Inter Arma Enim Silent Leges (*****)
Another one of DS9's masterpieces and my favourite episode of the show, I also reckon it has the hardest plot to follow (though after a couple of viewings it all makes sense) which is an oddity because usually trek episodes make you think about the higher moral concepts and not the actual plot itself.
What I love is how the episode jacks you around with who's doing what, who's plotting what and what is the desired outcome to all this intrigue. Finally the pay-off (and an episode like this needed one after all the complicated shenanigans) NOT only makes sense but is very VERY satisfying and I think portrays Starfleet Command in a very different light. The common perception (in the Trek universe) is that Starfleet is all about exploring the unknown and protecting civilians through honourable means.
But really that's an illusion -- something which this episode and others (Paradise Lost) have hinted at, but this episode suggests this far more strongly -- someone has to do the dirty, disreputable and sometimes immoral work to ensure the Romulans, Klingons, Cardassians and other races out there don't bury the Federation six feet under. Section 31 is the dark side of the Federation to ensure the Federation remains this peaceful utopia. The fact Section 31 was shrouded in such secrecy suggests to me a lot of blue pill (the Matrix reference to sticking ones head in the sand, ignorance is bliss, etc...) thinking amongst Starfleet's top brass, High Council and so forth- something which first the two Borg incursions and then the Dominion war made them completely re-evaluate such blue sky thinking (in which I think Ross was like that until the Dominion war came in).
But man this episode is tight; it all rested on that last conversation between Ross and Bashir and that scene nailed it! If anything that was the climax, whilst Sloan popping up to visit Bashir in his quarters as merely the icing in the cake.
It's a pity this is the last episode of Star Trek to really evaluate how the Federation works and to do so in an unbiased way. VOY never came close to touching this; it didn't have the balls to do so, as for ENT... I've only seen the first two seasons and part of season 3 so I wouldn't know. But Inter Arma Enim Silent Leges marked the last of the thinking man's Star Trek; you know episodes which really made you think about this made-up universe.