This character begins the story on the side of the villain but ends it on the hero's side. Why? Love.
Maybe she and the hero are both stuck on a spaceship at the other end of the galaxy and she discovers his kindness and her newfound feelings for him. Or maybe she finds out that she's been lied to by the villain all her life and has been working for the very people she thought she was fighting against while the hero has been honest with her and is the one she wants to be with. Somehow, she falls for him and decides to defect to his side.
This character will most likely never be truly evil, only misguided or manipulated. Since they are essentially an ordinary citizen of The Empire, they sometimes also serve to humanize their average citizen. While almost Always Female, males can just as easily fulfill the same role.
Most of the time, unlike the Mad Scientist's Beautiful Daughter, this character is the primary female lead, quite capable of taking care of herself, and her Character Development is a major part of the story. It's a good thing, too — she tends to have a few sources of angst in her past that require a lot of dealing with before she and her man can ride off into the sunset together.
If she doesn't switch sides, it's Dating Catwoman. While a High Heel-Face Turn may be done for a number of reasons, this trope's defining trait is love.
Milia Fallyna in Super Dimension Fortress Macross (and Robotech), who went as far as to get herself shrunk down to human size to hunt down the Human pilot who dueled her, and ended up marrying him after a knife fight. In The Movie, things go a little differently. He gets trapped on her ship when it leaves while they're still in their first battle, but things still turn out all right: He later shows up having been macronized to match her, becoming a Montague Counterpart, and they're fighting side by side, happy as can be.
Hilde Schbeiker from Mobile Suit Gundam Wing deserts OZ and ends up living with Duo Maxwell. According to the Frozen Teardrop novels, however, they didn't last too long.
Athrun Zala from Mobile Suit Gundam SEED is from the "empire" that is opposing the protagonist for most of the series (not that the Earth Alliance is exactly "good") and is pretty ignorant of what the top brass are really doing. In the end, he does oppose what they are doing and ultimately "betrays" and fights against them. He and Cagalli were in a similar situation. They were both from mostly opposing sides, they met as enemies, Athrun took her a prisoner, which led to them getting to know one another and found that they like each other.
X/1999 has Shiyu Kusanagi starting off as working for the antagonistic Dragons of Earth but eventually switches sides out of love for Yuzuriha Nekoi and even lives to enjoy his newfound happiness.
Caiera, the Incredible Hulk's eventual love interest in the storyline Planet Hulk was just misled. She believed her boss really was meant to be the savior of their world (specifically from the Spikes) and that thus Utopia Justifies the Means. When she found out that he had been in control of the Spikes all along, using them instill fear and enforce obedience, there was no more utopia left to justify and she changed sides to the new Messiah figure with some integrity.
Selene in Underworld is a vampire who hunts werewolves until she falls in love with a werewolf/vampire hybrid and starts to question whether what she has been told by the elder vampires was ever true (like who started the war, why, and who killed her mortal family). Though technically, her defection had more to do the truth than Michael.
Before her there was Sonja, and it ended very badly for her.
Sorsha in Willow betrays her Evil Queen mother and joins the heroes out of love for Madmartigan.
In On Fairy-Stories, J. R. R. Tolkien discusses this trope in the context of Norse myth — Frey, who married a giant's daughter — and the English legend of the marriage of Ingeld and Freaweru, and points out that even though they are named for the god, it does not prove their love is mythological, since human lovers who found enmity between their families were the real source of the Frey myth.
In Alethea Kontis's Enchanted, Rumbold comes to himself after losing his memories as a frog, and remembers the emnity between the royal family and Sunday's. He sets out to win her anyway.
The Firebird Trilogy features a straight and a peculiar example of this trope. The straight example is the titular Firebird Angelo, who defects from Netia to the Federacy largely due to loving and being loved by Breenen Caldwell. Terza Shirak is the second example of this trope, with the peculiar variant that it was not romantic but maternal love that drove her-she had fallen in love with her unborn daughter and could not bear having that daughter aborted or raised on the villainous world of Three Zed.
Caprica-Boomer, later named Athena of Battlestar Galactica initially sets out to seduce Helo in order to create a cylon-human hybrid child by getting him to fall in love with her. She eventually makes the decision to betray the Cylons and joins the human fleet.
Juliet on LOST. She was never very committed to the Others, and defects from them pretty quickly after meeting Jack.
Deconstructed in a famous episode of The Twilight Zone. An unnamed man and woman of opposing armies—implied to possibly be the only survivors of World War Three—find each other in the ruins of a small town. At first they shoot at each other, but eventually loneliness sets in and they try with varying success to communicate and by the end of the episode seem to have developed romantic feelings.
Princess Aura in Flash Gordon is a combination of this, a Mad Scientist's Beautiful Daughter and a Femme Fatale. She is physically attracted to Flash and betrays her father to keep him alive, but she doesn't end up with him and is paired up with The Lancer of Flash's group, Prince Barin of Arboria, who has been in love with Aura for quite a while already. In the 2007 series, Baylin is a much closer version of this trope, although she's not quite so innocent (she's a bounty hunter) and she probably won't end up with Flash, either (Dale's got dibs).
Kyle Katarn of the Dark Forces video games. In the backstory, Katarn is not unlike Luke Skywalker—a young Farm Boy who dreams of going to the Imperial Academy. Unlike Luke, though, he gets to, and becomes a promising officer. After meeting Rebel operative Jan Ors, though, finding out her secret, and letting her go... well, the rest was history.
Amelia from Fire Emblem: The Sacred Stones, although she's a minor character. She's a fresh recruit from the Grado Empire and one of the three characters that can make her pull a Heel-Face Turn is a cavalier who works for the Renais army, Franz, whom she can marry later via supports.
Tear of Tales of the Abyss fits the trope somewhat, although she and Luke are forced to work together starting quite early in the game, despite the fact that Tear works for the rival kingdom, the Malkuth Empire, and the Order Of Lorelei, the game's Corrupt Church. It's also played with via a Gender Flip: Luke is the one who has been working for the villain, as his Cool Teacher is the Big Bad.
In Worm, the villain Madcap pulled this off in his backstory, becoming the hero Assault because of his love for the her Battery.
Later, a reversed example occurs, with Flechette defecting to the Undersiders because she was in love with Parian.
The Tick had this between two sentient leftover Cold War super-weapons: an American moustache and a Russian beard.
Rose on American Dragon Jake Long. Essentially, she was taken from her parents as a baby and raised by the Huntsclan for the sole purpose of slaying magical creatures. Then she meets Jake in human form and falls in love with him. Then she finds out Jake's a dragon. She quickly betrays the Huntsmaster and becomes a Reverse Mole.
C.O.P.S. played with this with Nightshade and Mace. Mace stated openly that he'd be willing to marry Nightshade, if she gave up crime. He even gave her an engagement ring! She's shown clearly considering it, but the series ends before we see her answer.
Count on Jinmay from Super Robot Monkey Team Hyperforce Go! to be under this. She was found by the Skeleton King as he erased her memories of being a robot and sent her to Shuggazoom. He, along with his agent Sakko, puts her under his control of turning her into a giant robot to wreck havoc in the city. That is until Chiro manages to free her from his control by remembering the pictures of their date. After Sakko's defeat, she is sided with him and his team since then.