Lolita: Humbert Humbert never meets Quilty. Which one is the protagonist is conjectural. Quilty tries to hide his identity from HH through a series of masquerades. Quilty succeeds. I’m going by very old memory here, not sure if I remember it correctly.
Video game example: Conker’s Bad Fur Day. Conker only meets the ostensible arch villain, the Panther King, long enough to inadvertently insult him by calling him a “faery tale”, as in made-up, only for the Panther King die from the machinations of a henchman immediately thereafter. The Panther King never had anything against Conker per se, but desired a member of his species to function as an ad hoc table leg. It’s very silly.
The Unfought. Interesting they don’t link to each other despite the overlap
Vader’s TIE fighter interacts with Luke’s X-Wing.
And, specifically, R2-D2.
Randall Flagg and Mother Abigail never meet in The Stand.
Funny, this is the first thing I thought of!
Eh, I don’t think so. The Guy Pearce character, Leonard, is clearly the protagonist. He’s arguably not the hero, but he’s the main character and the movie is about his pursuit of his goals. There’s room to debate who the true antagonist is, but Leonard has met or knows about every other significant character in the movie. Most of them he can’t remember for more than a few minutes, but they all know that he exists.
There’s a case to be made that Leonard is his own antagonist and doesn’t even realize it, but he doesn’t defeat himself so that fails the OP’s #3.
The antagonist is Leonard when he writes down the license plate. Leonard the protagonist starts when Leonard the antagonist ceases to exist due to the dispersion of Leonard’s memory. The protagonist then sets in motion the antagonist’s plot that leads to the antagonist’s victory.
That still doesn’t meet the OP’s rules, though. #3 requires the protagonist to defeat the antagonist, not the antagonist getting what he wanted while the protagonist carries on without realizing what has happened.
I don’t think it’s accurate to call the version of Leonard who writes down the license plate number (I’ll call him Leonard A) the antagonist, as he’s not really working against the later version of himself (Leonard B). If Leonard B could remember what he briefly knew as Leonard A, he presumably would have agreed with Leonard A (they’re the same person, after all) that Teddy needed killin’.