Star Trek: Deep Space Nine was unique among other Trek shows in that it often featured serialized storylines from week to week. Once the Federation engaged in the Dominion War, the explosive action of the show was often too much to squeeze into one episode, and the two-part episode became commonplace.
Whether they were introducing rebellious factions like the Maquis, or weaving dark tales from the frontline of the Dominion War, the two-part DS9 episodes were often some of the best of the show. Even though most of the two-parters were well received, some garnered much higher scores on IMDb.
Image In The Sand/Shadows And Symbols - 7.6/7.9
By the start of the final season of DS9, there were a lot of threads that all tied together each week. "Image In the Sand/Shadows And Symbols" finds a defeated Sisko waiting on earth for a sign from the prophets. Meanwhile, the newly minted Colonel Kira is tasked with forming a blockade around a Romulan military hospital that is integral to the war.
Similar to a lot of Trek's other two-parters, the combo of episodes represent an overarching plot that is stuffed to the gills with many unique threads. While the story isn't as tightly plotted as others, the disparate parts eventually reunite and begin the narrative that would form most of the seventh season of the show. With Sisko's spirituality returning to the show, it adds another wrinkle to the already complex series.
The Maquis Part 1 & 2 - 7.8/7.8
Crisis negotiation is an integral part of the Star Trek mythos, and Commander Sisko was put under a tremendous test in the two-parter "The Maquis". When a Cardassian ship is destroyed by the resistance cell known as the Maquis, Sisko is tasked with de-escalating conflicts before it results in all-out war between the two parties. When Gul Dukat is captured and held for ransom, matters get all the more complicated.
Subtly sinister, and ultimately evil in the end, the Cardassians of the early seasons of DS9 are uneasy allies with their Federation counterparts. Despite being one of Star Trek, the Cardassian empire begins to slip, and resistance organizations like The Maquis hope to finish them off. As much as Sisko might not trust the Cardassians, it is his duty to find a diplomatic solution to the complicated problem.
Past Tense Part 1 & 2 - 7.8/7.9
This show's history is filled with great Star Trek time travel stories, and "Past Tense" sent the DS9 crew to the primitive world of 21st-century earth. A transporter accident sends Sisko, Bashir, and Dax back to San Francisco in the past, and they must find a way to get back without causing any temporal disturbances. However, an accident forces Sisko to take the place of an important historical figure in order to preserve the timeline.
With many of DS9's more lofty two-part episodes dealing with heady subjects like war and grief, "Past Tense" is a refreshingly simple story. Taking the characters off of the station was an interesting change of pace, and watching them interact with their unfamiliar surroundings is always humorous. Ultimately though, while DS9 is often regarded as one of the darkest Trek shows, "Past Tense" showed that it could be just as playful as classic episodes from The Original Series.
The Search Part 1 & 2 - 8.3/8.2
Sisko's brashness as a commander is well known, and few episodes showed that trait off quite like "The Search". Instead of simply waiting for the ruthless Jem'Hadar to attack, Sisko decides to infiltrate their quadrant in order to negotiate with the mysterious Founders who seemingly control them. Meanwhile, Odo comes face to face with his people for the first time, and has a crisis of faith in the process.
While his ruthlessness has served him well in negotiations, Sisko's boldness is a hindrance in the story. While most Captains in Trek come off as somewhat infallible, Sisko is far from perfect and it makes him a stronger character because of his flaws. "The Search" is great because it sets up many ideas that would further pay off over the rest of the series.
Homefront/Paradise Lost - 8.3/8.3
Moral dilemmas are the heart of Star Trek, and DS9 featured a fair smattering of episodes that challenged the moral constitution of its characters. "Homefront/Paradise Lost" sees Sisko travel to earth when a bombing at a Federation conference is revealed to be the work of the mysterious Changeling race. Martial law is declared planet-wide, and Sisko finds himself questioning who the real villain is.
Watching the pristine society that is cultivated on earth collapse under pressure was a shocking image for many long-time Trek viewers. Star Trek's utopian future was one of its biggest selling points, but "Homefront/Paradise Lost" showed that those ideas were extremely fragile. Unfortunately for Sisko and the rest of his crew, things would get only worse before they got better.
In Purgatory's Shadow/By Inferno's Light - 8.7/8.8
One of the things that placed DS9 among the best Star Trek series was its many complicated characters that walked the line between good and evil. "In Purgatory's Shadow/By Inferno's Light" follows Garak as he receives a coded message that leads him to believe that his mentor is still alive. When he and Worf travel to find him, they stumble across a Dominion plot to attack the Alpha Quadrant.
Garak is a fascinating character and he often straddled being dastardly and being reluctantly helpful. His mysterious past kept viewers invested through all seven seasons, and the two-parter helped to add more intrigue. The true power of the episode is that it manages to be a personal story about one character, while also kicking off an exciting new chapter for the series.
Improbable Cause/The Die Is Cast - 8.5/8.9
The two-part episodes of DS9 often represented two separate parts that were equally strong, and could be taken in a pair or singularly. "Improbable Cause/The Die Is Cast" finds Odo investigating the attempted murder of the Cardassian tailor Garak. Entrenched in his search, Odo is captured by the Cardassians and interrogated about his race, the Founders.
As the war heated up throughout the show, the loose parts began to solidify into cliques including the temporary alliance of the Cardassians and Romulans. Almost as evil as the Dominion themselves, the alliance's meddling nearly ignites the war for the worse, and it ends up harming individuals like Odo. Odo's emotional state is already rocky, and the actions of solids like the Cardassians and Romulans only helped to potentially push him towards his Changeling brethren.
Favor The Bold/Sacrifice Of Angels - 8.5/9.0
Coming as one of the best episodes of DS9 ever, "Favor the Bold/Sacrifices of Angels" was also one of the tensest moments of the entire Dominion War. With DS9 under Dominion control, the Federation plans an all out assault on the station in order to retake it. Meanwhile, Federation forces work to maintain the minefield at the wormhole to stop further Dominion reinforcements from crossing over.
Like a mix of the best War movies with the themes of Star Trek, the two-parter is unlike anything seen before or since in the franchise. With the station under Dominion control, it seems as if things are at their darkest point, but there is still a chance for the Federation. While many fans were somewhat turned off by the militaristic turn that Trek took with DS9, the tones of hope and perseverance are still present all throughout the Dominion War.