Prefect of Bajor
Dukat was once the Prefect of Bajor during the Cardassian Occupation and presided over the station of Terok Nor (which would become Deep Space 9 following the Cardassians' withdrawal). Dukat was the last Prefect of Bajor before the end of the Occupation. He was responsible for many atrocities committed against the Bajoran people, and became one of the most hated individuals in Bajoran history.
According to Dukat, he was convinced that a gentler approach was needed to quell the Bajoran Resistance and make Bajor suitable for colonization. Regardless of his apparent "compassion", the Bajorans continued fighting against Cardassian oppression and Dukat came to hate the Bajorans for shunning him.
Despite his latter admission of hatred for his charges, he conducted numerous affairs with Bajoran women, including Kira Meru, mother of Kira Nerys, and Tora Naprem, whom he claimed to love, and with whom he fathered a daughter, Tora Ziyal. The general implication is that in Dukat's inner fantasies, he wanted the Bajoran people to embrace him as their superior and beloved master. In microcosm, he enjoyed indulging this fantasy by manipulating Bajoran comfort-women into falling in love with him, as if they represented all Bajorans.
In the years following the Cardassian withdrawal from Bajor, Dukat - still holding the rank of Gul - played a major role in Cardassia's relations with the Federation. He made several visits to Deep Space 9 for various reasons, during which he established an awkward relationship with Benjamin Sisko, whom he would come to regard as a friend, though Sisko did not return the gesture. He also developed a borderline romantic fascination with Kira Nerys, though Kira despised Dukat completely. In spite of the animosity between Bajor and Cardassia, there were a number of occasions when Dukat and Kira worked together for mutual benefit, such as the rescue of Dukat's half-Bajoran daughter Ziyal from a Breen labour camp.
Following the fall of Cardassian Central Command, Dukat was promoted to Legate and became Chief Military Advisor to the Detapa Council, who ran the new civilian government. After he had rescued Ziyal, however, he was disgraced and reduced to running the freighter Groumall. With the aid of Kira Nerys, Dukat managed to hijack a Klingon Bird-of-Prey and decided to wage war against the Klingon Empire by himself. Ziyal was taken to Deep Space 9 so that she could live happily rather than get swept up in conflict and Dukat and his crew launched their own campaign against the Klingons operating in Cardassian space.
Alliance with the DominionWith the losses it had suffered in its war with the Klingons, the Cardassian Union was pushed to the brink of collapse. To save his people and also to gain greater power, Dukat began conducting secret negotiations with the Dominion, an empire from the Gamma Quadrant that had targeted the Alpha Quadrant for conquest. When the Dominion fleets first emerged from the Bajoran Wormhole, Dukat allowed them to make a foothold in Cardassian territory. Dukat was appointed as the new leader of the Cardassian Union by the Dominion, which normally would have allowed him the rank of Legate, but he preferred the title of Gul since it sounded more "hands on". As the leader of Cardassia, Dukat promised his people that the Union would be restored to its former glory and that with the Dominion's help, they would rule the entire Alpha Quadrant.
When war broke out between the Dominion and the Federation, Dukat led the Dominion task force that claimed Deep Space 9, which was re-christened Terok Nor. For five months, he enjoyed sitting in his old office and deciding on the restructuring of the Alpha Quadrant as the Dominion continued to push back the Federation and Klingon forces. He became increasingly confident that he would be victorious, but after destroying the minefield around the Bajoran Wormhole, no Dominion reinforcements arrived from the Gamma Quadrant (the wormhole aliens had seemingly caused the entire fleet to vanish out of existence). The Federation forces had managed to breach the Dominion defence lines and were about to surround the station, and so the Founder gave the order to evacuate and fall back to Cardassian territory.
Descent into madness
With victory snatched from his grasp at the last minute, Dukat was driven half-mad by his sudden reversal of fortune. Before he would leave Terok Nor, he tried to find his daughter Ziyal. The two found each other but Ziyal refused to join her father, deciding that she belonged on the station. Ziyal was then shot by Dukat's aide Damar and her death drove him over the edge. He remained on the station as the Federation reclaimed it and he was captured.
Sometime after the reclamation of Deep Space 9, Dukat was taken aboard the USS Honshu which was to take him to Starbase 621 to answer for war crimes. He had been treated by a number of doctors before being taken to trial and he was deemed "recovered", but in truth he still experienced hallucinations of Damar, Major Kira and Weyoun mocking him for his failure. Before he could be taken to trial, the Honshu was attacked by a group of Cardassian ships and destroyed. Dukat was able to escape and he took the injured Benjamin Sisko with him aboard a shuttle down on to a barren planet. While he seemed to help Sisko at first, his hallucinations pressured him to kill the captain and embrace his hatred for the Bajoran people. Dukat would later escape, but he vowed to return one day and destroy Bajor.
Emissary of the Pah-WraithsIn late 2374, Dukat believed he had found a way to destroy the Bajoran people and their Emissary, Sisko. Having immersed himself in the ancient Bajoran texts, he discovered that the wormhole was actually the Celestial Temple. He returned to Cardassia Prime and enacted an ancient Bajoran ritual to release a Pah-wraith into his body. Thus possessed, he traveled to Deep Space 9 and released it into the Celestial Temple via the Orb of Contemplation, causing the wormhole to disappear. In the process, Dukat killed Jadzia Dax, who was simply in his way.
His inhabitation by the Pah-wraith had turned Dukat into their believer; subsequently he retreated to station Empok Nor and founded a community of members from the Cult of the Pah-wraiths. He was worshiped as a messiah, and fathered another half-Bajoran child with Mika, one of his followers. Dukat never publicly admitted fatherhood. Dukat attempted to have the cult members commit suicide to conceal his attempt to kill Mika. When he was exposed, he fled again.In late 2375, Dukat secretly underwent cosmetic surgery on Cardassia Prime to pose as a Bajoran farmer, Anjohl Tennan. He then traveled to Deep Space 9 and gained the confidence of Kai Winn Adami and even became romantically involved with her - albeit for ulterior motives - and with the assistance of false visions given to Winn by the Pah-wraiths, he slowly convinced her to join him as a follower of the Pah-wraiths. The two plotted to release the Pah-wraiths from their prison in the Fire Caves, using the Book of the Kosst Amojan.
In DS9's final episode "What You Leave Behind", Dukat and Kai Winn entered the Fire Caves of Bajor, the ancient prison of the Pah-wraiths. As part of the ceremony to release the demonic beings, a sacrifice was required and so Winn killed Dukat by offering him a goblet of poisoned wine, believing that the Pah-wraiths would choose her to rule Bajor in a new age. The demons rejected Winn and resurrected Dukat, imbuing him with their power. Before Dukat could complete the Pah-wraiths' release, he was once more confronted by his nemesis Benjamin Sisko. Sisko attacked Dukat, but the possessed Cardassian was unfazed and used his newfound telekinetic powers to force Sisko to his knees. As he gloated over his imminent triumph, Kai Winn picked up the Book of the Kosst Amojan and attempted to throw it into the flames. Dukat snatched the book back from her and killed her, but his moment of distraction allowed Sisko to tackle him and send them both plummeting into the fiery pit. The book was destroyed in the flames, and apparently, so was Dukat.
Captain Sisko was saved from death by the Prophets, who told him that he had resealed the Pah-wraiths inside their prison and that Dukat was trapped with them.