Since we're having the Warpath love, my favourite scene is about half way through the book, where Taran'atar has just taken control of the noH'pach from the Klingons, and is flying it to Harkoum while Prynn is tied up in the back. Taran'atar gets into a fascinating discussion of what's gone wrong with him, using hallucinatory characters that go all the way back to Abyss. Meanwhile, we see Prynn untying her bonds in the back cabin. Just as Taran'atar's discussion comes to a climax, he gets an alert on his panels, and we're afraid that Prynn has accidentally set off an alert and he's about to catch her mid-escape attempt. He goes to stop her, and that's when we realise that she's set a trap for him and electrocutes him via a typical Starfleet improvised tech-job, and the alert was deliberate bait. We think he's down, and she rushes to the controls, tries to send a distress call. But then he's up again, prising the door open, and she's desperately working the panels, and he comes barreling at her, but he doesn't kill her, he just drags her back into the rear cabin and ties her up again. And Prynn is left dangling by her wrists while an even-more-pissed-off-than-before Jem'Hadar gets back to work, all in vain. The whole sequence has so many twists and turns in such a small space, and it's filled with such awesome pulse-pounding oh-shit-liness that I can happily just go back and read that scene over and over.
Another one of my faves, also from a DS9 book (no surprise there) is the opening scene from Fearful Symmetry. When I read that first scene, where Sisko shares a vision with all the alternate Siskos who explain that his trips to the alternate universe were deliberate and not random, and part of an ongoing plan by the Prophets, and that all Siskos are the Emissary, regardless of which universe, I just thought to myself "That... is... a... BRILLIANT idea." It redefines the entire Deep Space Nine series all in one fell swoop, stating that the Prophet storyline and the MU storyline, which had previously been two completely separate aspects of the show, were in fact one and the same, and both part of an even larger tapestry. F'ing genius. Suddenly everything you thought meant one thing about the entire show actually means something else altogether, and yet still makes complete sense. Loved it.
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