Some observations about thriller plot structure, after reading too many of them:
Hitchcock had a famous example about a bomb under a table. Two people sit talking. The bomb goes off. Fifteen seconds of surprise. But if the audience knows the bomb is there and the characters don't, you get fifteen minutes of suspense from the same conversation. Most thriller plot structure advice starts here and stops, but the harder lesson is that information asymmetry only works if the reader cares about the people sitting at the table. You can wire a bomb under any scene you want. If the characters are strangers, nobody leans forward.
Ticking clocks are everywhere in thrillers and the ones that actually work are the ones with consequences that can't be undone. Frederick Forsyth understood this in The Day of the Jackal. The deadline is de Gaulle's public appearance. You can't reschedule it, can't hide the president forever, can't simply remove the threat. The clock ticks because the world won't stop for your protagonist.
There's a difference between the reveal and the confrontation, and most first drafts collapse them into the same scene. The reveal is the moment the reader (or the character) learns the truth. The confrontation is what happens because of that truth. Gillian Flynn kept them apart in Gone Girl by a hundred pages. The reveal lands in the middle of the book. The confrontation takes the entire second half to play out, and the second half is better than the first because you're watching two people who now know the truth about each other try to figure out what to do with it.
False resolutions are the best structural tool in thrillers that almost nobody talks about. The moment the reader exhales, believing the danger has passed, is the moment you can make everything worse. But each time you pull the ground out, the new threat has to be different in kind from the old one. Same danger returning just feels like stalling.
In chess, there's a concept called "the intermediate move." You're expected to recapture a piece, but instead you play a move that changes the position first, then recapture. The best thriller middles work this way. The protagonist can't go straight at the problem. They have to solve something else first, and that detour changes the nature of the original problem.
I've never quite understood why so many thrillers let the hero win clean. The ones that stay with me are the ones where winning costs something the character didn't expect to pay. Thomas Harris did this with Clarice Starling. She catches the killer. She also carries Hannibal Lecter's voice in her head for the rest of her life. The case gets solved but Clarice doesn't get to walk away unchanged.
Escalation has a logic to it and when you break that logic the reader feels it even if they can't name what went wrong. The threats have to grow, yes, but they also have to grow in a direction that makes sense given what came before. A character dealing with a blackmailer shouldn't suddenly be dodging missiles. The escalation has to feel like the same problem getting worse, not a different problem getting louder.
The protagonist's flaw and the plot's structural weakness should be the same thing. If your hero can't trust people, then the thriller plot structure should hinge on a moment where trust is the only option left. The flaw is the fault line the whole story runs along.