The Best Star Trek Deep Space Nine Stories

The hugely ambitious Star Trek: Deep Space Nine has no shortage of classic episodes. We have a complete guide for you.

Star Trek: Deep Space Nine
Photo: Paramount

Spoilers lie ahead for Star Trek: Deep Space Nine

Overlapping with both Star Trek: The Next Generation and Star Trek: Voyager, Star Trek: Deep Space Nine‘s seven seasons had some very high points, It also had some very low ones that strayed a bit too far from the core of Star Trek for some fans, yet gave the show a unique texture that some savor.

If you only ever watch 25 stories from Star Trek: Deep Space Nine, these are they, at least in my opinion – the only rule being that multi-part episodes count as one story (but great big multi-season Dominion flavored arcs don’t!) 

Many Star Trek fans have long been hopeful that CBS may yet announce the remastering of Deep Space Nine for high definition and thus Blu-ray. One of the reasons HD for Star Trek: Deep Space Nine wasn’t greenlit a while back is that it has a lot more effects shots than Next Gen, and in latter seasons it used a significant amount of CG, all of which would need to be redone from scratch – a huge project considering all the ship types in the battles (but hey if the odd Sovereign class and some of the chimera ships, as depicted in the DS9 technical manual, turned up, that would be nice). One other stumbling block being the disbanding of the HD team. Perhaps targeting a 4K master based on the 35mm film would have legs?

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This list is presented in production order as they flow better that way, rather than in a rank order, with the season the story is from in brackets after the title(s). One thing I would recommend though is watching a little backstory from The Next Generation first in the form of the episodes “The Best Of Both Worlds,” “The Wounded,” “Ensign Ro,” and watch “Journey’s End” and “Pre-emptive Strike” as part of watching DS9‘s second season as they tie into key stories.


Starting a new show off in the middle of the Battle of Wolf 359 from Next Generation‘s “The Best Of Both Worlds” could be seen as giving a new show a crutch to help it stand, but Deep Space Nine was fortunate in that it was handled well enough to give Commander Sisko and his son, Jake, some serious backstory and grounding for the stories to follow.

Many of the themes and stories that followed call back to the events of this pilot, so it’s essential viewing prior to many of the other entries in this list, even with the cast clearly not having found their feet yet.


A Cardassian arrives on Deep Space Nine who appears to be suffering from a medical condition only contractable by being present at the time of an accident in a labor camp during the occupation of Bajor by the Cardassian Empire. Major Kira is convinced he is a war criminal and detains him, but in the course of interrogation and investigation, nothing appears as it seems… The result is a some real character development for the first officer of the station after the realization that not all Cardassians are, in fact, the same.

A wonderfully polished and powerful episode, it’s easily the best of the first season.


The failure of a Runabout’s warp field to collapse properly before entering the Bajoran wormhole throws it with Major Kira and Doctor Bashir into the mirror universe as first seen in the original Star Trek episode, “Mirror, Mirror.” It turns out the previous accident altered the path of the Terran Empire and led to a Klingon-Cardassian Alliance.

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Nana Visitor clearly relishes the role of The Intendant (mirror Kira), and this return to the mirror universe unlocks opportunities for the other cast members to stretch themselves in different ways in this and following episodes.

Blood Oath

The three Klingon Captains who famously came up against Captain Kirk in the original Star Trek series, Kang, Koloth and Kor, turn up on the station. They are on a mission of vengence to deal with the murderer of all three’s first born sons, one of which was the Klingon equivalent of a god son to Curzon Dax, the previous host/symbiont melding in the Dax line to Jadzia.

Any excuse to get John Colicos, William Campbell, and Michael Ansara on screen again and this was the first (and last) time we saw them together and also showed them with the full Klingon makeup that the original series could not have afforded to do, and Enterprise would later explain…. well, ish.

The Maquis

Set just prior to TNG‘s “Preemptive Strike” an old friend of Cmdr. Sisko and Lt. Dax arrives on the station after what appears to have been a Federation citizens attack on a Cardassian vessel. It appears the demilitarized zone between the Federation and the Cardassians isn’t as weaponless as it should be and colonists from both sides arm for war.

Introducing the terrorist faction known as the Maquis to Star Trek: Deep Space Nine, the episode lays the foundation for a lot to come both in this show and Star Trek: Voyager.

Ben Sisko and Jake take Quark and Nog on a planetary survey as a school science project, but unfortunately find the soldiers of the rumored Dominion instead. A solitary Galaxy class vessel, flanked by Runabouts, is sent to retrieve the Commander. It does not go well.

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With Star Trek: Deep Space Nine coming to an end, and Voyager still to come, the introduction of the Jem’Hadar, the Vorta and the Dominion really gets Deep Space Nine into its stride and the arrival of the heavily armed USS Defiant into the series does nothing but good.


Commander William Riker of the Enterprise turns up on the station and manages to catch Major Kira’s eye enough to get himself on the Defiant. Except things are not what they seem and the Defiant becomes a weapon of the Maquis.

Jonathan Frakes reprising his role as Riker in this episode which involves Cmdr. Sisko and Gul Dukat working together to find the cloaked Defiant before ships of the Obsidian Order (Cardassia’s secret police/intelligence force) and reveal their role in the demilitarized zone. It’s just a massive shame that this and TNG‘s “Lower Decks” were not followed up on when the Cardassian Empire falls apart later in the show’s run.

Past Tense

A transporter accident aboard the Defiant while in orbit around Earth maroons Cmdr. Sisko, Lt. Dax and Dr. Bashir in San Francisco… of 2024. The economy of the time period and apparent lack of social empathy has resulted in the creation of slum-like Sanctuary Districts where society dumps those down on their luck, the unemployable, and those with mental health issues that he government can no afford to look after. The only problem is that the man whose supposed to put a face on all of it has just been killed in front of Cmdr. Sisko.

The second part of the story is particularly powerful and got its director, Jonathan Frakes, his shot at directing his first film, Star Trek: First Contact. It shines a light squarely on the welfare and health care system in the USA in particular but also has a lot to say to many cultures as the gap between the rich and poor gets larger. Today food banks… tomorrow Sanctuary Districts?

Improbable Cause/The Die Is Cast

Following an explosion in (plain and simple) Garak’s tailor shop, Odo begins an investigation which reveals the reason why the Obsidian Order was building ships in secret. Odo’s and Garak’s travels leads them to Enabran Tain, the head of the Obsidian Order and apparently Garaks former mentor… onboard a Romulan Warbird, belonging tot he Tal Shiar – the Romulan equivalent of the Obsidian Order. A combined fleet is due to make their way to deal with The Dominion.

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This two parter lays some more groundwork for the Dominion War arc that is still in it’s infancy and throws Garak and Odo together in some major character development for both of them.

Way Of The Warrior

The Klingons decide that the Cardassian Union is riddled with Dominion spies and decides that the best way to deal with the situation is to simply conquer Cardassia. The Defiant rescues the higher officials of the Cardassian government, but even with proof they are not changelings, the Klingons attack DS9 to take the officials. However Chancellor Gowron and his General, Martok, are surprised by quite how well armed Deep Space Nine is suddenly.

This fantastic story, the double opener of season 4, shows a change of pace in DS9‘s story telling as well as its theme tune and brings Michael Dorn to the regular cast as Worf specifically to deal with the Klingons, who apparently do not forgive, or forget.


The Trill symbiont Khan(!) who, when in a previous host was married to Torias Dax, arrives on the station, joined with a new host, Lenara. This stirs feelings in both Lenara Khan and Jadzia Dax and the embers of their relationship appear to rekindle in defiance of the Trill culture where re-association of two symbionts from a previous relationship is a high taboo, the price of which is exile from the Trill and death of the symbionts at the end of their current host’s life.

The writing and direction (and this is an Avery Brooks episode) concentrates on the actual story rather than pandering to the fact Lenara and Jadzia are both women, regardless of what outcry brought in the headlines at the time of the original airing.

Little Green Men

Quark, Rom and Nog manage to find themselves in Roswell, New Mexico in 1947. Yes it’s all their fault. The episode starts with Nog getting ready for Starfleet Academy, but the trio of Ferengi end up creating the famous UFO incident, and expect every ’50s B-movie trope to be woven in if it’s your first time watching. Quark is astounded by the savagery and stupidity of 1940’s hoomans.

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Generally felt to be alongside “The Trouble With Tribbles” in the echelons of great comedic Star Trek, it’s one to immensely enjoy from beginning to end. Only thing is, watching it now, you’ll wonder why Hayley Atwell hasn’t walked in and taken over the investigation.

Shattered Mirror

Back in the mirror universe, the mirror Jennifer Sisko has lured the main (prime) universe Jake over, to in turn, gain Captain Sisko’s help in getting the ISS Defiant up and running to defend the, now, Terran hold Terok Nor from an attack by Regent Worf’s new flagship (Worf being leader of the Klingon /Cardassian Alliance.)

It’s dark, even darker than the other mirror universe episodes, and the cast get to really chew some scenery in their mirror universe counterpart mode, and it’s perhaps the highest point of the Star Trek: Deep Space Nine mirror universe episodes.

Our Man Bashir

A transporter failure due to an explosion has resulted in the physical patterns of Captain Sisko, Lieutenant Dax, Major Kira, Chief O’Brien, and Lieutenant Commander Worf being stored in the Holosuite memory systems while Doctor Bashir is running a 1960s spy holonovel. Due to the systems malfunction, the interruption of the program may result in the patterns of the stored screw being lost and thus not be able to be reintegrated with their neural patterns, stored elsewhere to rematerialize them. The Doctor and Garak are thus forced to play out the holonovel.

This is simply the most pure fun you can have in a Star Trek episode with it not being a specifically comedic one. The cast are clearly having a blast all the way through and it’s simply a joy to watch.

Home Front/Paradise Lost

The Founders (changlings) have made it to Earth and bombed a diplomatic conference the both Federation and Romulan diplomats were attending. Captain Sisko and Odo visit Earth where Admiral Layton makes Sisko the acting chief of Starfleet Security in order to drive the changlings from Earth. However it transpires that the Admiral wants to take things too far.

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An examination of what a man with too much power and little regard for the freedom of others can do to a paradise such as that Earth has become as the heart of the United Federation Of Planets. The story is thought provoking and perhaps foreshadows the revelation of Section 31 later on.

Apocalypse Rising

It appears that a changeling has infiltrated the Klingon High Command, and Odo is convinced it’s Gowron. The (now solid) Odo, Chief O’Brien, and Captain Sisko undergo surgery to look very Klingon, with Worf getting a slightly less drastic version to make him look like a different Klingon. The team inflitrate the Klingon’s military headquarters on Ty’Gokor to try and unmask Gowron as a Founder.

Is it me, or does Avery Brooks do Klingon a bit too well? The actor basically steals the scene he is in, in his Klingon disguise, but the story is pivotal in ending the hostilities between the Federation and the Klingons and focusing on the real threat. Though Sisko apparently missed the fangs afterwards.

Trials And Tribbleations

The Defiant is thrown back in time when a passenger they think is human uses the Orb of Time, recovered from Cardassia. The crew realize that they have ended up in the vicinity of Space Station K-7 and a certain starship. They realise their passenger is one Arn Darvin… who has a plan to stop himself being discovered as a Klingon spy at the Federation station, by killing one James T. Kirk.

Certainly the most enjoyable of the two 30th Anniversary TV episodes done for release in the autumn of 1996, and the effects work is fantastic. The images of the Star Trek: Deep Space Nine regulars appearing alongside the original Star Trek series cast will be some of the best remembered moments of any of the Star Trek series – a master stroke of a celebration.

Call To Arms

The Cardassians have joined the Dominion, and in an attempt to stop Captain Sisko mining the entrance to the wormhole to stop Dominion forces coming through, Gul Dukat takes a massive Dominion/Cardassian to take back his station – Deep Space Nine.

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This is possibly Deep Space Nine‘s answer to TNG‘s “Best Of Both Worlds” with a cliffhanger end of season resolved over the first six episodes of season 6. This however is a stand alone episode that kicks off the Dominion War proper with a combined Federation/Klingon effort to thwart the Dominion.

You Are Cordially Invited

Jadzia Dax and Worf follow through on their promise to each other, and prepare to marry. The House of Martok’s matriarch, and Martok’s wife, Sirella arrives on DS9 and immediately shows her disregard for Jadzia. Jadzia’s hen party and the Klingon equivalent of a stag weekend also are unexpected events for the other senior officers.

This is a perfect counterbalance to the prior six episodes without falling into farce and too much comedy, whilst unveiling some facets of Klingon culture that thus far had been left in the shadows.

Far Beyond The Stars

Captain Sisko has visions of himself as Benny Russell, a science fiction writer who takes his stand for civil rights and equality by writing a science story where a black Captain is in command of a futuristic space station. The rest of the regular and repeat guest cast get 1950s characters to play and the story grapples with themes that are especially worth revisiting today.

The beating heart, the core of what makes Star Trek, Star Trek is on full show in this episode… even if it does it by taking the Star Trek out of Star Trek. This episode certainly could not have been made this in the 1960s… or possibly even the 1980s. It’s understandable why Avery Brooks holds this as his favorite episode, even if you discount the fact he directed it. It’s also potentially the best episode of Deep Space Nine as a whole.

Tears Of The Prophets/Image In The Sand/Shadows And Symbol

Against the will of the Prophets, Captain Sisko plans and leads the start of the invasion of Cardassia, which results in a massive loss for him and the crew, and the Captain taking some time out on Earth (and this time he’s even taken his baseball).

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After some soul searching and the return of an old friend, Benjamin goes on a quest to learn more about himself, and his mother… who may have been a wormhole alien/prophet herself. Ben basically needs to find himself and his purpose before returning to the station and resuming his plan to end the war.

The latter part of “Tears Of The Prophets” isn’t pleasant, but the episode is very well done, and the journey that Captain Sisko goes on to finally reveal quite who, or what he is, is rather crucial to the full Prophet arc of the series, as well as dealing with the story of the Dominion War, and the consequences of it.

Field Of Fire

There’s a murderer on DS9, using a prototype Starfleet rifle that uses a micro transporter to beam moving projectiles near the target… which is found with a scanner eyepiece that acts like x-ray specs. The assassin can literally shoot anyone anywhere on the station… from anywhere else on the station. Lt. Dax needs to understand the murderer and turns to the Dax symbiont’s suppressed host, the murderer, Joran.

Nicole deBoer’s tour de force as Ezri Dax taking on the investigation of a serial killer on the station. Ezri summons the memories and personality of one of Dax’s formers hosts, Joran, whom Curzon and Jadzia before had suppressed with the best of reasons. Unfortunately for Ezri, Joran gets a bit too much sway of her mind for brief moments and it seems Ezri Dax may do the unthinkable.

The Siege Of AR-558

Captain Sisko, Lt. Dax, Doctor Bashir, Ensign Nog and even Quark end up marooned on AR-558 whilst on a supply run. The outpost is defended by a Starfleet unit with two thirds of it’s contingents dead and the rest severely low in morale. Then a much larger force of Jem’Hadar attack.

Deep Space Nine was always better at dealing with darker themes than other Star Trek incarnations, but this story dealt with reality and horror of warfare in a far more effective way than anyone had thought Star Trek could at the time. The episode was disturbing enough for the BBC to not show it on the first run through of Star Trek: Deep Space Nine on British television, though at 6pm that was probably a good choice.

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The Final Chapter: Penumbra/Till Death Do Us Part/Strange Bedfellows/The Changing Face Of Evil/When It Rains…/Tacking Into The Wind/Extreme Measures/The Dogs Of War/What You Leave Behind

I am kinda cheating here as I am counting nine episodes containing three story threads, two of which make Star Trek: Deep Space Nine what it is… so I am counting these as two stories. The final third of the last season of Deep Space Nine was marketed as quite the television event in the USA, bearing in mind that this was 1999 – prior to the onset of the concept of binge watching that downloads and low-cost multi-disc DVD boxsets would bring forth (a VHS season boxset was almost a nonsense). The idea behind this was to use these last ten hours, over nine episodes to properly wrap up every flapping loose end rather than rush to do it all in the two hour finale, especially with no plans for films, unlike The Next Generation.

There are three distinct story threads, but they are played out throughout these final episodes and are obviously hugely interconnected, with the Pah Wraith theme (with Gul Dukat and Kai Wynn ending up in bed together) tying into not only season one’s “Emissary” but other episodes too including season six’s “Tears Of The Prophets” and the conclusion to that story at the beginning of season seven.

Obviously though, the main event is wrapping up the Dominon War arc, which it does with aplomb. Kira is not only wearing a Starfleet uniform, but also teaming up with the Cardassian underground and frankly showing them how she and her cohorts drove the Cardassians from Bajor, while Odo deteriorates. Elsewhere Director Sloan of Section 31 makes the ultimate sacrifice in his deranged quest to protect the Federation, whilst Captain Sisko, Admiral Ross and Martok force the Dominion forces back into Cardassian territory.