EDIT: And to agree with Anwar as a second time, after Waltz it was only fitting that the Sisko/Prophets storyline came to a resolution with a battle with Dukat as the Emissary of the Pagh-Wraiths!
In theory, perhaps.

My rant from another thread:
The most serious problems with that storyline:Dukat and Winn and Dukat's Pah-wraith alliance. It makes perfect sense that Dukat would use the Pah-wraith to destroy the Bajorans, as well as giving him the power he also craved.
- it is a plot device rather than something that flows organically from the characterization, so Dukat is made to do and say things that make no sense, just in order to set up a Sisko/Dukat conflict: forgiving Damar completely for killing Ziyal, while blaming Sisko of all people. WTF? What did Sisko have to do with it? At least if he blamed Kira or Garak or anyone who was either 1) at the station at the time of the Occupation, or 2) was close to Ziyal, it could have made some convoluted sense - at least you could say that he blamed that person for influencing her and making her "betray" him. But Sisko?
About the only way I could have made sense of it would've been if it hadn't really been Dukat, but Damar's hallucination of Dukat, just like Damar, Kira and Weyoun were Dukat's hallucinations in "Waltz", since the whole thing is just like wishful thinking by Damar."Hello, Damar, old friend. Oh, I don't worry, I don't hold any grudges for you murdering my beloved daughter right in front of me! We're still pals and I'm totally supportive. I'll just choose to blame someone else who's got absolutely nothing to do with it."
And how weird is it that Dukat - just like the writers, apparently - seems to have completely forgotten by season 6 that he has 7 other children? Even though he used to talk about them in season 2, 3, 5... Now they just don't matter to him even to warrant a mention?
The only explanation of his behavior I can see is that he was insane at that point - but it is very lame when a TV show has to resort to "oh well, he is insane" as an excuse for making characters act in any absurd manner.
- the whole storyline was set up as being huge and incredibly important, with Dukat established as the main villain of the show again (according to the writers, that was what they were trying to do); but in the end, it had absolutely NOTHING to do with the Dominion war, nothing to do with Cardassia... and heck, it even didn't manage to do anything to Bajor, apart from killing Winn. And after all the build-up, it ended with a 2-minute first fight - what an anti-climax.
- the whole thing represented a shift from the intelligent treatment of religion and from the layered, complex storytelling and characterization that DS9 was known for, into a black-and-white supernatural tale of Good vs Evil, complete with demonic possessions and red-eyed maniacally laughing villains. Which I found really sad and disappointing. To quote Confused Matthew: "Come on! You are better than that!"
- The Pah-wraiths are never really explained - we don't get any insight into their motivations, they are nothing but boogey-men, or should that be boogey-beings. We're just supposed to think that they're eeeevil, so they'll naturally be allied with the eeeeevil Dukat. And I understand wanting to get back to the Celestial Temple, but WTF was that about "ending all life"? Why would they want that? Were the writers just wrecking their brains, trying to think of something that sounded eeevil enough?
The Pah-wraiths and Dukat in the end just served as a device to make the Prophets and Sisko look like a force of Good. But that just does not work, because...
- ... there is no reason to see the Prophets as Good; and it was OK as long as the show did not try to manipulate the viewers into feeling differently. But once they did, the Prophets just came off as arseholes who don't really care about the humanoids, but are ready to manipulate and use them for their ends. Did the writers ever realize just how creepy and disgusting what the Prophets did to Sarah and Joseph Sisko was?
- Maybe Ira Steven Behr should have just kept his mouth shut and pretended that he had always planned the Anti-Emissary plot, even though we know they just came up with stuff as they went along. But since he had to go on in public about how upset he was that Dukat was popular with the fanbase and how it was OMG oh so wrong! and OMG sending the wrong message! and OMG why did Marc Alaimo had to try to understand his character and play him as a multi-dimensional, realistic person rather than a caricature! and OMG why did he, Behr, allow Dukat to actually become an interesting and complex character! and OMG, we can't have people think that war criminals and despots are human and perhaps similar to the rest of us, can we! and OMG, that mistake had to be rectified!... I can hear very little in seasons 6 and 7 over the sound of Behr preaching and telling me what I am supposed to think.![]()