Rurouni Kenshin: The eponymous Himura Kenshin was a cold-blooded "Knight Templar" assassin for the Ishin Shishi who was willing to bury his humanity and kill on command if it meant bringing forth a peaceful era to Japan. It isn't until he accidentally kills his wife Tomoe that he realizes the hypocrisy of his ideals and vows to never kill again once the war has ended.
Magical Project S, Misao Amano is shocked to find out she is Pixy Misa (the evil magical girl that has tortured practically every main character, including her parents and her best friend). While it was initially thought her evil side was due to brainwashing, it was in fact her repressed self, despite having no memory of her actions.
Yamaki in Digimon Tamers has a particularly nasty one when he realizes that not only has he been killing sentient beings in the name of destroying "digital anomalies", but that it may have been his efforts to control what he saw as an invasion that made the real invasion possible.
Beelzemon, also from Digimon Tamers, has one when the ramifications of his lust for power finally hit him: he sold out and tried to kill his friends, drove one of them over the Despair Event Horizon by killing her partner right in front of her, and was at least indirectly responsible for the D-Reaper gaining the ability to invade Earth. This horrifies him so much that he actually has to be persuaded into Heel Face Turning, as he doesn't believe he deserves it.
Before them, three out of the four human antagonists of V-Tamer 01 quit after this realization. The one that doesn't is told You Have Outlived Your Usefulness and thus quits before it.
In the final episode of Planetes, Hakim experiences this after a simple conversation with Nono. Because Nono was born on the Moon and lived there for her entire life, she has absolutely no concept of what a country is. Hakim, who has resorted to terrorism to bring attention to the plight of the third world, realizes that development in space would eventually eliminate the borders between countries and loses his will to fight.
When a scrappy entrepreneur from The Old Country shows up, Claire (who was raised and educated in the USA since the age of eight and become a Workaholic ladder-climber) finds him annoying at first, until he reveals that his life's history is very similar to hers, at least before he went back to El Tanika to aid them with his education. Ultimately, this guilt bomb only serves to send her into a bit of a death spiral.
Lelouch has one in the first season after he Shoots The Dog completely by accident and kills his sister Euphemia. Although upset over his actions, Lelouch realizes he's gone too far to turn back, which could be seen as Ignored Epiphany...but he arranges his master plan around making his crimes public, and being executed at the hands of Zero (a disguised Suzaku), because in his mind, that is exactly what he deserves.
In Berserk, Griffith is made to realize at the Eclipse that rather than being the beloved leader that everyone thinks he is (including himself at times), he is an ambitious man who will do anything to realize his dream and uses people to that end, even into death on the battlefield. It's his spite for Guts' being the one person he couldn't control that sends him over the mother of all Moral Event Horizons.
Sadakiyo from 20th Century Boys realizes that he's been manipulated by Friend into doing evil when he bashes a former schoolmate's head in after the latter had come to him for information.
Also hilariously averted by Yanbo and Mabo: they never realized they were bullies to start with, and yet they manage to realize a Heel-Face Turn without noticing.
Suzumiya Haruhi in Sigh, when she finally gets called out by Kyon on her treatment of Mikuru. Directly after this is one of her biggest Pet the Dog moments, and she becomes much nicer after this. Made more obvious in the anime rendition, where she looks away from Kyon as he calls her out and it's clear that she's at the verge of tears.
In the 11th book, Kyouko Tachibana has one of these.
In Tegami Bachi, Sara has this realization after seeing the memories from the Shindan Lag used to finish off the Gaichuu. They had pretended to be part of the anti-government faction Reverse (with Hunt presented as the "Man Who Could Not Become Spirit" to prevent people from mistreating him because of the monster arms sewn onto him), and while keeping up that act, decided to prevent letters from coming to Honey Waters. A man took it upon himself to deliver the letters, but was attacked by the Gaichuu, lost his heart and died. After realizing that their lie caused his death, Sara turns over all the money they received to the villagers, and sets out with Hunt to start anew.
Fullmetal Alchemist. Most of these moments are in flashbacks, as soldiers in Ishval realize they're acting as Punch Clock Villains and become The Atoners we know and love. In the timeframe of the story itself, Scar gets a slower-acting one than usual, apparently beginning when he notices that he's standing menacingly over Ed and Winry in exactly the same way he remembers Kimblee standing over him and his brother.
In Mobile Fighter G Gundam, both Master Asia and Dr. Mikamura get them. For Master Asia, it was the fact that humanity was a part of the Earth as nature was and wiping them all out wouldn't solve a thing. For Dr. Mikamura, it was the realization that his own jealousy towards Dr. Kasshu lead them to the point where his own daughter was now the core of the Devil Gundam. Both of them suffer Tear Jerker-worthy Redemption Equals Death moments to atone.
In ∀ Gundam, Queen of the Moon Dianna Soreil learns that her policies, past antics and army have actually caused quite a bit of suffering both on Earth and on the Moon for years and allowed maniacs like Gym Ghingham to sieze ludicrous amounts of power. This turns her into The Atoner and causes her to undertake massive changes in policy upon regaining power.
Played for Laughs: This trope is the entire point of High School Boys and Panties peeping at a girl's panties does not make a guy feel good, but guilty and depressed... especially when you tricked a Ditz into unwittingly flaunting her panties. Motoharu slipped into a Heroic BSOD so hard he skipped school for three days.
The final climax of the 2003 version of Astro Boy. For the entire series, Dr. Tenma had been trying to guide Astro so that he would eventually become the most powerful robot in the world, able to rule over all humanity. However, all this time, Astro had been fighting for peaceful man-machine coexistence. So in their final conflict, Tenma and Astro meet in the abandoned Laboratory 7, where most of Tenma's angst originated, first with his real son then with Astro's original incarnation. What finally ended the battle wasn't strength of arms at all, but Astro forgiving Tenma for everything he did. He suddenly realizes that the robot he built himself had shown himself to be more human than him, and he finally surrenders.
Elfen Lied - At the very end of the manga, the DNA Voice that arguably drove Lucy to her murderous ways, is prepared to use its remaining power to destroy the world once Nyu and Lucy's spirits leave their melted body. Kouta has promised to kill Lucy, but cannot do it out of love. The Voice is shocked and impressed. In hideous pain itself, it now begs Kouta to end its existence, and he does.
Rock grows to realize the path he has chosen after he fails to save Yukio and the Washimine clan from destruction. He experiences this again after Fabiola calls him out on his plan that, while saving Roberta from herself, also nearly got Garcia killed.
In Kamisama Kiss while carrying out a Honey Trap ploy Jirou's actions (which Tomoe refers to as looking at a reflection of himself) causes Tomoe to admit what an asshole he's been to Nanami.
Happens rather often in Yu-Gi-Oh!. To start, Marik (the real one, not his Super-Powered Evil Side) had this moment after his dark side took over, so much that, during the Final Battle, he pleaded with the Pharaoh not to hold back and to strike his evil side down, despite the fact that it would cost him his own life. (Fortunately, Yami found a way to do it without killing him.)
This happened to Noah too. The Heel Realization for him came after Mokuba, despite everything that Noah had done, seemed willing to help Noah, even going so far as to call him his brother (even though that was only a technicality in the loosest terms, if that) and Noah double-crossed him anyway, stealing Mokuba's body in order to flee the Virtual World before Gozaburo put his plan into motion. He at first called Mokuba an idiot for trusting him... And thenthe full ramifications of what he had just done hit him. After changing his mind and going back to help the other heroes, he went so far as to say that he "deserved it" when Jonouchi apologized for wanting to slug him, and in the end, made a Heroic Sacrifice to defeat Gozaburo.
In Yu-Gi-Oh! GX: Saiou was an odd case. Due to his psychic tarot reading powers, he realized that evil would overpower him years before it actually happened, and warned his friend Edo Phoenix about it. Even when it did happen, his good side struggled with his evil side constantly, and at one time when his good side was briefly dominant, he gave the two keys to his Doomsday Device to Judai and Edo, pleading with them never to give them back.
Yu-Gi-Oh! 5Ds: Jack was the biggest example. His road to a complete Heel-Face Turn started when Yusei defeated him the first time, and it took longer than most. While he remained The Rival for the most part, he was closer to Yusei than other examples in the franchise.
This happened to most of the Dark Signers too, mostly because most of them had been Forced Into Evil. Kyru was the biggest example, forcing himself into a self-imposed exile to punish himself because of what he had done.
A lot of villains in Yu-Gi-Oh! ZEXAL, at least the first season. All three of Tron's sons, Tron himself, and even Dr. Faker at the end realized that what they had done was inexcusable.
Mewtwo: The human sacrificed himself to save the Pokémon. I pitted them against each other. But not until they set aside their differences did I see the true power they all shared deep inside. I see now that the circumstances of one's birth are irrelevant. It is what you do with the gift of life that determines who you are.
Neji: He helped me to understand just how selfish and narrow-minded I was being.
During the Fourth Great Shinobi World War, Gaara's father, the Fourth Kazekage (revived via the Edo Tensei), came to this realization when he saw that the son he made into a weapon and denounced as a failure ended up becoming a better Kazekage than he ever was. He admits his faults and his lies, and makes peace with his son before being sealed away.
In Bleach, Uryu is initially obsessed with proving the Quincies superior to the Soul Reapers, and he tells Ichigo about how his master and grandfather argued in favor of Quincies working together with Soul Reapers, only for the Soul Reapers to reject his plans and let him die against five Huge Hollows while Uryu watched. Ichigo then tells Uryu that while he wasn't paying attention to all of the story, he understood the part about his master wanting cooperation between Quincies and Soul Reaper, and proposes joining forces with him in spite of being angry about him using hollow bait and endangering innocents. At the end of the fight, while Uryu saves Ichigo's life, he realizes in an internal monologue the real reason he did all this in the first place — he was angry with himself for failing to save his master's life.
Uryu: Maybe I was trying to forget my weakness. My weakness in not risking my life to help you. By blaming the Soul Reapers, I tried to forget my own shame. Master... today I will help a Soul Reaper. Can you forgive me? I am a weak disciple. A weak disciple who wouldn't die for you. Can you ever forgive me? Master...
Suisei no Gargantia: Ledo does not take it well when he learns that the Hideauze are Transhuman Aliens, and not true extraterrestrials. The Hideauze whose children he just absentmindedly killed out of Forever War instinct. And then Chamber makes it worse when he follows his programmed directive and crushes a curious Hideauze child.
Ellen in Suite Pretty Cure ♪ gets one that leads to cementing her Heel-Face Turn as she's forced to watch a father and son drown in sorrow by the power of a Negatone, making her realize everything she's done was just hurt people. Hummy and the Fairy Tones who power her up as Cure Beat help find her resolve and allow her to finally become a Cure full time.
Quite a few villains from Attack on Titan experience this, but tend to follow it up with an Ignored Epiphany since they still believe their actions are necessary or justified.
Djel Sanes, a Corrupt Cop responsible for murdering Pastor Nick and several other innocents in order to protect the Government Conspiracy's secrets. He breaks down and admits that he is a monster for all he's done, but insists it was for the greater good.
Reiner Braun breaks down and admits to having lost their moral compass, later ranting about being a murderer and a monster. He's coped with his guilt via episodes of Trauma-Induced Amnesia, and is deeply shaken once he realizes it. Still, they resolve that there isn't any choice left but to take responsibility and see things through to their end.
Bertolt Hoover similarly breaks down, accepting that their actions can never be forgiven and that it isn't possible to apologize. However, they reject a Last-Second Chance by stating that they can't stop.
In Y: The Last Man, one of the characters mentioned that she had been working for a long time to try and make the post-Gendercide world a little easier to deal with—It turns out she had been flooding the entire Pacific community with heroin, but figured that it really was not a bad thing since the entire world is circling the drain, and this is just letting people have a bit of happiness before humanity goes extinct. However, the fact of Yorick's existence, which means that extinction is not a guarantee, changed her perception of her role - she's not The Hero, he is, and she's just one of the baddies. Things do not go so well for her after that.
The Superman nemesis Manchester Black thought of himself as a "realist", operating as an anti-hero (i.e. killing without remorse). He perceived Superman's boy-scout morality to be a facade bordering on stupidity. In an attempt to give Superman one bad day, he created a telepathic illusion of Lois Lane being murdered to provoke a homicidal response out of Superman. When it failed, and he saw the depth of Superman's dedication, Black realized that he had been a villain who had been lying to himself all along, and there was such a thing as a Good Guy. He then promptly killed himself. Sort of. Poor little Vera.
Magneto has one of these in Uncanny X-Men #150, after he almost kills Kitty Pryde with an electric shock. He's so disturbed by it that he actually reforms (and stays reformed for a hundred and twenty-five issues), and eventually becomes the headmaster of Xavier's school.
This is what ended the Marvel Comics Civil War. After the final battle causes lots of destruction calls in the rescue workers and he notices civilians begging to him not to kill Iron Man, Captain America realizes that he's putting innocent people in physical danger by his actions and country wants and has become one of the villains he usually fights against. Unwilling to become an Anti-Hero and force his ideals on the public he promptly orders his side to stand down.
In the Marvel The Siege story arc, Loki looks on in shock when he realizes that his actions were what led to the destruction of Asgard. He only wanted to restore Asgard's ancient glory, and never intended for these events to happen.
The Sentry's case throughout Dark Reign (and before) might also count, as he was constantly in doubt of his actions - 'course, the Void may be to blame for the most part, but Bob Reynolds himself is an extremely neurotic and superpowered individual. As he said in the first mission of the Dark Avengers, after ripping off Morgan's head: "What did I do? Was it good or bad?"
Enemy Ace, a series about an honorable German pilot flying in World War One, had a more recent series where the same pilot, now a gray-haired veteran, flew in World War Two. He was much unhappier about this war. At some point he got shot down and parachuted to safety near Dachau, saw one of the death camps, and underwent a textbook Heel Realization, even telling those under his command that they were fighting for the devil himself. He told them that he would no longer protect the Third Reich, and that he planned to fly to the nearest Allied airbase and surrender, giving them his undamaged fighter, then help them in any way he could.
Of all people, Superboy Prime seems uh, primed, for one of these in Blackest Night. Then again, he has been looking at his monstrous actions from a different perspective aka ours over and over again for months on end.
Happens twice in the Iron Man Armour Wars saga, once at the beginning when he realises his technology may have been responsible for some of the worst criminals in the Marvel Universe, and again at the end when he questions the extreme measures he has used in trying to solve the problem.
Nite Owl II in Watchmen finally begins to understand the potentially harmful social effects of superheroes during the Keene Riot.
This is played with in an issue of Nemesis the Warlock. The villain calls himself Torquemada, and in many ways models himself on the Spanish inquisitor of the same name. They meet through time travel, and the villain explains to the inquisitor what his philosophy has led to. It's the inquisitor who's horrified.
In ElfQuest, Knight Templar Rayek suffers a massive and acute Heel Realization just as he's about to kill all of the Wolfriders (for the greater good, he thinks). It's triggered when he meets his daughter Venka for the first time, who was trained her whole life to stop him. She refuses to, telling him that it has to be his own choice.
In Scott Pilgrim, the point of Negascott is not to be defeated as Scott initially thinks, but to get Scott to recognize his own faults as a person and to understand that he's played a part in the failures of his past relationships rather than just blaming others. When he accepts this, he absorbs Nega-Scott into himself and remembers all of his mistakes, which readies him to take down the last obstacle in his personal quest... Gideon.
Ironically, The Riddler had one after he had intentionally decided to become a "normal" criminal. Up until this point, he more or less did what he did either because he could or to prove he was better than the world's greatest detective. Finally, one day, he has enough, decides to drop the super-villainy and the gimmicks, and pulls a couple of last jobs like a "normal" crook to get the funding to get back on his feet. Batman stops him... Because he was subconsciously leaving clues behind. That's when Riddler realized he wasn't the brilliant mastermind he thought he was, he had an actual compulsion he could not control; "I might ACTUALLY be crazy". He asked Batman to take him to Arkham Asylum, and after being treated and eventually released, was one of the few rogues to pull a semi-successful Heel-Face Turn by becoming a private detective specializing in bizarre and unexplainable crimes.
Strictly speaking, this is a rehash of a Silver Age story where he has a nervous breakdown when he breaks into a jeweller's without leaving any clues and can't grab the loot because he can't bring himself to do it, and he tries to hypnotise himself into getting rid of his compulsion, which is when the subconscious clues ensue...
Doctor Octopus has ones during the finale of Superior Spider-Man. Otto, utterly confused by how easily the Goblin King brought down everything he built is left wondering what would Peter do in this situation, especially since the Goblin King kidnapped his Love Interest Anna Maria. When confronted with the child he helped saved (and used to convince Peter's spirit that he was the superior one when Peter was willing to leave her to die to save his skin), he's forced to act by Peter's spirit to save her, being told that the thing to do is to do what's right, not to plan. Through that, Otto realizes the one true Superior Spider-Man was Peter, mostly because Otto realized he was an arrogant man who overcompensated for everything while Peter was a man who knew he had everything, but kept sabotaging himself because he felt he didn't deserve it. He, then, erases his memories and personality from Peter's mind, restoring the hero once more.
In Transformers Dark Cybertron, Megatron has one in issue 10 while he is being repaired and taking time to reflect on how little he accomplished with millions of years of warfare. The moment he decided to use force to achieve his goals was the moment he lost the war for Cybertron.
Jason Stryker in the comic adaptation of X2: X-Men United, where Xavier helps him to realize his manipulation is the wrong way to gain his father's love.
Trian Aeducan has one in Dragon Age The Crownof Thorns and it's bad enough that he becomes unable to sleep properly, falls into a depression he can only distract himself from by abusing his body through incessant workout, and this is when he's not having a Heroic BSOD. Gorim, surprisingly enough, tries to get him out of it, but he doesn't have much luck because of how both of them are half-convinced the dwarven noble protagonist is dead, so he has his own grief to work out. Trian only really manages to emotionally recover, somewhat, when he discovers his talent for sculpting, something that happens weeks after the realization. Things aren't made much better by what happens with the king and the city-state itself afterwards. Let's just say those weren't the best few months of his life.
King Endrin Aeducan is a sort of aversion because he knows what he's doing is wrong from the get go. Still, his deathbed scene finally has him putting it into words, but it's far, far too late by then, or so he thinks. It actually wasn't, since everything had gone according to one of the DN's plans, but Endrin actually chooses to die because he didn't want to face his second son when he came back. It's just a very small point in his favor that part of the reason for his decision to give up on life before the second eldest prince has a chance to return is the fact that he doesn't want to put Raonar through the experience of having a second parent die in front of him. Needless to say, the second son in question quite rightfully calls him a stupid old man when he finds out.
In the Babylon 5/Mass Effect Crossover Fic The Babylon Effect Matriarch Benezia decides to stop at Beta Durani to have a little talk with a caputured Minbari Shai Alyt on the way to a Peace Mission to Minbar. After pointing out that the Minbari had killed an Asari Matriarch during an earlier battle during the war and that, by the Minbari's logic, the Asari had every right to exterminate them, among other things. The Shai Alyt has a combination of this and a Oh Crap moment realizing that there are only two ways their war with the Terran Systems Alliance will end; either they make peace with them, or the Citadel Council will crush them like a grape.
Colonel Dannett, a combat instructor for the Academy, realized what a monster he was becoming and had to decide between retirement and suicide. He chose to retire, but is still haunted enough by what he did that when River comes after him, he is willing to let her kill him for revenge. Fortunately, River spares and forgives him.
The second instance comes later on, with Inducer One-One-Nine, who is an eight-year-old psychic that can control emotions and thoughts, and went on a massive murder spree. She only comes to realize the horror of what she's done when Zoe shoots her in the stomach and she lays dying.
At the climax of the Rainbooms and Royalty sequel May the Best Friends Win, Rainbow Dash calls out Trixie on her behavior, which forces her to face just how vile she's truly acted, leading to her becoming a better pony.
All her life, the yellow pony had faced mockery from all sides but one, and it was the only difference between how Fluttershy and Derpy had grown. Rainbow Dash was the difference. Everypony made fun of Fluttershy everypony except for her. She had stayed by Fluttershys side through it all, defending her from the teasing at her constant fear and virtually non-existent flying skills. Fluttershy was still timid, still fearful, still a poor flyer, and just like Derpy, still hurt easily from the scars of foalhood. The only variation between her long-time friend and Derpy was that Rainbow Dash threw insults at Derpy instead of repelling them. It was time for that to change.
In the dark!HarryAUHeir after Voldemort tasks Harry and Tom with running distraction duty at Hogwarts by setting the Basilisk loose on the student body they had originally picked the muggle-born Hermione Granger to be one of their first victims, but after a week of stalking Hermione, Harry and Tom realize how brilliant she is and decide to choose a different target. When Harry and Tom give their report at the next Death Eater meeting and explain why they switched targets this even gets Voldemort thinking that maybe he was wrong about Muggle-borns.
Another My Little Pony example; Why, which expands on Discord's from "Keep Calm and Flutter On" (taking place between his Heel Realization and the final scene). When the Mane Six confront him over his change of heart, he explains his Heel Realization in more detail;
Kitty: You're right. You're right all this time. I'm the bad guy here, not Emma.
In the Total Drama story, Legacy, Heather reached out to Lindsay after the latter lost her baby, but Lindsay did not acknowledge the gesture. Lindsay did respond to condolences from Courtney, among others, so Heather assumed that old resentments still lingered. The incident left Heather questioning, for the first time, the wisdom of her game strategy.
"Look Mr L dude" dark said darkly. "I just want to blow up the world is that so evil?"
"Yes because then where will the kiddies live?"
Night looked shocked and stopped signing.
"BRO! I NEVER FORT OF THAT!"
In Perfection Is Overrated, Nao goes through a gradual one over time, as she realizes how much her mother's being put into a coma has affected her life by causing her to become a selfish and vengeful loner, starting when she is forced to ensure that it happens lest history be altered enough to cause a temporal paradox. After a chance encounter with Mai in the hospital, Nao realizes that Mai has, in the years since her parents' deaths, dedicated herself to something constructive in caring for Takumi, while Nao realizes how little robbing perverts eases her own pain. Eventually, she undergoes positive Character Development and becomes a better person, particularly after realizing her similarity with Natsuki.
Obsidian has one in the Hunger Games fanfic Some Semblance of Meaning after realizing how ruthless his fellow Careers are and recognizing that he feels guilty about the kills he has made.
The main character in This is the Life: A Tale of a Human in Equestria has one after hiding from Pinkie Pie so he won't have to attend her party, only to come to the realization she's trying so hard to invite him (read:literally hunting around town for him) because she thinks he doesn't have many friends and wants him to have a fun time and meet some people.
In one Harry Potter story, Harry explains to the Order of the Phoenix that given Snape's treatment of any non-Slytherin in his class, almost every job that requires a NEWT in potions (politics, aurors, healers, etc) is staffed near exclusively with Slytherins who buy into Voldermort's ideals. While checking the Order's reactions, Harry's surprised to note that Snape is one of those looking shocked.
In the ATLA fanfic Undone, Jeong Jeong has one after realizing that the Fire Nation has murdered children in the Earth Kingdom, and that while they may not be Fire Nation, the Earth Kingdom's people are still people. Iroh has one at the end as well, after Lu Ten dies.
Fai has a gradual one in Tsubasa Reservoir Chronicle fanfic Shatterheart after he confronts Syaoran on his drinking: he wants Syaoran to ask him for help but realizes due to his previous coldness he is the last person Syaoran would turn to. Kurogane points out that Fai treats Syaoran as if he's a ghost instead his own person, a problem not helped by the fact that Fai hasn't actually spoken much to Syaoran since Tokyo, which was several months ago in-story.
Cars 2 has Mater having a dream where he sees his activities over the past few days and finally realizes what an embarrassing jackass he's been to Lightning McQueen.
In Meet the Robinsons, after Bowler Hat Guy checked off everything on his villain agenda except the last entry, which he marked with a "?," he faced a "Now What?" moment and realized that whereas the Robinson family had vastly improved the quality of life in the world in the span of a couple of decades, Bowler Hat Guy's actions had been nothing but destructive for petty reasons. Without a direction for himself anymore, Bowler Hat Guy starts thinking about reforming. The bowler hat, Doris, figures this out (It Makes Sense in Context) and takes matters into her own robotic hands, and it takes the combined efforts of the Robinsons, Lewis, and the former Bowler Hat Guy to stop her.
In the film version of All-Star Superman, Lex Luthor has one of his only heel realizations in any continuity after he finally gets it. What is "it"? Everything.
Lex Luthor: "I could have made everyone see! If it wasn't for you, I could have saved the world!" Superman: "If it had mattered to you, Luthor, you could have saved the world years ago." Luthor: "... you're right."
Tommy Pickles suffers this in The Rugrats Movie. Having been abandoned by his friends and left to find for himself and his baby brother, Dil, Tommy finally snaps at Dil's greediness and attitude and plans to give Dil to the monkeys. However, as he's ready to dump banana baby food on Dil, the younger Pickles' demeanor changes to one of outright fear and Tommy sees himself in a puddle's reflection. This and Dil quickly clamering up to hug Tommy is enough to realize what he was doing was wrong. The monkeys, however, are less than thrilled.
In Monsters, Inc. Sulley gives a scare demonstration to some candidates, badly scaring Boo, which makes him realize how horrible it actually is to scare little children.
It turns out Zangief from Street Fighter was loyal to Bison because he thought the guy was the hero!
Zangief: Bison...?! He's a... bad guy?!
A pretty funny example from Machete. One of the Mooks has an epiphany, telling his coworkers that "I've been watching the boss, and the boss is a real scumbag." That same Mook, when confronted by Machete shortly thereafter, promptly quits his job and gives Machete his gun.
In The Elephant Man, Dr. Treves is shaken by the Head Nurse's observation that the arrangement he set up for John Merrick, which include receiving respectable callers, means he is still being treated as a freak on display, albeit in a high class cushy style.
Undercover news reporter Babe Bennett has one in Mr. Deeds when she finds herself falling in love with Deeds after lying to him in order to gather information to slander him with.
In American Beauty, the middle-aged protagonist spends the majority of the movie fantasizing about a slutty teenager, and starts working out to impress her. But when he finally gets a chance to fulfill the fantasy, he realizes that statutory rape laws are there for a reason: She's just as insecure and immature as any other teenager, and is actually still a virgin. He opts to be a Chaste Hero, not that it helps much.
Subverted in the Bill Paxton film Frailty: Fenton's father locks him in a cellar with minimal food and water until the boy comes to the realization that the family is destined to be God's warriors on earth, killing demons. Fenton later does have an epiphany... that he is one of the demons. He summarily kills his father with his own axe and instructs his brother Adam to bury him in the same rose garden all of the other demons were buried in, when the time comes for him to be killed.
Hostel Part 2 plays it both ways. Two brothers are in town to enjoy the "products" of the Murder, Inc.. One of them is looking forward to the main event, but gets cold feet after accidentally mutilating his victim instead of just scaring her. The other straps his victim back in after initially releasing her.
The final part of Pulp Fiction involves Jules explaining to a mugger that he has come to realize this, and he explains that before he had his epiphany, he would have gunned down the muggers without hesitation, but now he understands how bad a man he's been right before he lets the muggers go.
Boxer in Southland Tales realizes in his last scene that he's a facet of the Antichrist. He doesn't really seem to take it all that badly, even though he knows it means he's about to be blown up by the true Messianic Archetype.
Cass has one of these at the end of The Gamers: Dorkness Rising. Given that the Gamers and Dead Gentlemen in general are known for broad farce, pulling off such a vulnerable moment without Mood Whiplash is actually a small triumph.
Sybok from Star Trek V: The Final Frontier is devastated when he finds out that "God" is actually a malevolent alien entity, making his hijacking of Captain Kirk's ship worthless and potentially fatal.
In 12 Angry Men, when Juror #3, in the middle of explaining his 'Guilty' vote, sees the picture of his son in his wallet and tears it up ... and figures out why he really was voting the way he was.
A mild case with Jason in Mystery Team after Kelly chews him out for trash mouthing Charlie and Duncan.
The audience has one of these in Attack of the Clones; there is a scene at the end where troops ships are taking off from Coruscant to fight in the Clone Wars—the music playing in the background is The Imperial March. The audience realizes that for the past hour or so, they've been Rooting for the Empire.
Bjarnfredarson is all about this finally happening to the titular character, who failed to realise this over three whole series of comedy.
In Dogma, Loki has a moment like this when he hears Bartleby claim that God unfairly favours humans over angels and that therefore they are entitled to kill a bunch of them if that means they get to return to Heaven.
"My God. I've heard a rant like this before... You sound like the Morning Star... You sound like Lucifer, man! You've fucking lost it! You are not talking about going home, Bartleby, you are talking fucking war on God! Well fuck that! I've seen what happens to the proud when they try to take on the throne... I'm going back to Wisconsin."
In Iron Man 1, Tony Stark realizes this after being kidnapped and forced to see the damage his weapons have caused and how indiscriminately they are handled by the people he had uncaringly sold them to all his life (causing hundreds of deaths in collateral damage and easily falling into the hands of terrorists to be used against innocent civilians and soldiers). He is so horrified that the first thing he does after escaping is to shut down the weapons division of his company and call out the military-industrial complex, and the second is to build Iron Man and become a superhero. It's highly possible that he first realized this when, while trying to survive the firefight, a missile lands by him and he sees what's written on it: Stark Enterprises.
A meta example: during production of the 1976 version of Carrie, Nancy Allen and John Travolta didn't realize just how villainousChris and Billy really were until they actually saw the film. They thought they were the comic relief while filming.
In Mean Girls, Cady's response when Janis points out that she's become just as bad as the Plastics is to cry.
In a comic, do you know who the arch-villain is going to be? He is the exact opposite of the hero. And most times they are friends like you and me. I should have known way back when. You know why David? Because of the kids! They called me Mr. Glass.
No. I haven't been acting correctly. I can't hardly recognize myself sometimes when I'm greased. I go on journeys out of my body and look at my red hands and my mean face and I wonder about that man who's gone so wrong.
In Cube Zero, Wynn slowly begins to realize that the Cube masters are putting innocent people in the Cube who fall afoul of the state instead of death row inmates. After being forced to carry out his orders to kill one of his former colleagues he turns on them and tries to help the Cube prisoners.
In The Devil's Carnival, when John cries out "he shouldn't have been born!" he suddenly comes to realize how toxic his grief actually is.
Rachel of Animorphs has one after she threatens to kill David's parents.
Ian Hunter of The Unicorn Chronicles spends the first book, plus a great deal of flashback, being on the side of his great-great-and so on- grandmother, who is trying to destroy luster and the unicorns, all to 'rescue' his daughter. Upon finding her, she yells at him for hurting her friends, and after he gets dumped in the middle of nowhere, he realizes that Beloved is a monster and he's been on the wrong side for the past ten or so years.
A halfway one from The Secret River: Thornhill says that he is "not a bad man", but is doing "something only the worst of men could do"
In Witches Abroad, Lily Weatherwax ruled with an iron fist in order to make fairy stories come true (up to and including imprisoning a toymaker who serially failed to whistle as he worked) and didn't realise that this made her the bad one until her final confrontation with her sister. She goes to her not quite death still insisting she's the good one, but Granny's insistence otherwise has rattled her. Granny, though, has on multiple occasions made a point of saying that only people who don't know better can be bad; if you know the difference between right and wrong, you can't choose wrong. A position that is, incidentally, cribbed wholesale from Socrates.
Subverted in Wyrd Sisters when Granny Weatherwax forces the monstrous queen of Lancre to see her True Self. Instead of repenting, the queen declares that given the chance to start over she would've done everything the same, only harder. She then suffers Karmic Death...sort of. Which would make the above point "if know the difference... and are sane..."
This is also a theme in Going Postal, which focuses on the redemption of the main character, Moist von Lipwig, a professional conman. In the process, the novel subverts the trope Loveable Rogue by constantly pointing out to Moist that his past crimes were just that: crimes, with far reaching negative consequences for many people, up to and including his love interest, who lost her job at a bank as a result of one of his cons.
That had been a good day, Moist thought. At least, up until now it had been a good day.
Sir Apropos of Nothing has a variation: he's not the villain, but instead he's the weird side character to someone else's journey. He eventually kills the hero and takes over his duties, to disastrous results. Then in The Woad to Wuin, when he wakes up from a coma, he realizes what "he's" done while he was "sleeping" and is scared out of his wits. When he realizes the same force that controlled him then makes him indestructible... well, he falls into the evilwell face-first.
Though he'd been dangling just over the abyss to begin with, really. Kind of a self-serving-but-not-completely-evil-bastard/heel turn.
This is the source of the title of I Am Legend. The protagonist is indiscriminately killing the vampires who have reformed and learned to control their urges and realizes at the end he has become a monster to them.
What Skorzeny didn't get and wouldn't get if he lived to be a hundred - not likely, considering how the SS man lived - was that what we were supposed to do and what our superiors ordered us to do weren't necessarily the same thing. Soldiers didn't commonly had to make that distinction. Jäger hadn't worried about it, not until he had found out how the Germans dealt with Jews in the east. Since then, he hadn't been able to look away. He knew what sort of disaster awaited the world if the Lizards won the war. Like Skorzeny, he was willing to do anything to keep that from happening. Unlike the SS man, he wasn't willing to believe that everything he did was fine and virtuous. That made for another subtle distinction, but he clung to it.
Another Turtledove book late in his Timeline-191 series features a character who has become a guard at what is Auschwitz in the extermination of American Southern blacks, and considers himself doing vital work for the safety of his country. When he eventually realizes, through the simple decency of one of the prisoners, that blacks are * people* , he is overcome at the evil he has been helping enact and kills himself.
This is especially poignant, as earlier in the series the character somewhat identified with blacks (though in a way that only made him dislike them more). He himself was of Mexican descent, and commented more than once that in the eyes of most Confederates, he was at most only one step away from blacks.
In Ayn Rand's Atlas Shrugged, James Taggart is helping to tortureJohn Galt, and admits the latter's refusal to cry out is making him upset. When he realizes the significance of this, that he wants the man to be tortured to death — even though Taggart knows that Galt's the only one that can keep Taggart alive as civilization collapses, it dawns on him that he himself is total evil. At this point, he goes insane.
Reverend Hale in The Crucible has one of these and spends the rest of the play trying to make amends - by encouraging victims of the witch-hunt to confess and live rather than die for continuing to deny witchcraft.
Atonement gives one to Briony, the narrator, upon the realization that her actions sent an innocent man to prison.
In Ben Counter's Warhammer 40,000Horus Heresy novel Galaxy In Flames, after Abaddon and Aximand set out to lure Loken and Torgaddon to their deaths, Torgaddon points out to Aximand that he has doubt in his eyes — which doesn't keep him from killing him, but he sobs afterwards and speaks of how they had been their brothers. Abaddon thinks he needs to be watched.
In Graham McNeill's Fulgrim, Fulgrim realizes how great his betrayal is when he is fighting Ferrus Manus; his sword gets him to kill Ferrus Manus anyway, saying he will kill him otherwise, and then, when Fulgrim says "What Have I Done", it lets him realize the depths of his crime, and that his view of Ferrus Manus had been formed by spiteful misinterpretation of his deeds.
While we're on this, Sarpedon of the Soul Drinkers (another Ben Counter work) comes to the terrifying realisation at the end of Soul Drinker, upon finding out that his Chapter have essentially become Chaos Marines (although, had it not been for Chaos mind-befuddling, the mutations would have provided a pretty damn big clue). Having realised this, Sarpedon hauls himself and his Chapter back from the brink of Chaos just in time, and kills the Daemon responsible.
In James Swallow's Warhammer 40,000 novel Deus Sanguinius, Sachiel comes into Inquisitor Stele's rooms when forbidden, and realizes the man is working for Chaos, and so Sachiel and everyone else has been Chaos-tainted. (Nothing Laser-Guided Amnesia can't fix, though.) During the single combat between Rafen and Arkio, he realizes it again, and this time Inquisitor Stele murders him.
In Allegiance, a stormtrooper refuses to fire on unarmed civilians, deliberately shooting to miss. Later he thinks back on how much he looked up to the Empire as a kid, when it came down on the Space Pirates who used to raid his homeworld, and how he joined the stormtrooper corps and served for ten years because it meant making that same kind of difference. But the Empire itself seemed to sour - there was that time he and the other stormtroopers forced a town to stand out in the pouring rain while their identities were checked and rechecked, there was that fanatical obsession with finding and killing Rebels which let other problems go unchecked, there was the promotion of murderers like Tarkin, there were things like the Imperial Security Bureau, and there was Alderaan. After sort of accidentally killing an ISB officer, he and his True Companions steal a ship and go on the run, and end up helping people and finding that Good Feels Good as they try to figure out what to do. But they don't stop being stormtroopers, and they don't join the Rebellion.
Word of God, and the upcoming novel "Choices", holds that these stormtroopers are kidnapped by Thrawn and end up in his offshoot, the Empire of the Hand. The Empire of the Hand, judging by Survivors Quest and the short story Fool's Bargain, is apparently exactly what the stormtroopers used to think that the Empire was. Given that both of those feature stormtroopers who think for themselves and can make moral decisions, it's not surprising. They end up forming a sort-of vigilante group that hunts down pirates and ends up helping Mara Jade expose corruption within the Empire. They called themselves the Hand of Judgment until Mara Jade saved them from getting killed for treason, then told them that there was only one Hand in the Empire, and it was her, the Emperor's Hand. They lost the name, but haven't quit hunting lawbreakers yet.
Death Star has most of its viewpoint characters, all of them on the Death Star, realize this either slowly or after Alderaan. One of whom is the head gunner. His arc is a powerfully moving tragedy.
This is the central point in the The Wave, where a teacher wants to show his class how Nazi Germany came to be... and it all goes horribly right as they really begin to resemble Nazis. Various people have their Heel Realizations throughout the book, including the whole class at the end.
Jack McBride in Torch of Freedom, comes to the conclusion halfway through the book that promoting slavery and plotting to take over the known galaxy is bad and reacts by setting up a defection by a major researcher and then blowing up the Gamma center.
In other examples from the Harrington-verse, Alfredo Yu realizes what kind of sociopaths the Masadans he's been ordered to assist really are and wants nothing more to do with it (nor evidently do a good portion of his fellow Havenite crew). This eventually becomes a recurring theme with other Havenite characters until their second revolution and the overthrow of the Pierre dictatorship.
Pyotr Fursenko from the Dale Brown novel Warrior Class serves as the lead aerospace engineer for the Big Bad Pavel Kazakov. Detached from the atrocities by his distance from the fighting, the evil of his boss finally sinks in when he acts as Guy in Back on a bombing run on the German embassy in Albania, complete with civilian protesters surrounding it.
In John C. Wright's The Golden Transcedence, Gannis realizes that while he is technically not guilty of any crimes, his behavior has been petty, underhanded, deceitful, and disloyal, and he will be — quite justly — shunned for it.
In George Bernard Shaw's play Saint Joan, after Joan of Arc is captured, the English chaplain John de Stogumber pushes relentlessly for burning her at the stake; when he actually sees it done, he goes insane with remorse.
In Harry Potter, this happened to Dumbledore after the death of his sister.
Ditto on Dudley, who realizes exactly what he has become when attacked by Dementors in book 5
Also happened to Snape after his actions resulted in Lily Potter's death.
Valjean in Les Misérables had his Heel Realization after unthinkingly robbing a small child, right after Bishop Myriel had given him everything he'd owned, which got him to start taking his oath to the bishop seriously, and, ... you know the rest. Much later, Javert has his own Heel Realization when he sees Valjean's honest intent to save Marius shortly after having himself been spared by him, and realizes that the world isn't as black-and-white as he'd meant to believe; he doesn't take it as well.
"He had made me, if not an accomplice, at least an eyewitness to his vengeance! Even this was intolerable."
The In Death series: There is this one lawyer in Ceremony in Death who defends one of the Satanic cult leaders that Eve is trying to take down. This lawyer happens to be a cult member himself. When Eve shows crime scene photos of a murdered cult member, the cult leader acts all "Meh", and the lawyer can only sit there and stare at the photos. Eve tips him off that she knows about his involvement and that he should think long and hard about what to do next. Later, when the lawyer is by himself, he ends up experiencing a Heel Realization, where he realizes that ever since he joined the cult he's been having blackouts...and in one of those blackouts, the cult member in the photos was murdered in a sacrifice! Who knows what else happened in those blackouts? He ends realizing that he is in big trouble, and decides to pull a Heel-Face Turn...only to get murdered shortly afterwards.
"The Garden Party" by Katherine Mansfield is about the main character, Laura, having one of these and realizing just how privileged her life is.
Mrs Granger in Frindle, after overreacting to a student's creative attempt to invent a new word, is Genre Savvy enough to realize that her actions have placed her in the role of the villain and uses this status to help the new word along.
Sisterhood Series by Fern Michaels: Roland Sullivan in Lethal Justice apparently experienced this after Alexis Thorne was sent to prison. The good news is that it left him pretty wrecked up. The bad news is that it was an Ignored Epiphany for him.
Till We Have Faces spends its second half working towards this, with Queen Orual gaining revelation after revelation that complicates her perceptions of herself. It culminates in her long-awaited chance to read her accusation against the gods ... but it comes out the way her inner self meant it, not the way she wrote it.
Has one of these that he confesses to the avatar of his consciousness when a photocopy of the Fallen Angel Lasciel in his head. , his consciousness points out that Harry really doesn't have a choice, and that taking the high road means everyone dies. He then pointed out that Harry has the capacity to do good with the evil he agreed to working with. Later, Harry and Michael discuss this somewhat.
Then, Lasciel's copy has one of these. To emphasize, Harry is so stubborn that he got the shadow of a Fallen Angel to turn back to good.
Later, when Harry is dead in Ghost Story, he realizes what his decisions in the previous book did to his friends, especially Molly. It turns out that accepting a devil's bargain in front of your partially-reformed warlock wizardling apprentice is a bad idea, and that she learns from your example.
In one of the Iron Warriors short stories, the renegade Space Marine Ardaric Vaanes realises that yes, he's become a Traitor Marine. At first, he doesn't care.
Adventure Hunters: Ryvas wanted to use golems to end the lose of human life in wars. When he discovers that the golems are just as alive and sentient as himself, he surrenders and peacefully goes to jail.
Near the end of her life, Glory starts feeling emotions. This counts as an Ignored Epiphany, however.
Jonathan has one, which begins when he realizes the exact nature of a mind-controlled sex slave.
Andrew has one, which provides an in-story Tear Jerker moment from him when he finally allows himself to realize just how cruel his betrayal of Jonathan was.
When Faith switched bodies with Buffy, she eventually figures out that she could have taken a run at Angel for evil, and would reappear on his show as in the hope he would kill her. He sees right through this ploy and doesn't comply with it.
Another mild one crops up in the comics. Aside from the fact she is crazy enough to snap and try to kill Buffy despite her Heel-Face Turn due to a combination of liking the person she was going to kill, trying to protect her from Buffy and some belief that if she kills Buffy she'll be a hero; she has the realization she treats anyone who is the least bit decent to her like dirt. While she was nice before her Face-Heel Turn and after her Heel-Face Turn after she realizes this she makes more of an effort to treat people nicely for more than just getting what she wants.
At the end of one episode of Happy Endings, Alex realizes she's been running a child labor ring in the back of her store, and how terrible this is. Takes the intervention of her friends before she gets it though.
During the episode "Think Like a Peter" of The Mindy Project, Peter has one of these when dressing down Mindy's one-night stand.
Peter: This guy took advantage of your heartbreak, and that is a low move. That is disgusting. That is exactly the thing...that I would do. Am I a dick? Does everyone think I'm a dick?
And periodically through the entire series, both with series arcs and Angel's flashback-guilt. There's sort of an implication that if they're ever not hovering around one of these that something is seriously wrong.
Happens to Spike, oddly well after his Heel Face Door Slam. A deranged Slayer kidnaps and tortures him, mistaking Spike for a man who tormented her during her childhood. At the end, Spike realizes it didn't matter that he never laid a finger on the girl, because he'd done plenty worse to other people.
Iris Crowe in Carnivŕle, tells her foster-father Norman Balthus that she knows she's evil:
Iris: "I'm going to hell when I die. I know that. But if I am very fortunate, my brother will be there waiting for me with an embrace."
In The Middleman episode "The Obsolescent Cryogenic Meltdown", former Middleman Guy Goddard realizes that he's the villain when he finds himself saying the villainous Once an EpisodeCatch Phrase "My plan is sheer elegance in its simplicity."
Nicely played out in the Star Trek: Deep Space Nine episode "Waltz", although some fans feel it began Dukat's descent into a more simplistic villainy. Upon being asked by the hero to justify his occupation of Bajor, Dukat's calm rationalizations gradually give way to a rant about the Bajorans' lack of gratitude for his mercy, until he answers Sisko's sarcastic "you should have killed them all" with an excited "yes! Yes, that's right, isn't it? I knew it. I've always known it. I should have killed every last one of them. I should have turned their planet into a graveyard the likes of which the Galaxy has never seen! I should have killed them all." When he later makes his escape, he's dropped the claim of being a misunderstood hero that he'd always made before, and becomes an unapologetic, nihilistic villain for the rest of the series - one of the few examples where a character recognizes his villainy and actually embraces it.
This also doubles as a Nice Job Breaking It, Hero given what Dukat would go on to do after Sisko goaded him into embracing his darkside.
Damar has one in "Taking Into The Wind". He had, up to this point, romanticized the old Cardassia, particularly the occupation of Bajor, not seeing it for the genocidal campaign it was. It isn't until The Dominion murder his family in retaliation for him leading La Résistance (and a comment form Kira) that he realizes it.
Damar: They weren't a part of this rebellion. The Dominion knew that. The Founder knew that. Weyoun knew that. To kill her and my son... the casual brutality of it... the waste of life. What kind of state tolerates the murder of innocent women and children? What kind of people give those orders?"
Kira: Yeah, Damar, what kind of people give those orders?
Occurs in the Star Trek: The Original Series episode, "Changeling", for certain values of "hero" and "villain", as Kirk reveals to NOMAD that it has made an error. NOMAD realizes that it, too, is Faulty and Imperfect, and therefore must be Sterilized.
Also in "The Return of the Archons". Kirk must have studied Logical Judo in Starfleet.
30 Rock, Liz goes to her high school reunion and finds out that the reason she was so unpopular in high school was that her humor was seen as bullying by EVERYONE else in the school.
On Dollhouse, Mellie/November gives Ballard a creepy speech indicating (between the lines) that she's been programmed with low self-respect, and he responds with a dose of rough sex. The next morning she asks if he'll be looking for Dollhouse clients, and he mutters, "I found one."
Topher begins to have this realization, and tries to fight it off with noble goals, such as saving Priya from a lifetime of sex slavery. Nonetheless, his scientific progress leads nowhere good, he holds himself responsible for the destruction his discoveries cause, and he goes insane.
In "Her Charm", Sam leaps into an FBI agent assigned to protect a woman who testified against a crime boss. His attempts to hide her should be successful, but fail when an informant in the agency keeps giving away her location to her pursuers. Sam groans in frustration when he learns that he (or rather, the man he leaped into) is the rat in question.
In "Last Dance Before an Execution", Sam leaps into a man in the electric chair who is given a 48-hour reprieve, seemingly to try to prove the innocence of the man he leaped into. But as it turns out, he really did it after all - he was there to save the co-defendant, who was innocent.
Richard Woolsey in the Stargate SG-1 episode "Inauguration", beginning his long journey to becoming one of the heroes and ultimately a regular on Stargate Atlantis.
And Harry Maybourne as well, from slimy weasel to convicted traitor to grudging ally to beloved king of an alien planet.
Tomin has one early in "The Ark of Truth". The Priors have a collective one after the Ark is opened.
Supernatural has an odd version in season five when Dean realizes where his current path leads after he's sent into the future and meets himself.
Dean: (Chained up) What? You don't trust yourself? Future!Dean: No. Absolutely not. (leaves) Dean: What a dick.
The moment at the end of season four after Sam has killed Lilith and Ruby revealed that Lilith was the final seal, not the one who was going to break the final seal, is Sam's moment when he realizes he's just an Unwitting Pawn who screwed up big timeand brought about the apocalypse. His face during Ruby's triumphal and extremely ill-advised monologue conveys complete devastation. He's barely even paying attention when he and Dean subsequently kill Ruby.
As The Wire winds to its conclusion, McNulty finally realizes that being a Cowboy Cop did not make him a hero after his plan to get more funding for the police via a fake serial killer story blows up in his face.
In Alias, the agents of SD-6 are not happy to learn they've been working for the enemy all along.
Between seasons two and three of Breaking Bad, Jesse has one of these moments.
Jesse: I learned it in rehab. It's all about accepting who you really are. I accept who I am. Walter: And who are you? Jesse: I'm the bad guy.
Jesse returns to this fairly often, frequently being the one with a conscience this hits its apex in season 5 when the group's actions result in the death of a kid and Jesse decides to retire from the meth game, no matter how much Walt tries to guily him into staying.
Walt has these moments himself on occasion, but tends to move past them quickly — which is ironic since, by most standards, he's much worse than Jesse. The biggest one probably comes in season 4 in "Salud". As per usual, it doesn't stick. Until, "Gliding Over All" in season 5.
The message finally seems to get through to him in "Ozymandias". Unfortunately, it's not until Hank is dead and his entire family has been destroyed, their lives ruined by his actions and choices.
Skyler has it in the beginning of Season 5. While she was content with helping Walt with his crimes at first, once she finds out that he was behind the murder of Gus, she realizes how monstrous he's become and is terrified of him, doing everything she can to get the kids away from him.
Amy to Rory in "The Girl Who Waited", after realising that she doomed herself to wait thirty-six years being chased by killer robots to be rescued.
Sebastian the Vorlon Inquisitor in Babylon 5 had such a realization about his "reform" project for which he was "remembered only as Jack" (the Ripper).
Sebastian: The city was drowning in decay, chaos, immorality. A message needed to be sent, etched in blood, for all the world to see: a warning. In the pursuit of my holy cause, I did things, terrible things, unspeakable things. The world condemned me, but it didn't matter, because I believed I was right and the world was wrong. I believed I was the divine messenger. I believed I was... Sheridan: Chosen? Sebastian: I was found by the Vorlons. They showed me the terrible depth of my mistake, my crimes, my presumption. I have done 400 years of penance in their service. A job for which they said I was ideally suited. Now, perhaps, they will finally let me die.
Also from Babylon 5, Zack Allan. He was originally enticed into joining Nightwatch because of the extra pay it offered, but as he noticed Nightwatch get more and more oppressive, he began to resent his decision. Still, he stayed in and simply strove to involve himself as little as possible. All the time, his chief, Garibaldi, kept railing him for thinking it's a game when the consequences are getting very serious. Finally, as Nightwatch tries to take over the station, he lets slip that a bunch of Narns are coming in to replace them. The leader of the local Nightwatch musters every hand possible to capture them...putting all of them in one single secure location which Zack promptly has sealed. After both sides having told him he had done the right thing, it's only at this point, coming from a more-reassuring Garibaldi, that he feels he can believe it. Turning in the Nightwatch showed he was on the right side after all, and he would eventually become Chief of Security himself.
Done rather nicely in iCarly with Nevel, who was as close to a Big Bad as the show got. After spending the series doing everything he could to destroy iCarly, he gets caught on video being his mean, Jerkass self to a little girl who'd accidentally bumped into him. Not only does this ruin his life, it shows him what he's really been like. He says My God, What Have I Done? and makes a token effort to change his ways. Ultimately, the iCarly gang help him do so and he performs a Heel-Face Turn as a result.
The Big Bang Theory had an episode with two unrelated stories about this. One centered a around reunion between Leonard and a former bully, during which time he began to realize how much he'd hurt Leonard until he wakes up the next morning fully sober and reverts to his older self. The other centered around Penny realizing that she used to be a bully and trying to overcome her guilt upon realizing how much she hurt her classmates. This doesn't go so well, as her attempt to salve her conscience by donating clothes to Goodwill ends with her taking clothes from the box.
The final season of 24 saw, after 7+ seasons of being pushed around, screwed over, and betrayed, Jack Bauer snapping and going down a dark path where revenge actually had a precedence over justice for him. In the series finale, Chloe finally brings Jack back to his senses by making him realize that if he assassinates Yuri Suvarov, the Russian President dying on U.S. soil would lead to war between the United States of America and Russia and lead to the deaths of far more innocent than guilty.
One episode of How I Met Your Mother has Barney convincing Ted to have a night out with him, and getting him to live like there's no tomorrow. The context is that Ted has been having a bad time of it and is getting depressed about ever meeting someone. So they go to a bar and Ted ends up doing a bunch of not cool things, like charging a lot of expensive booze to someone else's tab, making out with a married woman (who he knew was married), etc. He thought it was all fun, until Marshall plays back the recording of the night that got left on his phone (from Ted butt-dialing him). Ted realizes what a dirt-bag he's been and that he is essentially becoming Barney.
In Once Upon a Time, Regina has done all manner of horrible things. In the second episode of season 2, a Meaningful Echo from Henry makes her realize she has become the one thing she swore she would never be... her mother. She lets Henry go, and begins to try to be The Atoner.
Tony Stonem in series 1 of Skins comes to this conclusion after his sister almost dies due to a revenge plot concocted by someone he screwed over in the previous episode and he relies on his best friend Sid, whose emotions he has been playing with for the entire series, to help save her. He then gets hit by a bus.
Henry gets one of these in Eureka after finding out that his wife used to be a Consortium agent. When questioning her, he finally gets her to reveal who she is protecting - him, or rather his alternate self in this reality.
Happens in "Cats in the Cradle" by Harry Chapin. Add a major tearjerker in that Chapin never lived to see his children grow up; he died in an automobile accident in 1981.
And as I hung up the phone it occurred to me He'd grown up just like me My boy was just like me
Happens twice in Razia's Shadow by Forgive Durden. First, when Ahrima goes into the darkness and Barayas (the Spider) convinces him that the only way to make people respect him is to make them fear him. He destorys the lamps, and is banished. In Toba the Tura, he laments "Oh, what have I done?". Second, Pallis. After accidentally stabbing his brother, Adakias, he begs and pleads for him to fight and stay alive. Though he was aware of his evil intentions, he didn't mean to take things so far.
The second half of David Bowie's "Cygnet Committee," wherein the second narrator first gleefully describes the violence he and his allies have turned to, but slowly sees it to be antithetical to his ideals.
I believed it would justify the means It had a hold over me Blinded to see The cruelty of the beast Here is the darkest side of me (Forgive me my sins) The veil of my dreams Deceived all I have seen Forgive me for what I have been.
Nick Cave and the Bad Seeds song "The Curse of Milhaven"
Since I was no bigger than a weavil they've been saying I was evil that if bad was a boot then I'd fit it that I'm a wicked young lady, but I've been trying hard lately Oh fuck it! I'm a monster! I admit it!
According to Christianity, acknowledging one's own "fallenness" is the first step to receiving salvation.
A specific example would be Saul of Tarsus, a notorious persecutor of the earliest Christians, who was knocked to the ground and struck blind by a vision of God on the way to Damascus ("Saul, Saul, why do you persecute Me?"). He converted within the week to Christianity, changed his name to Paul and found his sight restored, and "the road to Damascus" would become a popular metaphor for the Heel Realization.
In the New Testament, when Judas Iscariot realizes that he's betrayed Jesus, he gives back the thirty pieces of silver, and hangs himself. (The other account for his death averts this trope.)
David, though beloved of the Lord, was rebuked by the prophet Nathan when he had Uriah the Hittite put on the front lines so he would be killed, and David could take his wife Bethsheba for himself. Nathan tells him that the child Bethsheba was currently pregnant with would not live. Indeed, despite David fasting and clothing himself in sackcloth, the baby died after seven days. (And during this time, David alledgedly wrote the powerfully penitent Psalm 51).
According to legend, Joan of Arc's executioner showed up at his church for confession as a babbling wreck shortly after due to realizing he had "killed a holy woman."
In Ravenloft, having a Heel Realization is the only way a darklord can escape his/her Ironic Hell realm. The sourcebook does note that people actually capable of having a Heel Realization and actually admitting that they reaped what they sowed when they committed the Act of Ultimate Darkness that made them darklords would never have become darklords in the first place.
GURPS: Discworld has a spell causing this - forcing a fear roll upon the victim - but if they are truly evil, they snap back usually laughing, and the caster must make a fear roll!
Valjean and Javert in Les Misérables - see Literature, above, although the episodes with Petit Gervais and Marius are sometimes omitted, the realizations following directly from the Bishop's undeserved gift to Valjean and Valjean's decision to spare Javert. Here, with Javert having been upgraded from "recurring nuisance" to "deuteragonist," an explicit parallel is drawn, Javert having a solo that's a Dark Reprise of Valjean's.
In Deus Ex: Human Revolution, the character Hugh Darrow, father of human augmentation, justifies his actions in driving every augmented person in the world violently insane with a mass produced 'upgrade' to their biochips, by claiming they were necessary to show the world the dangers of mechanical augmentation, wanting to end human augmentation so that future generations may grow up without being surrounded by dangerous cyborgs and the torture of having to rely on an anti-rejection drug or die a slow and painful death, and is unwilling to let the Illuminati he conspires with control humankind through his technology. If Adam can make him see his own flawed logic and make him see the scale of his actions and the possible genocide he has caused he will recoil in horror of his actions and realize just how much innocent blood he has shed for his own selfish purposes. He gives Adam the code to the Hyron Project computer, making the final boss battle far easier, and meakly tells Adam to leave him for whatever may come next.
In Tales of Phantasia, the main characters' primary motivation the entire game long is avenging the slaughter of their hometown, but they go too far and they end up nearly dooming a planet because of it. There's a nice few minutes of angst (not quite enough, though) right after the Final Boss fight.
In Valkyria Chronicles one of the Imperial generals, Yeager, realizes that even though he's fighting to liberate his own country, his participation in the invasion of Gallia makes him a hypocrite. Inspired by the zeal and dedication the Gallians show in defending their homeland, Yeager decides to abandon his post and leaves the Imperial army.
An example from Knights of the Old Republic II comes from a conversation between Kreia and Jedi Master Atris, during which Atris realizes that she had fallen to The Dark Side some time ago through her resentment of those she feels betrayed her. Atris subsequently embraces the role of Darth Traya, although the Jedi Exile has the opportunity to redeem her.
It's worth noting that Atris wasn't Darth Traya, or at least not the original Darth Traya. In the version of the game that shipped, which had quite a bit of story cut for time, Atris doesn't get a Sith name. The full story, including the bits that got cut, seems to be canonical, though. It's also hinted that Kreia went through the same realization sometime in her past, as well as Atton Rand, whose story you can find out more about.
And then there is the original KotOR, where at tho-thirds point in the game you learn that you were the amnesiac Sith Lord all along.
White Knight Leo from Lunar 2: Eternal Blue is a Knight Templar who's really a Knight in Shining Armor at heart...which is why he flip-flops between Heel and Face. By the time he's mostly sided with Hiro, he's had to accept that the Althena he served was a fake goddess, put into position by the real dark god, Zophar. Oh, and that he's slaughtered an untold number of other innocent people by unquestioningly following the orders of his false goddess. It's a tough pill to swallow.
Xenosaga has Canaan, who actually does this twice: first as Lactis during the cellphone game Pied Piper, then a hundred years later during Xenosaga III: Also Sprach Zarathustra as Canaan. Both times, Redemption Equals Death. Reincarnation is fun, kids.
This "Let's Play" of Galactic Civilizations 2 was intended to be a peaceful attempt at attaining galactic superiority through advanced culture. Half way through comes the realization that something has gone terribly wrong:
God, look at me. This was supposed to be my quest for peace, and I've become addicted to destroying suns.
Anyone who has read the Mass Effect: Revelation prequel book will know that he was an asshole with an agenda even before his indoctrination. He would abuse his Spectre status and openly lie to prevent Anderson from becoming the first human Spectre.
At the end of Mass Effect 3, Shepard can convince the Illusive Man into committing suicide by convincing him that he has become indoctrinated and that his delusions of controlling the Reapers are just the tool they're using to control him. The method of doing this is more subtle than most of the other reputation-related checks in the game: you have to consistently pick Paragon or Renegade options during every single conversation with him over the game to successfully convince him how far he's fallen.
The Paragon Ending of the Citadel DLC has the Clone Shepard end up being Driven to Suicide after witnessing Shepard's squad rush to help them from the ledge both are dangling off of, while their own ally Maya, callously left them to die. Without a word, you can see the realisation slowly sink-in, answering their earlier rant about what it was that made Shepard so special andnotthem? The very thing that Clone!Shepard derided the real one over when they first met face to face: Shepard has friends.
The ultimate villain of the Overlord DLC, if you chose the Paragon solution, seems to have realised between 2 and 3 how horrific what he did actually was, and erased his notes and left Cerberus when he was asked to repeat it.
"I...don't think I can think that I can continue. Continue? To have done the things I have done in the name of progress and healing. It was madness. I can see that now. Madness. Madness? There is no hope. Leave now. Leave while you still have hope..."
In Dead Money, Dean Domino enacted a scheme with Vera Keyes to ruin Francis Sinclaire's happiness out of petty envy in the backstory. Assuming he survives to the end, he will experience remorse when he hears Sinclair and Vera's side of the story. He doesn't understand why he feels so sad, but it's enough to convince him to finally let go of the Sierra Madre.
Eden: Perhaps...Perhaps there is a problem. I—I am unsure how to proceed.
If you spare Loghain in Dragon Age: Origins and increase his approval, he will eventually go through one of these. His last words if you allow him to slay the Archdemon make it clear that he knows his past actions are unforgivable, and all he wants is a chance to atone for them.
In the sequel, when you get Knight-Commander Meredith down to her last bit of health, she nearly has one of these, but unfortunately for her, the realization doesn't stick.
In the original God of War, Kratos, when flashing back to the day when he cried out to Ares for help, thus starting the whole cycle of events that lead up to the present, says to himself "By the Gods, what have I become?" This is the only time we ever see Kratos expressing sorrow and regret for something other then being tricked into killing his wife and daughter.
Throughout Persona 4, Namatame (manipulated by the real killer) has kidnapped people he saw on the Midnight Channel and thrown them into the TV to protect them from a Serial Killer. He sincerely believes that the TV is a safe place, and he can retrieve them once the killer's found. What he doesn't realize is that they can't escape on their own, and once the fog lifts, they will be killed by Shadows. Once he himself enters the TV to escape police pursuit, it hits him just how wrong he was, and he does everything he can to assist the party as atonement... assuming you aren't cruel enough to kill him.
Quite possibly the entire reason Raiden attempts to change history in Mortal Kombat 9, coupled with Shao Kahn's victory. His revival of Liu Kang is one of the key events shown in the flashback message he sends to his past self.
In Back to the Future: The Game, Edna Strickland is hit with one of these in the fifth episode, after admitting that she accidentally burned Hill Valley to the ground when trying to destroy a saloon in the 1800s.
In Asura's Wrath, Yasha spent the last 12,000 years going along with the plans of the same people who killed his sister and his brother-in-law, enslaved his niece, and regularly slaughter people for their souls. All for the sake of the "cause" — preventing the complete destruction of humanity at the hands of the Gohma. He justified it by believing with all his might that it truly was the only way to save humanity in the long run. Confronting Asura again and seeing how much power he's attained without mass human sacrifice helps Yasha realize that Deus' plan isn't the only way to save the world. When Asura calls Yasha and the other Deities fools for killing seven trillion people as part of their plan to "save" the world, Yasha agrees.
If the Arcade Endings of Blaz Blue Chrono Phantasma is any indication, then Litchi Faye-Ling finally had this. On top of being told that Kokonoe has not just abandoned her, but made her an enemy that she would not hesitate to kill, she is also told by Rachel that her efforts and insistence in saving Arakune and siding with NOL is going to bring the Day of Destruction, killing many people when she thought she wasn't planning to hurt anyone in her quest. On this realization, she broke down in tears, and we're gonna have to see if this characterization will stick in the console Story Mode, or ignored.
Skullgirls: Let's face it, Cerebella is a very sweet girl, so sweet that she has Incorruptible Pure Pureness. So why is she on this list? Because she's working for a mafia responsible for many murders, yet she faithfully stays with them because she considers them family, and seeks the affections of the mafia boss she considers a father. Only when she ends up crushing a Cat Girl to death to retrieve a stolen jewel does she start to feel remorse for her actions.
In Prototype Alex Mercer gets one when he discovers Alex Mercer has been dead all this time. He was actually The Virus in an Alex Mercer suit. He at least takes some consolation in the fact that as bad as being The Virus is, the person he thought he was before that was even worse.
In Dragon Island Blue, many high-ranked Guild Trainers switch sides and join La Résistance after the increasingly ruthless missions that The Guild was sending them on convinced them that The Guild had become corrupted by power and turned despotic. The player is a fully-licensed Guild Trainer too, and rapidly rises to become their main enforcer (though the mass desertion of their elites might have helped with that) - and so, the player will likely have a Heel Realization at some point too... but you never switch sides, and indeed, proceed to effectively destroy La Résistance. Not because you aren't sympathetic to their cause, but because you feel that overthrowing The Guild in an armed uprising will only lead to unacceptable bloodshed.
In the Flash game King's Ascent, the entire game is the King's own sorceress and general's plan to force the King to face his flaws and mistakes. The King eventually agrees that he wasn't a very good ruler and throws away his crown to spend the rest of his days as a farmer. The sorceress has a Heel Realization of her own. She acknowledges that she was being driven by anger and hate, and refuses to take the now empty throne.
One of the Mooks in Max Payne discusses this in a bit of Enemy Chatter, he's not a bad guy, he's just trying to provide for his family and is in over his head but can't get out. Of course, you have to kill him anyway.
In Tsukihime, Akiha route, you can, at one point, kill Ciel (thus, failing her test of Shiki's humanity), prompting Shiki to assume he IS a natural-born killer, after all, and give in to The Dark Side. Needless to say, it's a bad ending game over.
Part of Kohaku's route has her realize much quicker than in Hisui's route that maaaaybe she should have picked a different hobby than plotting the utter annihilation of the Tohno family, even if Makihasa wasn't the world's nicest guy after his Inversion Impulse began.
Part of Kotomine's backstory in Fate/stay night is his realization that nice people do not enjoying watching others being tortured or that sort of thing. That's fundamentally why he can't actually become a Card-Carrying Villain; he actually has a sense of morality. The end result can be considered an Ignored Epiphany but he did try. For years.
In Phoenix Wright: Ace Attorney, Miles Edgeworth starts to have "doubts" after you demonstrate two defendants to be innocent, but it's not until he's the defendant in two murder trials in a row in which he's innocent that he really decides that striving to get every single defendant found guilty to maintain a "perfect record" might be a bad thing. Furthermore, he finds out that although he became a prosecutor because of the fatal shooting of his father, it turns out that the real killer is the senior prosecutor who mentored him, and instilled those beliefs in him to begin with!
Also, in the fifth case, Edgeworth finds that he's already guilty of using forged evidence, and the forged evidence was used to give a death sentence to a serial killer. He wasn't aware of it at the time (he himself didn't forge it, and he was convinced that it was the real deal), but it really came to bite him in the ass when people found it out and started to call him out on it. Even when they find out who forged the evidence and why, sort of clearing his name a bit, he couldn't forgive himself for it...and it's implied that it's one of the many things that pushes him to leave the prosecutors' office for a year, leaving what appears to be a suicide note.
Acro has one in case 2-3. When the Judge asks if he's a victim, he says he's nothing but a murderer.
In Katawa Shoujo, in Act 4 of Shizune's route, she realizes that she has been taking those closest to her for granted and pushing people close to her away. She thus resolves to, with Hisao's help, repair her friendship with Misha, and also says she will be less competitive in the future.
In Exiern, Tiffany hates Theresa for several bad reasons: They are both under a Gender Bender spell (and Theresa doesn't share Tiffany's whiny attitude about it), the guy Tiffany tries to tell herself she's not in love with seem interested in Theresa, and they (Tiffany & Theresa) are equally bigoted against each other's culture. After Denver give her the appropriate "What the Hell, Hero?", Tiffany finally realize what a bitch she has been to Theresa. See page illustration above.
Axel: We've faced worse than this. Remember when Disneyworld was destroyed? Marluxia: Larxene did that. Axel: Well, what about that plane that got hijacked? Marluxia: You hijacked that plane. Axel: Okay, but there was that corrupt government. Marluxia: That was, and still is Zexion. Axel: Wow, we're assholes.
Agatha: And I'm the evil mad girl with the death ray and the freakish ancestors — and the town full of minions — and the horde of Jagers — and the homicidal castle full of sycophantic evil geniuses and fun-sized hunter-killer monster clanks and goodness knows what else- [beat] Agatha: -And you know what? I can work with that!
In fact, multiply parodied: Baron Wulfenbach gets a few lovely moments too - mostly in the vein of knowing he's the "bad guy" and being all right with that. He's not really the bad guy - but his "heel" turn happened because he was drugged and dragged out of his continent, only to find upon his return years later (and with a new son in tow) that the Heterodynes have vanished, their base was annihilated, zombie-like people are running rampant, and the few nobles alive who still have power are engaged in petty squabbling instead of banding together to fix the utter chaos. The Baron quickly gathers all the allies he can, makes all the death rays he can, and just starts killing everything that is killing something else, until everyone finally bows to his rule. He's one of the only two reasons that the continent has general peace, and the other reason was a woman who made a Heroic Sacrifice to stop the zombie threat from being worse than it had. It hasn't stopped the world from considering him an evil tyrant, but at this point, he's stopped caring what anyone else thinks.
In Darths & Droids, the PCs have always been skirting the border between merely Off the Rails and Obliviously Evil, casually trashing the GM's carefully scripted story and messing things up far worse than they were originally. The GM loves to point this out to them, but it isn't until #454 that Pete finally gets it. His reaction subverts the trope: "So we're the bad guys now? Cool!"
Played a little more seriously in #571, where Anakin slaughters the younglings. Jim can no longer sympathize with Anakin. In this continuity, he's probably right.
Parson arrives at this fairly quickly after arriving in Erfworld (what with his side having all the classic evil minions like dwagons, gobwins, twolls, and giant spidews), but gets chewed out by his new boss and told that the whole "Good Guys/ Bad Guys" concept is just stupid. Comes up again after the climax of the Battle of Gobwin Knob, when the full impact of his plans and actions (tens of thousands of Erfworlders are DEAD) hits Parson and he has to wonder how much he was influenced by the spell that summoned him and how much by his own free will and genuine desire to command a battle.
King Slately, too.
"I am facing facts," he repeated, softly. "My friend. Hard, hard facts." The two rulers looked at one another for a long moment. "My son is more of a man than I am. All my sons have been. And you always knew it. Did you not?" Don said nothing. "You never would listen to me about Royal ideals," Slately said, frowning. "Honor, sacrifice, dignity, decorum, station...loyalty, bravery... You were too polite to me, Don. You couldn't simply say I was no Royal ideal myself."
In El Goonish Shive, Abraham realizes the error of his ways after Nanase persuades him that in trying to fulfill his oath by killing Ellen he was actually violating it. This leads him to become The Atoner.
Bobby Jacks in Survival of the Fittest, who realizes he's one of the bad guys very early on but then decides that now that he's killed somebody there's no going back. Lenny Priestly also arguably fits this, although he is less somber about it.
The Escapist series Doraleous and Associates had an episode where the titular heroes-for-hire realized they were working for the bad guys. They immediately switched sides.
In this short video made for Christmas 2009, Jack Bauer begins to interrogate and tortureSanta Claus. (Santa's flying over the US without a passport delivering mysterious packages, after all). With only a few sentences Santa makes Jack (who has just threatened to cut out Santa's eyes) realize that what he's doing is wrong. The video ends with an emotionally distraught Jack leaving the room and nearly having a breakdown in his car.
In the Global Guardians PBEM Universe, the original Dove was a vigilante crimefighter who was active between 1989 and 1995. He considered himself a hero helping to defend ordinary people from street criminals. His usual modus operandi was to hunt any criminal whom he thought "got away with it"; that is, whenever he disagreed with a "not guilty" verdict. When captured, he was confronted with the fact that he wasn't a defender of the public, but rather just another serial killer and the idea horrified him to the point that he hung himself while awaiting trial.
Phase of the Whateley Universe is a fourteen-year-old who was kicked out of the richest family on the planet, the Goodkinds, when he turned into a mutant: the Goodkinds are notoriously anti-mutant, supporting the Knights of Purity and the semi-governmental Mutant Commission Office (MCO). Goodkinds, including the boy Phase used to be, have supported the MCO with billions of dollars over the years. Phase has defended the MCO to his new (mutant) friends at Whateley Academy, even though there are rumors that the MCO has kidnapped hundreds of young mutants who were never seen again. In "Ayla and the Grinch", Phase has to face the fact that the MCO really has been kidnapping, and "disappearing", young mutants, and he is partly responsible, since he helped fund the MCO.
Later on, Epsilon, in the form of Church and with his memories, angrily blows up at the entire Blood Gulch crew...perhaps not unjustified due to all the things that have happened to him, not all of which were his fault. However, he finally realizes what kind of an asshole he's been to them when Tucker, his friend for the longest time, and Caboose, the poster child for stupid yet earnest loyalty, both leave him and Carolina, walking out with the rest of the Blood Gulch crew.
In The Venture Bros., Dr. Killinger, a villain adviser who previously made massive changes/improvements to both The Monarch's villain career and personal life, shows up to advise Dr Venture. Killinger saves Venture Industries and helps Venture face his numerous childhood issues, especially about his father, but at the end produces two papers, one of which would officially make Venture a supervillain, the other would dismiss Killinger and the "Venchemen" that Killinger had assembled to be Venture's army of mooks. The semi-sociopathic Venture eventually chooses not to become a villain, but is left deeply shaken by the whole encounter.
Dr. Venture: What? My brother? Dr. Killinger: Bingo! Isn't it perfect? It's a classic Cain und Abel story. Dr. Venture: But... But... But he can't arch me, he's not even a super- (Beat) oh my god...
Brock: Are you okay, doc? Dr. Venture: I... I don't know. He thinks I'm a... Brock, am I a... bad person? Brock: The hell just happened? Dr. Venture: Am I, Brock!? Brock: (pauses, then rocks his hand in a "kind of" gesture) Ehhhh.....
In the final regular episode of Daria, Daria has a painful flashback memory about a loud argument her parents had over her. At this, Daria is wracked with guilt that she had been an unfair burden to her parent when she thought she was being herself. However, her parents make it clear that as much as they tried to encourage a more social attitude from her, they also accepted that her loner and iconoclastic ways were worth the price to have a daughter who is admirably intelligent, perceptive and principled.
In Megas XLR, Coop tries to protect the Earth, though it's usually his fault, and he does far more damage than anyone else. The S-Force and their evil nemesis, Ender, spend an episode pointing this out to him (aptly titled The Bad Guy), and nearly everyone else does at some point. In the series finale, an AU version of him actually was the bad guy. It was intended to be revealed at some point that he created the Glorft on accident, too.
In an episode where Stewie has learned he is actually a masochist as he tries to goad Lois to hit him he says, "Dear Lord, I really do have problems don't I?"
In another episode, Peter and friends are in jail and being targeted by a vengeful prisoner. He turns up at their cell with a knife only to find that they have already been released, giving him some time to think:
I wonder what this feels like. [pokes himself in the chest with his knife] OW! That hurts! ...My God, is that what I've been doing to people? I belong here.
Jeong Jeong and Iroh both had one before the series, leading to them working with the Order of the White Lotus to stop the Fire Nation.
Fire Lord Sozin who began the war, left his best friend Avatar Roku to die, and wiped out the Air Nation realized this at the end of his life, but it was far too late to turn back, and his descendants turned out to be largely worse than he was.
In the Sequel Series, The Legend of Korra, Tarrlok goes through one of these after Amon takes his bending away, realizing that he's become the horrible man that his father wanted him to be. To atone, he commits Murder-Suicide, killing both himself and Amon and ending Yakone's evil legacy. It's also possible that Amon went through one at the end but, like most things about his character, it's left ambiguous.
In the South Park episode "Crack Baby Athletic Association", Cartman talks Kyle into joining his business of getting crack babies to play basketball which, after some karaoke and bacon pancakes from Denny's, he accepts. He then tells Stan about it and Stan doesn't reply, making Kyle give a monolouge how him and satire target NCAA do good by using players like slaves. Then towards the end of the episode, Stan says he's starting to sound like Cartman and Kyle replies "No I'm not goddammit!" then cups his mouth in shock.
In The Movie, most of the Mothers Against Canada drop what they're doing when they realize that the war is putting their children in danger. Sheila's doesn't come until it's almost too late.
In "The Glass Princess", an episode of the original My Little Pony, Porcina has been turning Ponyland and the ponies there into glass at the encouragement of her Raptorian minions. But when confronted by some of the ponies face-to-face, she can't do it. She had only been able to do it to the others because they didn't seem real through her scrying glass, and ends up seeing the error of her ways.
In the same continuity, in the episode "Baby It's Cold Outside", an evil penguin king tries to freeze the entire world so that only "worthy" creatures like himself will survive in such "perfection". In the finale, when our heroes try to stop him, he tries to freeze our heroes...but accidentally freezes his own son instead. In an interesting take on his trope, he actively tries to resist the realization at first, telling himself that it was his own son's fault for getting in his way (even his own guards don't swallow this). Megan and the ponies sing a song to him about how he could be so cold, which finally causes the heel realization because the song made him remember all the happy times he used to have playing with his son, and he cries over his son's frozen form...which thaws him out.
The episode "Secret of My Excess": Spike's draconic hoarding instinct is triggered on his birthday, and he starts going through dragon puberty which means growing to prodigious size and snatching everything he likes the look of. This culminates in an adult-sized Spike rampaging through Ponyville and kidnapping Rarity. When she snaps at him when he tries to steal the wrong necklace (one made with a stone he gave her earlier) and he realizes that not only does his beloved Rarity literally not recognize him anymore, but actively hates what he's become, the Heel Realization is so powerful it reverses the draconic growth and he immediately shrinks back down do his familiar size.
Fluttershy in "Putting Your Hoof Down." After becoming more and more violent and then proceeding to brutally tell off her own friends until they're driven to tears, she becomes horrified at the monster she's turned into after looking into a puddle and seeing her own rage face. She's subsequently so remorseful that she endeavors to tie herself up inside her own barricaded house so that she can't hurt anyone else.
The episode "One Bad Apple" had Apple Bloom's cousin Babs Seed goes from Shrinking Violet to bully on a level above even local Alpha Bitches Diamond Tiara and Silver Spoon. The Cutie Mark Crusaders plan payback prank for all the turmoil Babs has caused. Both sides get the Realization. The Cutie Mark Crusaders upon learning Babs's Freudian Excuse, and Babs when the Crusaders immediately abort their plans and save her from their prank.
Amazingly, Discord gets one in "Keep Calm and Flutter On" when he realizes that what he does could cause him to lose his friendship with Fluttershy. It is also during this moment that he first realizes Fluttershy's friendship actually means something to him.
The Wonderbolts have a few of these thanks to Rainbow Dash - when their star cadet puts her friends in danger in "Wonderbolts Academy", and when they choose her over their teammate Soarin' in "Rainbow Falls".
In Gargoyles, Demona comes oh-so-close to hitting this multiple times, but always turns it into an Ignored Epiphany at the last second. John Canmore winds up doing the same.
Played With with Germaine of Xiaolin Showdown. In his season 2 reappearance, he's studying under Chase Young, in hopes of becoming a warrior like the monks. Though it takes the entire episode to convince him, he eventually bows out, realizing that studying under Chase technically makes him a part of the Heylin.
Roger Papermouth has one of these after he shoots up his daughter's teddy bear (which was a gift from his ex-wife).
Arthur has a Jerkass Realization after he realizes how he manipulated his son Clay which caused him to become what he is.
Bloo went through on in the Foster's Home for Imaginary Friends episode, "Cuckoo for Coco Cards". Coco had been making trading cards featuring each of the friends in the house, but refused to make any for Bloo unless he apologized for being being rude to her earlier in the episode. He ended up gaining them by other means, but it wasn't until the very end when he read the stats on his own card; "Big, insensitive jerkface", that he realized what a JerkAss he had been, and apologized to Coco.
Megatron in the finale movie of Transformers Prime, Predacon Rising. After spending the whole movie as Unicron's unwilling slave, he realizes the oppressive evil he has inflicted on Cybertron, and disbands the Decepticons.
Danny Phantom has a rare case where the villain (namely Vlad) goes through this twice. The first happened in a Bad Future where being without his powers for ten years made him realize what a fool he was. The second occurred in the Grand Finale when his ultimate plan backfires and he loses everything, even Jack's respect. This trope is made clear when he shows a look of guilt before sadly flying away from earth in exile. Definitely an Alas, Poor Villain moment.
In MetalocalypseRock Opera special "Metalocalypse: The Doomstar Requiem", Magnus Hammersmith, The Pete Best of the band Dethklok, sees firsthand the unnecessary and evil actions of his partner, as well as the righteous vengeance of his old band, and realizes that the revenge he was seeking wasn't justified. Though he spends the whole special assuring Toki, who replaced him, he was really attempting to assure himself he was good. When that facade is broken, he states "I am not the hero, I am the villain, and I too must go down..."
The New Adventures of Winnie the Pooh has an instance of this in "Groundpiglet Day". After unfairly harping on Piglet for lying about the weather forecast, Rabbit learns from a calendar that Groundhog Day wasn't for another three months and starts to really feel guilty about his actions. Upon realizing his mistake, Rabbit goes to Piglet's to apologize to him, only to find a note that says Piglet had set off to look for a real groundhog.