After The Original Series and The Next Generation, Deep Space Nine remains one of the most popular of the Trek series. Over its seven seasons, it delivered just as many great episodes and in some ways the on-going storyline through the last four seasons outdid The Next Generation and really put Voyager to shame.
Duet came at the end of the first season of DS9 and many still consider it to be the best hour the series ever made. It’s a Kira episode and dealing with the ramifications of the Cardassian Occupation of Bajor, and obviously has many parallels to the Nazis in WWII. It’s still one of the best episodes of “Star Trek” ever made, and if DS9 had its “Inner Light” this would be it.
In the Pale Moonlight
If there’s one episode of Star Trek that would make Roddenberry swirl in his urn, it’s this one. When Sisko gets sick of the Federation’s losses in the Dominion War, he decides to do anything necessary to get the Romulans on their side. He lies and cheats, and doesn’t regret a second of it. Garak is awesome here as always, and this is the episode responsible for the “It’s a Faaaaaake!” Internet meme.
What You Leave Behind
DS9′s series finale is actually part nine of a nine-part mini-series within the series. That was needed in order to wrap up all of the many story lines in the series, and What You Leave Behind definitely brings DS9 to a satisfying conclusion and doesn’t leave room open for movies or sequels.
Far Beyond the Stars
Where DS9 has one of the least-Roddenberry Trek episodes in the franchise, it also has one that is extremely true to the core of Star Trek. This is the one where Sisko is an African American science fiction writer in 20th Century Earth who has an idea for a story set on a space station that resembles Deep Space Nine. All of the DS9 actors appear in this episode, including those who normally wear extensive alien make up.
Trials and Tribble-ations
Where TNG had Original Series guest stars, this extremely popular series took the DS9 crew back in time to the Original Series itself and did an amazing job melding in with the original footage.
While the whole Mirror Universe thing got a bit out of hand by the end of the series, the initial Mirror Universe episode is the best. In it we learn what happened to that universe after Kirk turned goatee-Spock good and it was just so much fun to see the evil universe again. It was a sequel to an Original Series episode done right.
While the end of this episode was a massive Star Trek reset button being used, it was still one of the most memorable episodes of the series’ run. This is the one where Sisko suffers an accident and Jake spends the rest of his life trying to fix it to bring his dad back.
Sacrifice of Angels
Look up the definition of “Epic” in any Star Trek Encyclopedia and you’ll see this episode listed. Massive space battles where the Federation is outnumbered two-to-one results in the retaking of Deep Space Nine and sets up a lot of characters for where their stories will take them in the final season.
In September of 1994, The Next Generation was off the air and Deep Space Nine was out there all by itself. So they had to start the third season off in a big way to establish DS9 as a series that can survive on its own, and they did that by revealing that Odo’s people were the leaders of the Dominion and would cause massive trouble for the Federation in the remaining seasons of the show.
Little Green Men
This episode is a rather forgettable little one that doesn’t have anything to do with the overall Dominion War, but it’s included here solely due to the great idea behind it. What if the Roswell aliens were Ferenegi, and it just happened to be Quark, Rom, and Nog? Really fun idea.