Star Trek: Deep Space Nine (1993)

In the first episode, Starfleet Commander Benjamin Sisko takes charge of Deep Space Nine. He and Jadzia Dax stumble upon the first stable wormhole ever found and discover that it is inhabited by beings who are not bound by normal space and time. To the strongly religious people of Bajor, the wormhole aliens are their gods (the Prophets) and the wormhole itself is the long-prophesied Celestial Temple, where they reside. Sisko himself is hailed as the Emissary of the Prophets, through whom the Prophets primarily act.

This provides the basis for a long-lasting story arc. Sisko initially considers his role as a religious icon with open discomfort and skepticism, referring to the Prophets simply as "wormhole aliens" and striving to keep his role as commander of the station distinct from any religious obligations that the Bajorans try to place on him. Later, he becomes more accepting of his role and, by the end of the series, he openly embraces it.

The station crew early on has to contend with a human resistance group known as the Maquis. Rooted in the events of The Next Generation episode "Journey's End", in which Native American settlers refuse to leave when their colony world is given to Cardassia as part of a treaty, the Maquis is an example for the show's exploration of darker themes: its members are Federation citizens who take up arms against Cardassia in defense of their homes, and some — such as Calvin Hudson, a long-time friend of Sisko's, and Michael Eddington, who defects while serving aboard the station — are Starfleet officers. The show's sharp departure from traditional Star Trek themes can be seen in episodes such as "For the Cause", in which Eddington complains to Sisko, "Everybody should want to be in the Federation. Nobody leaves paradise. In some ways, you're even worse than the Borg. At least they tell you about their plans for assimilation. You assimilate people and they don't even know it."

The second-season episode, "Rules of Acquisition" marks the first mention of the Dominion, a ruthless empire in the Gamma Quadrant, though they are not fully introduced until the second-season finale, "The Jem'Hadar". It is led by "the Founders", a race of shape-shifting Changelings, the same race as station security chief Odo. They were once persecuted by non-shape-shifters (whom they call "Solids") and they seek to impose "order" upon any who could potentially harm them, which includes nearly all Solids. The Founders have created or genetically modified two races to serve them: the Vorta, sly and subversive diplomats, and the Jem'Hadar, their fearless shock troops. These races worship the Founders as gods.

At the start of DS9's third season ("The Search"), with the threat of a Dominion attack looming from the other side of the wormhole, Commander Sisko returns from Starfleet Headquarters on Earth with the USS Defiant, a prototype starship that was originally built to fight the Borg. It remains stationed at Deep Space Nine until its destruction in season seven, providing an avenue for plot lines away from the station. With the third season, the writing took a substantial upwards turn in quality as the best Star Trek writers turned away from the now completed Next Generation and began to write regularly for DS9.

The Dominion forms an uneasy alliance with the Cardassians in the fifth-season episodes "In Purgatory's Shadow" and "By Inferno's Light" and goes to war with the other major powers of the Alpha Quadrant. Throughout the series, loyalties and alliances change repeatedly: pacts with the Cardassians are made, broken, and remade; a short war with the Klingons flares up and is settled, and (through Sisko's secret machinations) the formerly neutral Romulans ally with the Federation.

An example of DS9's darker nature is the introduction of Section 31, a secret organization dedicated to preserving the Federation way of life at any cost. This shadow group, introduced in "Inquisition", justifies its unlawful, unilateral tactics by claiming that it is essential to the continued existence of the Federation. Section 31 features prominently in several episodes of the Dominion War arc; such plot elements, as well as DS9's relative lack of exposure compared to its predecessor, garnered the show a reputation as the "black sheep" of the Trek family.

In DS9, the Ferengi are no longer an enemy of the Federation, but rather an economic power whose political neutrality is, for the most part, respected. A number of episodes explore their capitalistic nature, while others delved into the race's sexist social norms. Unlike their depiction in Star Trek: The Next Generation, where they were generally portrayed simply as sexist buffoons for comedic purposes, in DS9, they received a more complex depiction, with the female partner (Ishka) of the Grand Nagus leading a women's rights rebellion on the Ferengi homeworld, and Rom, Quark's brother, leading a strike against unfair working conditions in Quark's bar. Also, Jake's best friend, Nog, has to deal with Starfleet's more liberal attitudes towards women as a Starfleet cadet while Jake learns to deal with his friend's more backward ideas in a respectful manner rather than risk the loss of their friendship.