Deep Space Nine remains one of the most beloved (and controversial) entries in the Star Trek franchise. It bridged the gap between Star Trek: The Next Generation and Star Trek: Voyager, separating itself from its predecessors by taking place on a space station, not a Federation starship exploring the universe. It focused more on the interpersonal relationships of its inhabitants, rather than external situations.
This changed in later seasons, when it diverged from the normal episodic format of Star Trek and became a more serialized program with over-arching plots and inter-connected storylines. It's dark and gritty tone differed from Star Trek's normally upbeat and altruistic mode, but it never failed to capture fan's imagination with intriguing narratives and colorful characters. It was full of the most exciting plot twists and reveals of any Star Trek series. Below you'll find ten of the biggest, ranked.
10 ODO AND KIRA HAVING A RELATIONSHIP
Odo had a seemingly unrequited love for Kira, the brash Bajoran militia member for the length of DS9, and it made for some emotionally moving episodes. His feelings aside, viewers never expected Kira to return his affections, since nowhere in the series was it hinted at that she might have feelings for him in the same way.
Despite fans misgivings, Odo and Kira got together anyway. Their relationship was saccharine and pejorative, doing neither of their characters any favors. It never really made sense why someone like Kira would end up caring for Odo the same way he did her, and why Odo would sort of abandon their life together in pursuit of the Great Link.
9 QUARK BECOMING THE GRAND NAGUS
Gentle, obedient Rom was one of the most wholesome characters on the show, and by that token, the worst Ferengi. Still, him ending up as Nagus was a great twist, if only because the position of the Grand Nagus had been previously offered to one of the most unscrupulous Ferengi, Quark.
Despite Rom's bumbling, in the middle of the series it was revealed that he actually had hidden talents. He may not have been the mathematician that Quark was, but his engineering prowess knew no bounds, which endeared him to his people and to the Bajoran militia. Quark on the other hand, though he was offered the position of Grand Nagus, turned it down to tend bar and run the holodeck.
8 WORF AND JADZIA'S MARRIAGE
On the surface it might have seemed like a contrivance to have Worf (the newly minted DS9 cast member) and Jadzia become an item. Worf was fresh off of Star Trek: The Next Generation, and seemed like an odd fit to the motley crew of established DS9 characters.
However, his bristly demeanor and abrupt candor matched well with Jadzia's forthright nature. They were both characters whose personalities had a way of making their fellow crew members uncomfortable. It was certainly more logical pairing than Worf and Counselor Troi. Plus, the wedding ceremony between Jadzia and Worf was a highlight amidst DS9's doom and gloom.
7 MILES O'BRIEN TURNING OUT TO BE A CLONE
In one memorable episode, Miles O'Brien's behavior is just off enough to cause other members of the crew to grow suspicious. Viewers spend the entire episode thinking they're following the real Miles O'Brien on a bad day, only to discover at the conclusion it's actually a clone of the real Miles O'Brien, who ends up taking down the rogue version of himself.
In reality, the clone was an operative of the Dominion, sent to retrieve Federation intelligence from Deep Space Nine. As though that wasn't bad enough, Miles O'Brien also had an instance where an alien implanted memories from a 20 year stint in prison that he never experienced, but had to deal with emotionally. Poor Chief O'Brien!
6 GUL DUKAT BEING A TURNCOAT
Gul Dukat turning out to be, well, Gul Dukat wasn't that much of a plot twist, but if you consider he had started to get in the habit of helping Sisko and Co. in a period of grey morality for his character, it came as a punch to the gut. In some ways, the greater twist would have been for Gul Dukat to not side with the Dominion Empire in the last season of the series.
His perspective that the whole of Deep Space Nine and the Federation were doomed with the advancement of the The Founders was in line with his character's rationale, but many fans would have liked him to stay a part of the DS9 crew and possibly have explored his feelings for Kira.
5 BASHIR TURNING OUT TO BE AUGMENTED
Of all the doctors in all the Star Trek series, Dr. Julian Bashir had the best bedside manner. Dr. Beverly Crusher on Star Trek: The Next Generation comes a close second, but even she didn't have the natural charm and warmth of Dr. Bashir (we won't even touch Doc McCoy's ornery nature or the EMH's stuffy efficiency). The best parts of his personality turned into a lie when it was revealed that he had been altered as a young child.
His parents had allowed all sorts "upgrades" be given to the young boy to improve his reflexes, stamina, intelligence, and even his physical appearance. The best parts of Bashir's character turned out to be the product of genetic experimentation.
4 GARAK BEING A MEMBER OF THE OBSIDIAN ORDER
Garak was one of the most sensationalized characters on the series, if not all of Deep Space Nine itself. By day, he was a mild-mannered tailor on the promenade, and by night he was gossiping at Quark's bar, fishing for information. The fact that he was so congenial yet so private made him one of the most mysterious inhabitants of the station.
Fans eagerly awaited when Garak's past would finally be revealed - it was sure to be something juicy, especially since he was a Cardassian ex-pat. Garak turned out to be a high-ranking former member of the Obsidian Order, the Cardassian intelligence agency.
3 BASHIR BEING A SPY AND RECRUITED BY SECTION 31
In many ways Section 31, the Special Ops of the Federation with the ability to manipulate time and space, was a plot twist in and of itself. Suddenly, no plot-line was safe if Section 31 members were involved - it could go pear-shaped at a moment's notice depending on the episode narrative.
One of the most sudden reveals was the recruitment of Dr. Julian Bashir into their clandestine ranks. This was at the same time that Bashir was being accused of being a spy for the Dominion Empire. Apparently his augmented self was a prize for both agencies!
2 SISKO GOING OFF TO JOIN THE PROPHETS
Early on in DS9, Benjamin Sisko meets one of the religious leaders of the Bajoran people. As Commander of the space station Deep Space Nine, he has vowed to let all inhabitants peacefully practice their faiths, from the Bajorans (whose planet DS9 orbits) to the Cardassians that seek asylum. He takes a particular interest in the religious leader called Kai Opaka, the spiritual guide for all Bajorans.
It's through their initial meeting, and subsequent spiritual encounters that Sisko begins to learn of his true nature as a prophet, and spiritual guide to the universe. When he leaves at the end of DS9 to fulfill his duties, it seemed an odd twist for a Starfleet officer.
1 JULIAN BASHIR BEING A CHANGELING
Julian Bashir was part of several plot twists, some of which were received well by viewers and some of which that were considered ridiculous. One of the most effective occurred when Dr. Bashir turned out to be a Changeling, an operative sent by the Dominion Empire to infiltrate Deep Space Nine.
What was so fruitful about this plot twist was the fact that fans realized Dr. Bashir had done all sorts of things as "fake Bashir," including perform surgery on Commander Sisko! Not really knowing how long they'd been dutifully watching Dr. Bashir made for a twist no one could see coming (fans concede it was about five episodes, or a month's time).