In the years before the United Federation of Planets intervened in Bajoran affairs, Dukat was the head of the Cardassian ore processing facility Terok Nor and the prefect of the occupied Bajor. Dukat maintains that he attempted to rule Bajor with a "softer" and "gentler" hand than the Central Command asked him to, such as by abolishing child labour. But subsequent murders of Cardassians on Bajor forced him to take retributionss.
When the Cardassians finally left Bajor, the Federation moved into Terok Nor, renamed it Deep Space Nine, and discovered the Bajoran wormhole. This made Dukat very unpopular with Cardassian government, and as such made Dukat very annoyed at Sisko, vowing one day to get back Terok Nor.
Dukat eagerly tries to suppress his image as a harsh ruler in non-Cardassians, and yet he still maintains strongly that Cardassians are more advanced "militarily, technologically, and culturally" than Bajor, so the Occupation was justified and to improve the lives there. And if the Bajorans do not appreciate the Cardassian superiority and resist with a false pride and religious faith, then the Bajorans deserve to be killed systematically. Because of what she deems as hypocrisy, Kira Nerys have always detested Dukat, and Sisko comes to the conclusion that Dukat is "pure evil" in a world of grey.
However, there are also those who interpret Dukat from a different light. One such person is Dukat's long-lost half Bajoran daughter, Tora Ziyal. Ziyal's murder caused Dukat a temporary severe loss of control over his emotions and sense of reality. He desperately seeks approval during this time, but never received any from those he deemed important.
In the series finale, Sisko and Dukat fought each other physically, and Dukat was imprisoned with the Pah-wraiths.