In the third season of the legend of korra, a group of people try to get rid of a monarchy (which is long established as especially unequal and oppressive) in favor of self government. They also try to get rid of the avatar, because she is an infallible being with incredibly outsized power. I love the avatar universe and get how they needed to fight them, but the group wasn’t wrong
Voyager kinda fucks with my ability to set spoiler tags, so here is your Spoiler Warning.
The Cabin in the Woods (even tho the organisation is run by complete assholes, they also happen to postpone the end of the word)
Mass Effect series (the Geth are actually ok having peace with everyone. They just happen to be in a civil war with Reaper worshippers)
Witcher 2 (Letho turns out to be the good guy)
Wanted (the father turns out to be the good guy)
Battlestar Galactica 2004 series (yes, the Cylons enacted the nuclear holocaust on humanity, but there is a case to be made that the vast majority of them have been manipulated by a faction of ancient Cylons, which leads to a civil war later in the show)
Falling Down. Prendergrass is the good guy.
Kill la Kill, at least with the primary antagonist as the main villain isn’t really introduced until pretty late in the story.
God Emperor Of Dune. Leto II needs his bath time.
The French version of La Femme Nikita, although it's more of a redemption arc than "villain turning out to be a good guy." She starts out as a junkie petty crook who murders a cop in cold blood, spends most of the film assassinating people for the government, and in the end seems to have gotten her life together.
But she starts out as a very not-nice person.
Harry Potter and the Prisoner of Azkaban comes to mind.
The Rock, starring Sean Connery and Nicholas Cage
Xenoblade Chronicles
The Good Place, season 2.
"Villains by Necessity" by Eve Forward.
Sophia, Garden of Eden, Genesis
Interview With a Vampire ... kind of ... Lestat was by no means good to Louis, but their portrayals in the rest of the series was quite different ... I think that Anne Rice was trying to show that neither of them should be considered reliable narrators and Louis will always try to portray his situation as awfully as possible and Lestat is a narcissist and will always try to portray himself in the best light even when acknowledging what he did incorrectly.
But, when I saw that book 2 was about Lestat, I was like ... wtf ... I hate this guy, why would I want a story with him as the main character and then I read them all, lol.
...so the (racist af) Tsukimichi series/manga/webnovel has this Demon race, right? Whole isekai happens because they instigate a war against the h(y)umans outta nowhere and the Goddess needs a hero.
spoiler
Well~ turns out these mofos had it comin'... and so does the Goddess. 🤷🏿♂️
it only sorta works for this post since the main character is quite indifferent to the
conflictwar for quite awhile
interestingly, the story primes you up for that reveal with a precursor villain of sortsspoiler
Lime and his cohort are quite villainous until you learn what brought that fate upon the Rembrandt family 😐
Terminator. Arnold was reprogrammed.
The Quarians vs the Geth...the Quarians did the Geth dirty
In a sense, Bleach - twice!
spoiler
Sousuke Aizen used deplorable methods in his attempt to achieve godhood and conquer the "empty throne of god", but was ultimately justified when the forces of Yhwach, the legitimate son of God decided to invade and lay waste to the Soul Society. Subverted yet again when it is revealed that the current "Soul King" (the lynchpin that hold reality together and the pretend-ruler of the world) is in fact an empty husk of the original God, who was assassinated by the Shinigami because they feared his powers, and Yhwach's bloody conquest was in fact an attempt at revenge. Some of his final words before dying are "I will create a world without the fear of death".
