No, no, Doral is “Kevin Spacey” and Leoben is “That Other Guy” and Cavil is “Father Al” and Simon is “Black Cylon”. Get it straight, will you? (Tigh is “John McCain”. Ellen Tigh is “John McCain’s Wife”.)
Meanwhile on Babylon 5 (or Battlestar Five or whatever we call it) we have Barack ODoctor and Company.
There must be about five thousand stories in which the tough teacher turns out to be the best influence on the student, or the tough military officer for the private, and that kind of thing. My brain has mercifully blasted all those Arrow Books/Boys’ Life memories away, though the feeling of betrayal the stories gave me remains.
FBI Agent Dwight Harris on the Sopranos. Through most of the series he’s out to get Tony, but at the end he tries to help him out with information during his mob battles.
Slugworth! Hmm. Maybe even Willie Wonka, himself.
There are a lot of middling characters I could name, in that they aren’t necessarily evil but they start out with the motivation to undermine the protagonists, then more or less abandon that motivation: Lassie from Psych, Cordelia from Buffy, Sue from Glee, Sesshomaru from Inuyasha, Oded Fehr’s character in The Mummy movies, Commodore Norrington from the Pirates movies, Hansel from Zoolander, Juno from The Descent.
Characters thought to be evil but were good: Billy from Hocus Pocus, Cotton Weary from Scream, the servants in The Others, The Beast (Hercules) from The Sandlot, Megumi from Shutter, the usual trope that a criminal turns out to be an undercover officer from various movies.
Characters that transformed from evil to good: Drakken and SheGo from KimPossible, Regina George from Mean Girls, Sideshow Bob (temporarily in “Brother From Another Episode”; he changes back), that one Predator on Aliens vs. Predators, the giant guy from Get Smart (the movie, sorry but I forget the character’s name), that one guy from Metalocalypse (the one whose brother was killed), Vin Diesel’s from Pitch Black (he started out as a prisoner), Forrest Whittaker’s character in The Panic Room.
Yeah Pitch Black is a good example, most characters in it tend to be far more than what you thought, even more efficient since most of the characters are presented as somewhat archetypes. How they reveal themselves to be far more complex is one of the big assets of the movie.
In The Sting there is a character who is only seen to be a black gloved figure who we are led to believe is a hit man out to get Robert Redford. In the end, it’s revealed that he was actually sent by Paul Newman to protect him.
In the Order of the Stick webcomic, Elan’s Lawful Evil father Tarquin (who is enough of a bastard to crucify and set fire to a bunch of people on a hillside just to spell out his son’s name for a celebration) is perfectly happy to let Elan go about his business for much the same reason - Elan is on a quest to save the world and Tarquin’s plans for conquest require the world not to be destroyed.
G’Kar from B5 is a phenomenal example - he is set up early to be a nasty piece of work but we get an early view of his “enlightened self-interest” when he saves Sinclair’s girlfriend from crashing into Sigma 957. His eventual transformation into a far more enlightened being thus starts not from a point of being evil but merely from a point of being overzealous in the interests of his people.
I know. I love that movie. Twohy’s best movie by far.
Heck, I even adored Chronicles of Riddick.
I’m glad they are making a 3rd one.
How about Sam Gerard (Tommy Lee Jones) in “The Fugitive”?
Now that’s a good one: can’t believe I didn’t think of it for the OP.
It was the first one I thought of when I read the title, and I scanned through the thread hoping that no one else had mentioned it. 
Perhaps Renfield in Stoker’s novel DRACULA and as portrayed by Jack Sheppard in the 1977 BBC production.
I can’t believe it didn’t occur to me until just now, but I may have thought of the ultimate example of what the OP is talking about (at least in book form): G.K. Chesteron’s The Man Who Was Thursday.
In fact, “antagonists are revealed to be the good guys” is not just the climax, but more or less the entire story.
As do I. I will say, though, that I’ve a somewhat higher opinion of Londo than you do. Yes, he makes mistakes - horrible, horrible mistakes. But as an agent of his government, it’s hard to say that he makes irrational or foolish mistakes. He’s trying to arrest and reverse the decline of his state - and since the Narn Regime is both hostile and on the ascent, this could well be an existential issue for the Centauri Republic. Londo miscalculated the scale of Shadow ambitions - but once he realized that, he did everything in his power to remove the Centauri Republic from its alliance with them.
And no one can doubt the man’s bravery - when the Vorlons were ready to destroy Centauri Prime because it harbored Shadow influences, his reaction was to demand that Vir kill him immediately. When the Drakh threatened Centauri Prime with annihilation unless he accepted a Keeper, he submitted to that nightmare without hesitation.
Vir is a better man than Londo, certainly. But calling Londo pathetic does him too little credit.
This is a slightly obscure sci-fi film, but it fits the topic well.
In “The Monitors,” aliens have taken over the Earth and are trying to control every aspect of human existence. Through most of the movie, the hippie protagonists are working to undermine and oust the Monitors, and restore government by humans.
When the movie ends, it becomes evident that, for all their faults, the Monitors were truly benevolent and were TRYING to do what was best for humanity. The Monitors are finally made to see that their ways can’t work, and they voluntarily (if reluctantly) leave forever. But as soon as they do, and the old President takes power again in the USA, we realize that we might have been better off with the aliens than with the power-mad human bozos we’re stuck with.
71-hour Ahmed.
I meant that I felt pathos for him. I genuinely felt bad for him and I do agree that he was brave. Hey, nuking an entire island was amazing.