On the eve of the election for Bajor's new Kai, Vedek Winn suspects Vedek Bareil of being a Cardassian collaborator and recruits Kira to help her find the truth. Kira—who is in love with Bareil—finds herself in a very difficult bind where her personal feelings are at odds with her duty to Bajor and the truth.
I like seeing characters put through the wringer like this; it's a good way to see emotional performances emerge, and Nana Visitor is one of the most credible and effective when it comes to projecting emotion onto the screen. There's never a question of whether Kira will find the truth or not; it's more a question of what she will find, and how she'll react emotionally to it.
The plot's twists and turns are probing, bringing up the issue of how to deal with Bajorans who sold themselves out to the Cardassians, and, further, looking at the reasons why people would be tempted to do such things. Odo makes a keen observation when he notes that in extreme circumstances everybody is capable of terrible things. (Was he referring to Kira's murder in "Necessary Evil"?)
Vedek Winn's political intrigue takes the character in some unexpected directions, particularly when she declares "peace" with Sisko in a scene that makes one wonder if she's being sincere or merely self-serving. Similarly, her belief that Bareil could be a collaborator gives her the perfect opportunity to milk the situation to her political advantage—yet her motives somehow seem deeper and more sincere than her superficial arrogance and condescending persona let on.
Kira's investigation takes her where she doesn't want to go—straight to proof that Bareil did help the Cardassians destroy a rebel base. His noble motives were to save Bajoran lives—an admission that will still cost him his political career. A last-minute twist privately confounds the situation even further, showing Bareil as a truly honorable man. If there's a subtext flowing through here, it certainly highlights how brutal and painful the Occupation was, even apart from the often-explored issues of killing.