Paths of Disharmony was the best; great use of continuity from various series without drowning the story in recaps. It was a convincing and "natural" continuation of the "Deep Space Nine Relaunch" Andor arc, while building skillfully on "Destiny", "Vanguard" and the "TNG Relaunch" too. I could easily except Andor finally pulling out of the family; it had the feeling of inevitability while also working as a shock due to the weight of the decision. When the Andorian ambassador was meeting with Bacco, I knew what was coming, but in the sense that I found it gripping, not boring. Well played. The novel didn't actually focus on the Typhon Pact very much at all, which was surprising but actually very effective - after three books focused on internal politics of Pact members, it was interesting to have a Federation-focused story that then used the Pact "intrusively" to interrupt the Federation's internal concerns. It gave a real sense that both the UFP and the Pact have their own "lives" (so to speak) separate from one another - that there's of course a lot more to both than the rivalry the series is built around, but that neither can avoid the other's agendas either. In that sense, this book was actually the most effective in using the Pact, despite placing the least focus on them. The Pact is simply there now, and the Federation has to take them and their various members' agendas into account, even while most of its concerns have nothing to do with the Pact at all.
The Tholians suddenly showing up was a real "aha" moment, another of those "I know what's coming (more or less) but that excites me rather than bores me".
Oh, and points for clearing up the Flute continuity issue in a manner that really worked as a character piece rather than merely a explanation for the sake of it. Not that I of all people mind explanations-for-the-sake-of-them, but I was impressed at how the explanation was integrated into a genuinely enjoyable character piece for T'Ryssa (who continues to be a great character). Her evolving relationship with Picard is proving one of the highlights of the TNG novels.
PS: Poor Shar. He finally agreed to "do his duty" and make a child and now it was all for nothing. It was nice to see him again, though, definitely.
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Second, I'd place
Rough Beasts of Empire, for its great politics, good use of the Romulans (particularly in terms of continuity) and rather surprising twists. I was a little disappointed to see the IRS and Donatra out of the picture so swiftly (while I'm certainly not saying this
was the case, it couldn't help but come across a bit like "well, we had a situation with the Romulans - two states - and now we have another - the Typhon Pact - and we can't have
two situations, so let's drop one") but then again it served as a genuine and successful surprise, so no fault there. And I must say, after all the Romulan Star Empire's been through - and the lengthy debates we've had on here about their newly second-rate position, it was rather satisfying to see them back where they belong, so to speak. I couldn't help but share Tomalak's pleasure at "Romulus ascendant!".
Ave Ch'Rihan! 
A shame they're going to get reversed again a few years down the road...
The Tzenkethi were satisfying, and I hope to see more of them now we have an established Trek lit identity for the Coalition. I would like to see Alizome herself again, actually. She seems like she'd make an effective recurring character.
Now for the controversy...Sisko. I was indeed concerned over his behaviour and choices, but I don't see it as a weakness of the novel. Rather, are we not supposed to feel that way? Sisko's clearly in a bad place (and unlike many, I
do think he's in character, or, rather, this out-of-character behaviour falls within the established boundaries of Sisko's out-of-character behaviours, if that makes sense?). I'm anxious to see where future novels take him, and I hope he can take back his life a second time. So, disturbing, but not, in my mind, a fault of the story.
I found the other Deep Space Nine parts interesting and fulfilling - I'm excited to see the Ascendants are now apparently allies, and despite my earlier concerns about Kira-as-a-religious-leader (you might remember my thread on that) I was pleased with what we got. It seemed to fit with Kira's earlier character development, and I can accept that this is where she is now. So, good job there; my concerns are put to rest on that front.
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Then
Zero Sum Game, which was good (I wrote a very extensive and favourable review as I read through it) but doesn't get marked as high simply because it was less involved with the wider high-stake politics that the "Typhon Pact" series is, in my mind, geared to. That's not a complaint - it's nice to have variety, and a more action-based thriller with in-depth exploration of an alien society that needed fleshing out is great. So it was certainly a success, but I can't help but favour "Paths..." and "Rough Beasts..." ahead of it here.
As I said in my initial review in the ZSG thread, the novel's ending gives it a boost in significance, by redefining the events of the book as part of an ongoing plotline that really did need follow-up. In that sense, it worked as a Deep Space Nine novel - and it certainly worked as an exploration of the Breen. I recall
Christopher suggested it could possibly be seen as "Worlds of DS9: Breen": a good description. This is not in any way a bad thing, but because (and only because) this book reads slightly more like "Worlds of DS9: Breen" than it does "Typhon Pact" (the great Breen-Romulan-Federation political tussles and slipstream issue aside), it gets third place.
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Last,
Seize the Fire, which while it certainly had its good points was indeed a bit of a misfire. Oh well, not every book can be a great one. I usually like Martin as an author (particularly paired with Mangels), but this was his weakest. I
did like the insights into the Gorn, and the character of Gog'ressh (however it's spelt) was particularly fun. I really liked having an antagonist who was truly mad. Not mad-with-power, not overly paranoid or extremist, just...genuinely insane. I particularly liked how as he deteriorated his stated goals became more and more ridiculous until they clearly weren't supposed to be taken seriously. What disappointed me about this book was the lack of references to past novels, which really were needed in terms of the themes and content. I mean, we have a civilization without interstellar travel but using advanced warp-style technology anyway, and extensive talk about Prime Directive matters in terms of civilizations that don't easily fall into the Federation's rather simple classification system. Why didn't the words "Orisha" and "Droplet" come up? And the Sentries, while at least mentioned, should have had more focus. Basically, the novel's major weakness could easily have been its major strength - all that was needed was for the book to reference the previous novels and what the characters learnt and discussed in those. Make it overtly a continuation of those debates. That way, the rehash of theme could have worked really well and cemented
Seize the Fire as the next installment in a series; as it is, it felt too much like a lack of originality for the
Titan line.
I don't agree with the "shouldn't have been published" stance - it may have been a misfire, but it had its good points and was still enjoyable. It certainly comes last on my list, but every writer has off-days. I hope to see Martin and
Titan bounce back soon.