Being somewhat meta, somewhat on the subjects of both villainy and religion, and somewhat Dukat-apologistic, because I have Just That Much Moxy. And it's for
selenak, because she asked, and because we're having lots of sex.
BUYER BEWARE: There's a point (commonly referred to as post-Waltz) where characterization slaughter interferes with any proper analysis of Dukat's character, so I'm taking some liberties, shaping Dukat from his own point of view, or from an objective point of view, but leaving aside any (post-Waltz) positioning the series did to force us to see him through Sisko's eyes as puuure eeevil. I don't think that's terribly constructive, or terribly interesting, and all that puuurree eeevill business really bastardized a character who, in my mind, was both more complex and more sympathetic than he was given credit for. That being said:
Dukat is of Bajor, But He Will Find No Rest There
From day one, Dukat is established as Sisko's foil, or, more properly, Sisko is established as Dukat's, as Dukat is the one with history and reputation and Sisko's new and untried.
Where Dukat was Prefect of Terok Nor, Sisko comes in as Commander of DS9; they sit behind the same desk, make the same kinds of command decisions, and both are driven by a desire to shape Bajor (the squabbling orphan) in their own image. As the audience, we're asked to take it on faith that Sisko's decisions are better, that the Federation's plans for Bajor are kinder, more sincere, more humane.
Flashbacks to the Cardassian Occupation are seen through that lens, because we're a human audience of a human series. Where DS9 is sterile, pristine, Federation, Terok Nor is soot-covered and littered with the bodies of exhausted slaves. The depiction is insidious -- even before we meet characters from the old days of Terok Nor, we're disposed to seeing them as evil because they're colored that way.
What's interesting is that the two credible eyewitnesses to both Occupations (in this case, the first Cardassian Occupation and the subsequent seven-year Federation Occupation), Odo and Quark, seem far more willing to defend their actions during the Cardassian Occupation -- and far more willing to defend the Occupation itself -- than any of the Federation officers who were never there.
Odo insists that he was just, and fair, and served Dukat with the same law-upholding honorability that he later served with Sisko. Quark insists that he was magnanimous and righteous, that he treated all people (who could pay) equally, during both the Cardassian and the Federation's tenure on the station. Neither one of them up and had a hissy fit and left in protest of Dukat's actions. Neither one of them suggests that Dukat did anything other than his duty while assigned to Terok Nor. Whether his duty seems cruel to us or not is beside the point -- he served, they served, just as Sisko served later.
"Things Past" is the obvious case in point here, where Sisko et al get a first hand look at life during the Cardassian Occupation. And it's Odo who made the mistake there, Odo himself who got the slaves killed. And it was because he didn't serve justice, because he failed to uphold his own morals that he always swore by. Not because of anything out of the ordinary that Dukat did; Dukat did his job. Odo failed to do his.
Odo makes similar mistakes while serving on DS9, lets his emotions get the better of him (see: the Dominion War arc), and I think if you got Odo in a room and asked him, he'd be just as guilty of the crimes he committed by not serving justice during the Federation Occupation of the station as he was during the Cardassian Occupation.
So, with the understanding that both Dukat and Sisko have jobs to do, both which, they believe, are in the best interest of Bajor but are overwhelmingly -- in both cases -- in the best interest of their personal governments (Cardassia and the Federation respectively), I think it's interesting to look at those two characters side by side and come to realize that they're not nearly as different as they would think they are.
Even "Waltz" -- which has its own set of characterization problems, some of which are the fault of the writers for trying too hard to construct a Dark Enemy, but that's aside for now -- covered that, at least in its artistic structure. It's a waltz, a metered dance with two equal partners, facing off. Dukat came to Sisko seeking understanding, insisting, in his uniquely megalomaniacal Dukatish way, that what he did he did for the good of the Bajoran people. And while, over the course of the episode, we come to see Dukat as way more reprehensible than we'd ever seen him before, and while over the course of the episode we're forced -- both by Dukat's song and dance and by the triggerish puuurree eeevill words he uses -- to "realize" that Dukat is completely insane and dangerous, we still believe that he believes he did what he did for the good of Bajor.
Like Sisko, everything Dukat ever loved is of Bajor, from the world itself to his job on the station, from Naprem to Ziyal to Kira Nerys. Sisko's love for Bajor estranges him from his family, from Kasidy and Jake (it's worth noting that Sisko never even said goodbye to Jake when he went off to be with the Prophets in the last episode); his obsession with Bajor and the Bajoran people makes him quite entirely insane. No less insane, really, than Dukat became, after a lifetime of watching Bajor seduce him and then, just as readily, take everything he loved away from him.
The series starts with Sisko taking on the mantle of Emissary to the Bajoran gods; it ends, in a way, with Dukat taking on that same mantle. Posturing aside, we don't know any more than Winn does whether the Prophets or the Pah-Wraiths are Bajor's true gods; we don't know which set of puppet masters truly has the best interests of Bajor in mind. So when Sisko goes to the air, to be with the Prophets, Dukat goes to fire, to be with the Pah-Wraiths.
Dukat's emotional break comes, understandably, with the death of Ziyal. In that moment -- evacuating Terok Nor for the last time -- Dukat loses his last ties to Bajor. Up until that point, he had love, and he had hope; the Dominion tears that from him, the unkindest cut of all. Imagine if the game had been played differently, if the Federation aligned with the Dominion, if Sisko were torn from DS9 and Bajor; if Admiral Ross killed Jake. With Sisko's love for Bajor so profound (think of the scene on Earth where he sings Bajor's praises to the Admiral, fairly disappears into reverie in the middle of a war talking about the house he's going to build in "Eden itself" -- and Bajor has proven, on many occasions, to offer the double-edged temptation of that fabled garden), I think a psychotic break would not be out of order. Betrayed by the Prophets, he could easily have turned to the Pah-Wraiths himself -- anything of Bajor that would offer him love is better than nothing at all.
Dukat's rage against Bajor in "Waltz" is the ranting of a spurned lover. When you're dumped on your ass by someone you've loved so hard, and so long, the script writes itself. "They never understood me! I was only trying to love them! They are fools! Kill 'em all!" And Sisko, who, as we know, holds a grudge against people who hurt the ones he loves (cf. his relationship with Picard), would likely have had a similar reaction.
Bajor is DS9's harsh mistress. She plays fast and loose with those who love her, and everything that touches her dies. At the end, there's no one left but Kira -- the blank-slate stand-in for Bajor itself -- alone in a Federation uniform, with everyone who was close to her either dead or far gone.