Of course, she ends up dying crying and begging on the floor to not die.
Pythos of AJCO pulls one of these at the end of the Trial To End All Days, confessing to the court that she believes AJ was guilty of everything she had been charged with and more. It's especially impressive considering she had been antagonising Egg constantly up to that point, and even more impressive considering she was AJ's defense attorney.
Happens with several characters from the Darwins Soldiers RPs, most notably with Hans.
Possibly The New Adventures of Captain S: in the last episode of the first season, NES digs up a Sega Menacer for Captain S to use against Game Genie (NES's former master). Although, the series ended with NES's fate unknown, so his motivation for doing this is just as unclear.
In most of the Madness Combat shorts, Jeebus is the enemy of the protagonist, Hank. However, in Part 8, he is featured as trying to stop the Mooks and new Big Bad.
Ralph from Dead Ends pulls one of these when he realizes that he is hunting down an unarmed teenager and her friend during a Zombie Apocalypse because his best friend, Ephram, has gone batshit crazy.
Battle betrayed Tarot to save the life of her son, Stone.
Gadgeteer villain Knick-Knack retired from his life of crime and became the custodian of the Hyperion Academy.
The Redeemers are a team made up of former super-villains.
Gross Sword does this at the end of The Sick Kids, but only because his lawful-good siblings nearly kill him.
Firebrand from the slenderverse web series Tribe Twelve pulls one of these in INTERCEPTION, when it is revealed he is not only working on behalf of Noah to save him from being abducted by the Collective, he is actually Noah from a future/alternate timeline.
Bogdan from Water-Human does that after he develops a liking for a prisoner that his partner tells him to kill. He proceeds to attack his own partner.
Kelly from We're Alive is easily the most hated character among both the cast and audience during Season 1, but eventually pulls one of these after her attitude indirectly kills Tommy.
Demonking does this in TOME. Then he becomes bad again, but then ascends again and is currently more of a rival to Nylocke than a bad or good guy.This entire process is subverted when it's revealed the hackers aren't really bad guys anyway.
The King of Thieves and Assassins reforms after hearing the Harp of Remorse.
In The Gamers Alliance, a bunch of antagonists eventually switch sides and become more heroic. Some examples include Dalthas, Jemuel, Kagetsu I (he joins the Alliance because they saved his wife, but he still more or less pursues his agenda albeit with different means while being bound by his oath to the Alliance), Omaroch, Titaniel and Viirsa.