There are decided differences between heroes and saints, and while Deep Space Nine tried to separate itself from its Trek forerunners by painting its characters as the former rather than the latter, "In the Pale Moonlight" is when the series finally embraced that distinction and found a whole new layer of storytelling, depth, and relevance.
Sisko and his Cardassian ally Garak are trying to convince the Romulans to join Starfleet and the Klingons in repelling the Dominion invasion of the Alpha Quadrant. They do so by first attempting to find proof of the Dominion's long-term intention to subjugate the Romulan Empire. The plan fails, so Garak convinces Sisko to manufacture the necessary evidence — a moral concession that Sisko rationalizes by declaring that clearly the Dominion will eventually invade Romulus and the only way to save the Romulan people (and the Federation) is to bring them into the war before it's too late.
In the NextGen episode "The First Duty", Capt. Picard declared that Starfleet was above all devoted to the truth. Here, Sisko declares that Starfleet is devoted to protecting the Federation, truth be damned. From there, the moral line becomes grayer and grayer until Sisko finds himself complicit in what could be termed the assassination of a Romulan Senator — a betrayal of his principles that not only brings the Romulans into the fight but, far worse, Ben Sisko can live with.
In this war, the ends justify the means, and Ben Sisko is a hero, but far from a saint. This is the day that Star Trek grew up, and no episode showed how much or how far DS9 expanded and enriched the franchise more than this one.
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