Anti-Villain/Fanfiction

• Sympathetic or not, it's undeniable that Aeon Natum Engel's version of Migou got a valid point for justifying their war against humanity. Namely, about possibly causing a ruckus with their Arcanotech that will wake up certain cosmic horrors, Cthulhu included.
• Ashley in the Battle Royale based 72 Hours starts out as this before her Heel Face Turn. Like many other students, she's just trying to stay alive, though unlike the overtly Technical Pacifist students, she has no qualms with killing. Indeed, she has an innate streak for sadism and intends on destroying SABRE from within. Luckily for them, however, her infiltration efforts lead her to realise that she's on the wrong side, and she becomes one of their greatest assets in the end. Not to mention, she winds up the only character who ends the book alive.
• Deadlock, the Big Bad of The Legend Of Spyro: A New Dawn. She didn't want to be evil and admits that she has her regrets. She's just lost everything, including her sanity, and feels that Spyro and Cynder are responsible for her tragic life, prompting her to attempt revenge. She also feels like her present plan is the only thing she hasn't tried in order to get something extremely important to her. On top of this, she's a very good queen to the Naga and treats them with respect, even being called the best queen they've ever had by some of them.
• In the Sonic the Hedgehog Alternate Universe Fic Prison Island Break, the protragonists are barely even Designated Heroes. Their goal to escape prison isn't particuarly noble; all admit guilt, and most intend to commit more crimes on their escape. Their crimes include murder, rape, bank-robbery, fraud on a global scale (Tails claims to have nearly made himself the sole owner and stockholder of Sony), escaping other prisons, and what boils down to terrorism. It's the Morality Kitchen Sink. However, since the story is told mostly from their perspective, and their jailer is a Complete Monster, Sympathy for the Devil ensues to some degree.
• In the Final Fantasy Tactics a 2 fanfic The Tainted Grimoire, a character named Crow is this. He is regretful about the evil deeds he did and the author has written him as such. Eventually, he did a Heel Face Turn.
• Numbuh 86, along with the rest of the Decommissioning Squad, oddly enough were given the Anti-Villian treatment in Operation:REBEL In the story, they seek to capture and Decommission a trio of 13-year-old KND Operatives who are looking for a group of anti-decommissioning rebels called the Kids Eternally There to seek protection from the Squad, the now teenaged Operatives honest don't see themselves wanting to betray the KND for any reason, but Numbuh 86 is worried that betrayal from escaped teen Operatives would be inevitable and strongly believes decommissioning the 13-year-old Operatives is the only way to assure that doesn't happen.
• In Mega Man Defender of the Human Race, a story based on the Mega Man cartoon, Protoman has a policy to not kill, and it's clear that Wily's programming is what makes him unable to defy the doctor. He was also very conflicted over the Heel Face Mole part of "Brothers".