Stories where the big twist is that the protagonist is actually the bad guy (spoilers

One more Agatha Christie to add to the list: Endless Night.

Icebreaker has three protagonists who aren’t what they seem.

An awesome film, sadly its pretty much unknown in the US- great ending, great job of showing how certain events could be perceived differently, etc. One of my all time favs.

Does Mulholland Drive by Lynch fit this category? It’s pretty twisty/twisted.

how about “The Third Man”?

Agreed, that was a cool twist. I’m concerned that it might continue to be unknown in the US though if nobody points out that its english title is “He loves me…He loves me not”.

I would also submit a movie called “The Usual Suspects”.

And from the horror genre, “Happy Birthday to Me” starring Mary from Little House on the Prairie.

Pretty sure that your misremembering the plot of the film (hey, its ironic!). I just double checked wiki’s plot synopsis. The protagonist’s wife is dead (there is some ambiguity about how she died), he kills the cop because the the cop confesses he is setting him up to kill people (knowing he won’t remember the confession) not because he’s annoying, and it isn’t just likely that the cop isn’t the first person he kills, it’s shown explicitly that they killed someone else (Trinity from the Matrix’s boyfriend).

And let’s not omit The Mousetrap - probably her most famous work, and the longest-running play ever.

The “narrator as perpetrator” theme is one that Agatha Christie used throughout her career. As well as the ones already mentioned, there’s another variation on this theme in The Man in the Brown Suit.

It’s been a while since I’ve seen it, but doesn’t Tape qualify?

Yet another Agatha Christie: In A Glass, Darkly.
The Doctor Who story arc Trial Of A time Lord where the prosecutor turned out to be a future incarnation of The Doctor.

I think you have to have a plot before you have a big twist, let alone protagonists/antagonists.

(FTR, I love Eraserhead.)

Here’s what I remember:
A certain Lou Cyphre (Robert de Niro with a pointy beard and reeeeeally long fingernails) hires private detective Harry Angel to find disappeared person Johnny Something. During the investigation, people questioned by Harry Angel die right after Harry Angel has interrogated them.
Plot twist:
Lou Cyphre is - guess who? Johnny Something had sold his sold to Satan to achieve success. Then Johnny tried to avoid paying his debt by performing a magic ritual to hide his soul in someone else’s body - Harry Angel’s. Harry Angel is actually Johnny. In flashbacks we see that all the murders were committed by Harry / Johnny. Lou Cyphre knew this all along and the whole “investigation” was Lou’s plan to bring about Harry’s awareness of who Johnny really is.

Interesting, I hated Eraserhead & loved Mulholland Drive. Of course I didnt love it until I read this explanation. It’s weird, and surreal, but it adds up if you watch it again with this in mind. Of course its not exactly what the OP had in mind - the shift is more of a dreamworld vs reality thing, not a good guy = bad guy thing.

Now if someone could give me an explanation for Lost Highway, I’d love to hear it. I LOVE that movie (specifically, the first half before the inexplicable character shift), but it just does not make any sense.

In Richard Matheson’s short story, Mad House- The twist is the opposite of the OP.

(Personally, I don’t see the big deal about Matheson’s, I am Legend. This was a much better story, stylistically (literary).)

We Have Always Lived in the Castle, another creepy delight written by Shirley Jackson. If you liked The Haunting of Hil House and have not read this one, do. I’m not going to spoil it here. It would have made a great Hitchcock film.

Also, Thomas Tyron’s The Other.

Also, the cop (Teddy) was setting him up to kill people not only to take care of “bad guys” that the cop wants to dispose of (?) but also because when Leonard (the protagonist) managed to find and kill the guy he’d thought was the killer, with the cop’s help, he then forgot that he’d done so and went back on his quest.

When Teddy explains all of this, Leonard gets pissed off, and before he forgets, he writes down a couple of “false” clues that implicate Teddy as the killer. And so, after he forgets, he pieces the clues together, and kills Teddy. I say “false” because Teddy says that there are a lot of "John G"s (what Leonard thinks is the killer’s name) out there to kill; even his real name happens to be John G., and Leonard’s written note that he is not to be trusted is in fact correct.

The 2002 film Spider directed by David Cronenberg.

If you look on Iain M Banks “Culture” as good, I suppose you could have the character Horza from Consider Phlebas as a sort of protagonist we like who turns out to be bad.

In his other book Use of Weapons the protagonist has assumed the identity of someone else more heroic who actually committed suicide (IIRC) that he pushed to commit suicide.

In The Book of the New Sun, Severian ultimately saves Urth, but at the cost of countless deaths. The Ascians and anti-government types are opposed to him not because they’re evil but because of the high cost of fixing the sun.

The Atreides family from Dune is similar, IIRC.