Crowning Moment of Awesome: The Pah-wraiths, in the War of the Prophets timeline, blow up the universe in order to reunite with the Prophets and end the war. The universe gets better.
Foreshadowing/Harsher in Hindsight: The trilogy was written after Deep Space Nine concluded. It takes place shortly before Jadzia's death in the season six finale. There are multiple moments that are either hopeful poignant snapshots into her state of mind in the weeks leading up to her death or heavy anvils being dropped on the reader's head that scream 'she's going to die' in giant blazing neon letters. Although the heaviest of them all is likely when she kills the Pah-Wraith crazed future version of Dukat, the man who will kill her, at the end of the final book.
Fridge Brilliance: Vic's rescue of most of the crew from the holosuite might be one major reason they are so willing to help him out in "Badda Bing, Badda Bang"; they feel they owe him one for his help here.
Fridge Logic: How come the present-day Garak isn't shifting forward and backward through time when Sisko encounters him around the time the past versions of Garak, Quark, and Odo are brought to Terrell's lab? It's true that we don't see him for a long while, but the only way that could have happened is for him to have encountered Weyoun, who put him "in phase", and then Garak somehow got away...and that's a rather farfetched situation at best, even for Garak.