in the process.
In Spider-Man 3, after freeing himself of the black suit, Peter sits alone in his apartment depressed after all his crimes he did while under the black suit. Aunt May comes in and checks on her nephew to see how he's doing and if he proposed to Mary Jane. Peter tells his Aunt that he's not ready for marriage because he had hurt Mary Jane and feels he is now lost on what to do. Aunt May then tells her nephew that he needs to forgive himself and that she believes that Peter will make things right again and that he is a good person, despite how Peter feels at the moment.
Aunt May: Well, you start by doing the hardest thing: You forgive yourself. I believe in you, Peter. You're a good person. And I know you'll find a way to put it right.
Roland, the "good guy" in The Dark Tower, ends up letting Jake, a boy he has grown to love, fall to his death by dropping him off an underground railway into a bottomless cavern in order to continue his quest. However, Jake is only in the same universe as Roland because he re-incarnated there after being killed in New York City. Roland unexpectedly ends up in Jake's New York, and, because Roland still loves him and regrets his previous decision, takes the opportunity to prevent the original death. This not only saves Jake, but creates a horrible paradox solved only when Roland helps him cross again to his world, where he embraces him as a son and trains him to take part in his quest.
It is said that this is due to Stephen King's own guilt at having killed off the character of Jake, whom he liked, in the first place, in which case Jake's role in the next six books is nothing more than a successful attempt to make amends.
Prince Galrion later named Nevyn in the Deverry books spends several hundred years trying to teach magic to various incarnations of his lover Brangwen, after he had caused her death.
"Brangwen, my love, forgive me! If we ever meet again, I swear I'll put this right. I swear to you—I'll never rest until I set this right."
This is a major theme in the Discworld novel Wintersmith. After a moment of thoughtlessness, Tiffany attracts the romantic attention of the personification of winter, messing up the cycle of the seasons. Though she insists that she's sorry for her mistake, the ever-blunt Granny Weatherwax informs her that sorry won't cut it, invoking this trope by name. She does eventually manage to fix things.
Harry in The Dresden Files to an extent, during Ghost Story, when he realises the effects of some of his actions during the last book. Easier said than done since he happens to be dead, and the 'action' in question was dying and leaving his apprentice all alone.
Harry also feels at least a little bit of an urge to set right all the innocent people he is told (several times) whose deaths he caused by destroying the entire Red Court and thus creating a HUGE power vacuum in the supernatural world.
Live Action TV
The titular character of My Name Is Earl starts a list of all the things he must make amends for at the beginning of the series, being a newly-converted believer in karma. The entire series is Earl and his friends completing the list, one item at a time.
DG in Tin Man is already motivated to take down her evil sister, but then sees a vision in a cave revealing that, as a small child, she accidentally freed the witch possessing Azkedellia.
Connor does this in Primeval, in episode 5 of series 5, though he shows the intention a little before hand.
Connor: I helped build this. I need to make it right.
Also happens in Law & Order: Special Victims Unit when Elliot realizes that a little girl falsely accused an innocent man of being her rapist, under pressure from Elliot himself and the shrink. The guy does not forgive Elliot since his life is already ruined, but Elliot throws himself wholeheartedly into finding the true culprit - and does so.
And it's happened on the original Law & Order. When Claire Kincaid died, a drunk driver picked the worst possible time to kill someone in a hit-and-run. Jack covered up evidence to get him a murder one conviction—and death penalty. Only at the last minute—and after much shaming by Jamie—did he change gears and let evidence of the defendant's drunkenness in.
This happens with Londo in the second season of Babylon 5, right after he realizes that he's basically started an interplanetary war by being an idiot and working with the Shadows.
The end of Life On Mars has the main character betray his friends and leave them all to die, in order to return home. However, he decides he isn't really all that fond of 2006 after all, and jumps off of a roof in order to go back and save them. He still thinks he's in a coma, but he likes his coma dream better. Maybe. See the WMG for more speculation.
This happens with Clark in Smallville as he tries to go back in time to save Lana Lang from dying but in turn causes his father's death.
Interestingly enough though, a version of the future that Peter visits during that arc shows what would've happened if Syl-erm, Gabriel Grey did complete his Heel-Face Turn. That one didn't work out for long either.
In the fifth season of The Wire, McNulty's plan to fake a serial killer probably loses all sympathy with the audience when he kidnaps a crazy homeless man to use as a "victim" and then dumps him in a homeless shelter in Virginia to ensure he's never found. McNulty's final action in the series finale is to track him down and drive him back to Baltimore so he can fix at least one consequence of his screw-up.
This is mainly Tommy's reason for staying as the Green Ranger in Mighty Morphin' Power Rangers. Despite the fact the Rangers knew he was under Rita's spell, he felt horrible for the trouble he caused and stayed on.
In The Duchess Of Malfi, Bosola strangles the duchess, but almost immediately attempts to revive her once he learns that her brother, who hired him to commit the murder, is refusing to pay him. It doesn't work. He tries to make amends by spending the remainder of the play trying to protect the life of the duchess's lover. That doesn't work either, in fact, he ends up killing the guy he's trying to protect.
Chell of Portal made a huge mistake by putting Wheatley in charge instead of GLaDOS, and spends the rest of the game trying to put GLaDOS back before Wheatley's incompetence blows everything up.
From Tales of the Abyss, we have Luke, who ended up destroying the mining town Akzeriuth from his blind loyalty to his mentor Van. He spends some time in denial, but after some soul searching and an Important Hair Cut to boot, he starts almost going to become a Martyr Without a Cause thanks to the overwhelming guilt.
The Nameless One from Planescape: Torment. The entire point of him seeking out Ravel Puzzlewell in order to sever his body from his mortality — thus making him immortal and accidentally causing his amnesia — is that he knew he would never live long enough to make up for all of the crimes he had committed before he became good. It didn't work out too well.
Arguably, Roxas from Kingdom Hearts fits this. After killing offXion, he tries his best to respect his dead friend's wish—by setting all the hearts that both he and she had collected free from Kingdom Hearts and foil Xemnas's plan for gaining ultimate power. The way he goes about doing so wasn't really what Xion had intended him to do to begin with, and it was all because he wanted his life with Xion and Axel back. Riku stops him from going about his suicidal rampage to confront Xemnas, setting the stage for Kingdom Hearts II.
Considering how he beats down Saix, quite possibly the second strongest member of the Organisation at only a fraction of his strength, he probably could have done it too.
Scorpion from Mortal Kombat cannot get over the fact that Sub-Zero, who at the time was Noob Saibot, murdered his family and clan and is constantly after revenge.
Victor Lazarin from WildStar invented the "Everlife Elixir," which mutated into the Contagion that nearly wiped out his species, and then invented the Vitalus Serum that lets them keep together what little shreds of themselves—physically and mentally—they have left. These days, he's working tirelessly for a cure alongside being instrumental to solving numerous epidemics on the Exile fleet.
Atop the Fourth Wall: An enraged Linkara destroys a pocketwatch belonging to the mysterious antagonist known as the Gunslinger, and is horrified to find out a) that the Gunslinger is trying to free his home dimension from a ruthless tyrannical government, and b) without the watch, he can never go home. Linkara immediately pledges all his resources to trying to fix the problem.
In Worm, Taylor discovers that the first job she went on with the Undersiders served as a decoy for Coil so that he could abduct and imprison a nine-year-old girl with precognitive powers. Taylor dedicates her life to rescuing the girl.
In Waterworks, Connie in a fit of rage destroys a fish, which was the only thing protecting a roomful of Innocent Bystanders from a villain with a fish-related Weaksauce Weakness. She realizes it is her duty to fix the situation somehow.
Justice League: Hawkgirl was already torn between loyalty to her home planet and her feelings for the teammates on whom she was spying. After she sold out the Earth and the League to her Thanagarian brethren, she discovered to her horror that they intended to destroy Earth in a bid to save Thanagar. Hawkgirl turned on them and provided the League with information crucial to defeating the Thanagarians. Ashamed by her prior actions, Hawkgirl resigned from the Justice League and secluded herself in Dr. Fate's household in order to think long and hard about what to do with the rest of her life. She came to the conclusion that resuming superheroism would be her best means of atoning for her wrongs and reconciling with the League. In a Crowning Moment of Heartwarming, the League let her know that they voted to let her stay a Leaguer with Superman being the tiebreaker ("I believe in second chances").
This also makes a nice Call Back to Superman: The Animated Series, where Superman has a similar need to make amends after Darkseid brainwashed him and turned him loose on Earth. A popular fan theory is that Superman's actions in the first episode of Justice League (essentially trying to become the world's policeman) is him still trying to make up for that.
Futurama followed the old trope title (Resuscitate the Dog) quite literally. Fry finds his old dog from the 20th century fossilized in a construction site. Feeling bad for abandoning him (despite not meaning to) he arranges for the professor to actually revive him. With Science!
In that same episode, Bender, in a fit of jealousy, literally kicked said dog's fossil into hot lava, but after realizing what he did, he went in to save him and recovered him.
Constantly happens in the Thomas the Tank Engine series starting from season 8 to 16. After an engine makes three mistakes in their given job due to their Fatal Flaw or is just being plain incompetent, and after The Fat Controller calls them out for causing "confusion and delay", the engine will begin making things right with absolutely no problem at all. The engine finishes their job on time and The Fat Controller praises them by calling them "really useful engines".
One could consider the scientific efforts to clone extinct animals this.
Many of the scientists who participated in or were otherwise linked to the development of nuclear weapons became fierce and vocal opponents of the nuclear arms race and advocates of nuclear disarmament. This list includes:
J. Robert Oppenheimer, head of the Manhattan Project
Andrei Sakharov, developer of the Soviet hydrogen bomb.
He later parlayed his disarmament campaign into a campaign for human rights and democracy in the Soviet Union. This naturally got him exiled to Siberia, but he was later rehabilitated and was elected to the first, last, and only (more or less) freely elected Supreme Soviet of the USSR. He was shaping up to be a major leader of the Soviet democratic transition until his sudden death in December 1989.
Otto Hahn, part of the team that discovered nuclear fission (with Lise Meitner and Fritz Strassmann)
Niels Bohr, who had been on the Manhattan Project. He didn't quite advocate disarmament, but he was an architect of the "Atoms for Peace" vision that led to the creation of the IAEA.
Any suggestion of overt nationalism, interest in military conflict, and especially any allusions to the Holocaust or other deeds of Nazi Germany tends to go over badly in modern Germany. Nearly seventy years after the fall of Nazi Germany, making amends is still Serious Business to the Germans.
Earl Warren was Chief Justice of the Supreme Court of the United States from 1953 to 1969, and he led the Court in a highly liberal direction that included major rulings in favor of equal civil rights for African-Americans and other minorities, voter rights, rights of the accused, freedom of speech, and freedom of religion. Before that, during the 1940s, he was Attorney General of California and pushed the federal government to intern the Japanese-Americans living on the West Coast. Many people believe he realized just how awful that decision was and tried to make up for it with his time on the Supreme Court.