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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)
Cylons being manipulated by other cylons doesn't absolve them of guilt.
BSG did have a few instances of the reverse of OP's question tho -- where the "good guys" turned out to be bad" -- trying to say this without spoilers; it's a 20 year old show but ffs of you haven't seen it, go see it now.
- the (temporary) new admiral
- several main characters during the part where they live on the dirty planet
- a very specific set of seven main characters (wink wink) ... .and more,..
And there's one specific example of the full 360 -- a character that starts good, turns bad, but turns out they were actually good all along. I won't give the name, but they were passing messages to the resistance.
That show was awesome.
One note tho, on the topic generally: flipping character alignments is a frequent pre-shark-jump thing, and is often bad writing. In BSG, tho, all of the "flips" are pre-planned, or at least 100% true to their character (eg the 360 example above).
BSG is one of the best shows I have ever watched and not a single twist came across as forced or unnatural.
If I think about that I started watching it years after it was made and only started because I was bored out of my mind at that time. I could have missed it so easily.
Same here, I think I started it during the lack of new content after the 07-08 writers strike. I thought it would be a mid sci-fi show I would put on for background then it turned out to be awesome.
From someone who has never seen anything about BSG besides jokes here and there in media, where would I start? The 2003 miniseries into the show? Should I start farther back?
I watched the miniseries then the show, and there was some additional stuff I watched also but I don't remember exactly when. There was a spinoff called Caprica, it was good but never got a second season.
Here is a watch order that includes a couple movies and webseries, but it puts Caprica at the beginning. It is a prequel but I think it would be better watching it after everything else like it was released.
Edit: if I remember correctly Caprica either has some serious spoilers or there are some things you wouldn't understand if you hadn't seen the main show, I don't want to say anything more but I don't know why they recommend it first.
Watch the mini-series, then the show from the 2000s.
He doesn't "turn bad". He's good all along, but he's a target of a witch hunt, understandably gets jaded by it and gets absolved at the last moment. It's the judging commission or however they called themselves who are the bad guys there. Gaeta is innocent all along, even if he is annoying at times.
You're right, I'll concede that -- but only because BSG is an amazing show and very few characters can be reduced to "good" and "bad" -- even the "antagonists" (in the traditional sense of those characters working against the stories' progression) have pretty valid reasons for doing what they do.
Gaius (sp?) is one of the closest characters to "bad" -- but not because of the bad things he does, but because of the bad things he is -- ie, vain, selfish, etc -- and the fact that he lets those negative characteristics drive his actions.
All the characters have flaws, but the "good" characters do their best to mitigate their flaws, and let their positive traits motivate them. For example, Adama often acts before he thinks, a trait that is awesome in combat, but can be less positive other times -- and he (as best he can) seeks advice and counsel from the people he trusts (eg Saul Tigh) -- he knows he can be impulsive and he knows his "instant judgement" decision making isn't perfect.
Cavil (that's his name I think) is close to "evil" but he does have reasons for his actions -- preservation of his "species" (though really it's just himself) -- but he's evil because of the fact that he doesn't listen and acts with disloyalty and dishonor.
(There's an amazing comeuppance for the titular character of the show Nathan Barley that epitomizes this idea: Barley doesn't actually do anything wrong, but his motivations are repugnant, and his motivations are what's revealed... Shit I should write a whole essay on that....)
Are there contemporary shows that are as good as BSG? I kind of gave up on TV after Firefly.