From its inception, Star Trek: Deep Space Nine was intended to be morally darker than other incarnations of the venerable franchise. It took a look at the shady gray areas around the edges of the Federation, bringing realpolitik to Gene Roddenberry’s previously utopian vision of the future. Much of that centered around the show’s lead, Ben Sisko, a man who had to shoulder the practical burden of those ethical choices throughout the show’s seven-year run. And unlike previous Starfleet captains, he sometimes made unconscionable decisions in the name of a greater good, particularly during the Dominion War.
That was by design, allowing the writers to explore moral dilemmas in a way that hadn’t appeared on Star Trek before. The Dominion were conceived as a threat unlike anything that had appeared in Star Trek before -- a fascist theocracy whose rulers, the Founders, acted as living gods. They possessed vast military resources, cunning political saboteurs and the shape-shifting Founders, who could perfectly imitate anyone they wished. They launched a war of conquest against the Alpha Quadrant, forcing the Federation to join forces with longtime enemies in order to stand a chance. And in many cases, they had to do much worse.
Sisko became the fulcrum for that, making calls in the name of the greater good that routinely violated the Federation’s principles. Some of them even went so far as to be classified as war crimes. He committed them for the sake of the Federation, allowing it to survive and ultimately claim victory in the war. But the cost to his soul was enormous, and while the greater good prevailed, it often took the moral compromise of a good man to do it. Indeed, fans can point to these four specific points as instances in which Sisko crossed a clear moral line in order to secure victory.
Sisko Launches Biological Weapons
Sisko’s first definitive break with Starfleet's principles came in his pursuit of Michael Eddington, a former underling now leading the terrorist Maquis. Eddington attacks Cardassia with a biogenic weapon, and Sisko threatens to respond in kind, launching bombs against a Maquis colony made of trilithium resin that will render the planet uninhabitable to humans but won’t affect Cardassians. When Eddington calls his bluff, Sisko launches the bombs, poisoning the planet and forcing its civilian population to flee or die. He threatens to do the same thing to every Maquis colony unless Eddington surrenders, and as his foe notes, it makes him everything Starfleet is supposed to stand against.
Sisko Massacres a Jem’Hadar Force
Season 5 ended with the Dominion and their Cardassian allies in control of Deep Space Nine and Sisko commanding the Defiant. Season 6, Episode 2, "Rocks and Shoals" presented the crew of a crashed Defiant facing off against a similarly crashed Jem’Hadar vessel. With supplies of ketracel-white running out -- turning his forces into mindless killing machines -- the Dominion commander plans to attack the Federation position and shares his plans with Sisko. Doing so guarantees his forces an honorable death and allows him to surrender to the Federation. Sisko tries to convince the Jem'Hadar soldiers that they have been betrayed, but they attack anyway, forcing him to cut them all down.
Sisko Convinces the Prophets to Destroy a Jem’Hadar Fleet
The Federation’s main method for holding off the vast majority of Dominion forces was a field of self-replicating mines at the entrance to the wormhole. When the Dominion finally disables the field in Season 6, Episode 6, "Sacrifice of Angels," Sisko and the Defiant enter the wormhole in a hopeless last stand against an invading fleet of thousands of ships. Victory arrivers when the Prophets make contact with him, and he convinces them to destroy the enemy fleet. They promptly wipe it from existence -- every single being on every single ship constituting perhaps hundreds of thousands of combatants destroyed in the blink of an eye.
Sisko Lies to Bring the Romulans into the War
If any moment could be called Sisko’s damnation, it comes with Season 6, Episode 19, "In the Pale Moonlight." Facing long-term defeat in the war, Sisko relies on deception to try to convince the Romulans to join the rest of the Alpha Quadrant. When the ruse falls through, Garak murders the pertinent Romulan before word can spread and frames the Dominion for the crime. When Sisko learns what Garak did, he does nothing. The Romulans falsely blame the Dominion and join the war based on a straight-up lie Sisko is prepared to perpetrate. And as he notes, he can live with it. The needs of the many prevail, but they exact a brutal cost in the process.