Perhaps you have had a Heel Realization. Perhaps you are Dying as Yourself and have just learned the enormity of your deeds. Perhaps you have learned too late that the act you sought Revenge for was fully justified. Perhaps you have failed in your one and only chance. Perhaps you were responsible for another's death; perhaps you know in your heart that you can never be forgiven for what you have just done. Now you can do nothing but cry. Maybe you are sobbing uncontrollably; maybe it's just a Single Tear — at this point you don't know or care. All you know is that the tears are going to fall and you cannot hold them back.
These are universally the sign that some spark of goodness resides in the one who sheds them. No matter how far gone s/he seems to be, a character who weeps for an evil act is not yet a completely evil person. This does not always mean that reform is possible (tears may be the last gasp of the conscience before plunging completely over the Moral Event Horizon, for example). But they can be the start of redemption, especially if the hero can apply The Power Of Trust; or better, The Power of Love.
A Sub-Trope of My God, What Have I Done?. Common in a Villainous BSOD — though Ignored Epiphany can still ensue. A good character Fighting from the Inside may shed these, even if s/he has shown no previous ability to resist the control.
May be a form of Manly Tears. Tender Tears combine when they are grief-stricken by minor injuries to others. Note that crying because you didn't get away with it is Water Works.
Contrast Tears of Joy.
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Anime & Manga
ItachiUchiha cries after Sasuke pursues him after Itachi was forced to kill the clan.
Sasuke after his battle to the death with Itachi, only to learn his older brother had done all of those horrible crimes to protect his beloved little brother.
Gaara also cried a single tear after he realized that Sasuke was never gonna stop obsessing over revenge/darkness like he used to and that he was forced to fight him.
Magical Project S's Misao cries and suffers realy hard when Sasami and herself discover that she is Pixy Misa.
The sixth arc is full of this, actually (hence why it's called the Atonement Chapter). Rena does this there too.
Towards the end of Meakashi-hen (which is right before the Atonement Chapter), Shion does this combined with Dying as Yourself, at least in the anime adaption.
Squad from One Piece does this after he betrayed Whitebeard and stabbed him in the chest. When he realizes that the Marines played him like a fiddle, and that Whitebeard still considers him a "son", Squad breaks down sobbing.
Lucy from Elfen Lied quite a few times, most notably from murdering her love interest Kouta's family in front of him in a jealous fit.
Digimon Adventure 02 has former Big Bad Ken Ichijoji who cries upon realising he's been sadistically torturing and killing living beings as catharsism for his The Unfavourite and Dead Big Brother complexes without realising they were sentient. Plus there are the real kids who's life he's been making a misery with his actions...
Mikael in the final episode of Tenshi Ni Narumon upon realizing what his actions have led to, broke into tears.
Shizuru, after being resurrected in Mai-HiME. Considering her usually calm demeanor, this comes off as quite shocking.
Also Yukino in an earlier incident; after trying to kill Mai to save Haruka's life, she later helps Mai to find Takumi when he's being attacked by Nao and Shiho. Mai thanks Yukino, with the implication of having forgiven her, and Yukino breaks down in tears before apologizing again.
Zeref from Fairy Tail does this whenever he kills anything. It makes it a little hard to take the rest of the cast seriously when they talk about how he's pure evil.
Kahlua from Rosario + Vampire might as well be the codifier, as every time she weeps, it's because she's about to kill somebody, despite her truly gentle nature.
In Ginga Densetsu Weed, after being offered to heal their wounds in the hot spring by Gin, three of Hougen's generals (Baruge, Bat, and Kite) were so moved and touched by his kindness that they regret what they have done and cry tears of remorse, promising to never follow Hougen ever again.
Also happens with Teru's father...just before he dies.
In Codename: Sailor V Minako cries only twice: the first because the first youma she killed happened to be the boy she was crushing on, and the other after killing the Big Bad Danburite, as he was her true love.
At the end of the first volume of Monster, Dr. Tenma breaks down crying after Johan (whom he had saved as a child) reveals to him he murdered his boss "just as he had wished" and then casually kills another man right in front of him. The remorse in this case isn't so much for the deaths as it is for the fact that Johan is alive because of him.
In Attack on Titan, Reiner Braun and Bertolt Hoover break down in tears on separate occasions while admitting to the terrible things they've done.
In the Kalos arc of Pokémon Special, Shauna does this after it appears that she may have killed Viola, while brokenly asking if she really did this. While she was possessed and brainwashed at that moment, this shows that she's not under complete control.
In Booster Gold, at Blue Beetle's funeral, what finally has Booster in tears is that he stood up to eulogize him, and couldn't speak. What sort of friend can't pay tribute Due to the Dead? When Wonder Woman tries to console him, Booster speaks bitterly of how he failed Blue Beetle, not having been there to help him.
Navarone does this in Diaries Of A Madman after making his first sapient kills. Celestia also later breaks down in tears when she sees what Navarone has become, partly due to her actions.
Films — Animated
In Tangled, they are trapped in a cave rapidly filling with water and will drown. Rapunzel blames herself and cries.
Meg in Hercules crumpled to the ground in tears after Hades revealed her betrayal to Hercules. This was made even worse by the fact that the hero had given up his incredible strength to rescue her.
Films — Live-Action
In The Abyss, the most emotional character in the entire sequence of Lindsey Brigman's drowning and resuscitation, besides Bud, is "One Night". Earlier in the film, she said and thought some rather nasty things about Lindsey. Obviously her probably dying brought out a great deal of regret; she was the only one besidesBud (Lindsey's husband) to openly have an emotional breakdown.
Kathryn at the end of Cruel Intentions, once she is exposed as the manipulative bitch she is and, upon reading about herself in Sebastian's published journal, she finally seems to grasp how messed up a person she is.
In a daydream sequence from A Christmas Story, Ralphie's parents shed these after they find out that the cause of Ralphie's blindness was from a bar of soap used to wash out his mouth when he said the "F-dash-dash-dash word."
X-Men Origins: Wolverine would have Kayla pulling this when the titular character muses the folktale that he is just a fool who got played due to the fact that she is blackmailed into working for Stryker.
In both Thor and The Avengers, Loki is in full tears every time he fights his brother and even occasionally wells up when he's planning evil.
In Oz: The Great and Powerful, Finley suggests confessing all rather than facing the wicked witch. Tears might help — he suggests an onion.
Amazing Grace has a variation; a former slaver has been haunted by the atrocities he oversaw for decades, and finally writes his confessions during the film. He cries as he describes his crimes, but since he says he couldn't weep until he stopped hiding and running, the tears are seen as a cleansing force.
Ian in An Echo in the Bone (Outlander series) after he kills Mrs. Bugg accidentally
In Graham McNeill's Ultramarines novel Dead Sky, Black Sun, after Uriel has learned that Pasanius's augemtic arm was tainted, and he knew it, he finally has a chance to confront Pasanius over it. Pasanius sobs as he says how could he have told Uriel that he was tainted, unclean.
In The Killing Ground, the gravely wounded Lord of the Unfleshed weeps with horror at the killing he and the other Unfleshed did while their minds were controlled; Uriel comforts him before the Mercy Kill.
In Dante's Divine Comedy, in the first few cantos of Purgatorio, a soldier mentioned had been a brutal, bloody bastard his whole life, but when struck down in battle, he cried a Single Tear of repentance, which is enough to send him to Purgatory instead of Hell.
In the original No. 6 light novels, Shion ruthlessly shoots a guard that harmed Nezumi. Shion is so horrified by what he has done that he attempts to shoot himself. After stopping him, Nezumi is so overcome by guilt that he breaks down and weeps on top of Shion.
In A Song of Ice and Fire, The Hound literally sobs when he recounts not interfering when the kingsguard beat Sansa, threatening her with a knife, and trying to rape her, to her younger sister. However, it's also implied that he might regret not having raped her, although he may have just said that to piss off the sister.
Sisterhood Series by Fern Michaels: Alexis Thorne in Lethal Justice says that Roland Sullivan was apparently shedding these kind of tears at her trial, after he helped Arden Gillespie frame Alexis. However, Alexis knows that Roland must have Ignored the Epiphany afterwards, so she has little sympathy for him.
In Galaxy of Fear: SporeActual Pacifist Fandomar weeps openly as she tries to contain The Virus. She hasn't killed anyone, but even when people are in spacesuits, throwing them out of airlocks isn't something she's happy about.
In Smallville, Phantom, Chloe cries over Lois' body when she arrived too late after she is stabbed. Then it turns out her tears has healing properties, and Lois is completely healed at the cost of Chloe's own life.
Andrew in the Buffy the Vampire Slayer episode "Storyteller". After several attempts to justify the murder of Jonathan, he breaks down crying as he realizes he killed his only true friend in cold blood.
Faith in Angel episode "Five by Five". She agrees to take assassination contract to Angel, but keeps giving him openings he doesn't use. Eventually she's rendered sobbing wreck, revealing that she was trying to get Angel to kill her in order to stop her past crimes from haunting her.
Criminal Minds offers us some examples. For example, in "Mosley Lane", as he's spreading the ashes of a boy his wife has cremated alive, Roger Roycewood tells a woman in the graveyard that he likes to think to roses as the souls of forgotten people. Although he doesn't acutally shed tears, his voice breaks and he sniffs. Then he gets back to his role as accomplice of the Monster of the Week.
In an episode of the Fantasy Island remake Secret Self, a man's fantasy is to have no conscious so he could be the greatest business man. Over the course of the episode, he slowly becomes more demonic, paranoid he will lose it so he trusts no one until he is alone in his office when his dog he scared away earlier returns. With this act of kindness, he sheds a tear, saving his soul.
A major point in the Merlin episode 'Beauty and the Beast'. Uther must cry tears of true remorse to break the troll enchantment. To accomplish this, Arthur takes a potion that makes him appear dead. Cue frantic, remorseful, crying Uther.
Breaking Bad: Walt sheds these after being forced to kill Krazy-8. As the series goes on though, killing becomes easier and easier for him.
Jesse sheds these right as he is about to shootGale. And again after realizing he almost shot Walt over a false accusation which turns out to be true, but Jesse doesn't know.
At the end of the season 1 finale of "Once Upon a Time", Regina's curse is broken and all the characters remember who they are and what she's done to them. She tearfully tells Henry that no matter what he may think, she does love him. Later, she is shown in Henry's room sobbing into his pillow.
Thomas Light has this during Funeral for a son, when he realizes He sent his son off to fight a battle he knew in his heart was unwinnable.
At the end of Metal Gear Solid 3, Snake stands before the grave of his mentor The Boss, with his newly awarded title of Big Boss marking him as her successor. As he reflects on the conspiracy that forced him to have to kill her, Big Boss does all that he can do given the top secret nature of what really happened and salutes the grave of his mentor. As this happens, a single tear of remorse flows from his eye as the gravity of what he had done and what he has lost weighs down on him. This marks the Start of Darkness for Big Boss's character, nothing would ever be the same after this.
In Homestuck, Terezi tricks Dave into creating a doomed version of himself, and then tries to persuade him to kill his doomed clone. Dave refuses, and leaves his clone sleeping on the Quest Bed. As soon as doomed Dave wakes up and steps off the Quest Bed, Jack Noir teleports in, and slices his throat. This causes Terezi to feel guilty for killing the Dave, and runs away from the lab to cry.
Wakfu has an absolutely pitiable breakdown from Nox, when he finally realizes that his dream is truly impossible and all the people he's killed to reach it died for nothing.
Animated Punky Brewster episode "Punky To The Rescue": Punky and her pals are in a swamp looking for Henry and they think a so-called swamp monster may get him. After several attempts to find him, Punky sits on a log and cries, blaming herself for sending Henry to Florida for a photo assignment to start with.
Max from Capitol Critters cries these when he thinks he killed a cat. Keep in mind that Max is a mouse and he was saving a girl mouse by knocking the cat unconcious with a stage light. Goes to show you Max is really pure of heart.
The Brain of all people in Pinky and the BrainChristmas Special, after scolding Pinky and brushing off his Christmas letter (which he didn't deliver in time) in his obsession with his new scheme for world domination. He eventually reads the letter to discover it is nothing but good words of his "best friend in the whole world, the Brain", and that Pinky asked Santa for nothing but to give all his presents to him instead, since he never gets any reward for all his hard effort. The letter plus a sight of Pinky sobbing from their row leaves Brain a blubbering mess.
In The Ren & Stimpy Show episode "Stimpy's Fan Club", Ren doesn't as much shed tears as bawl them out screaming after finding out Stimpy (the focus of all his contempt and jealousy throughout the episode) was the one person who wrote him a fan letter.
My Little Pony: Friendship Is Magic sees Celestia crying Tears of Remorse during the flashback in Princess Twilight Sparkle Part 2, as she is left with no choice but to banish Luna to the Moon after her transformation into Nightmare Moon.
Helen Keller on the day she learned to communicate.
On entering the door I remembered the doll I had broken [earlier that day, in a tantrum]. I felt my way to the hearth and picked up the pieces. I tried vainly to put them together. Then my eyes filled with tears; for I realized what I had done, and for the first time I felt repentance and sorrow.