Newly-promoted Sisko and Co. have been dispatched to "show the flag" near the border of a hostile race known as the Tzenkethi, with whom the Federation have already fought one war. Once they reach the aliens' space, though, they lose control of the ship, which is then programmed to attack a Tzenkethi colony. There is a shapeshifter on board, and Sisko and his crew have to work hard to figure out where (or who) it might be. At this point, if you haven't seen the episode, you might want to stop reading or you'll accidentally learn that it's Bashir, not Eddington, who the Changeling is impersonating.
It's a wonderful ruse on the part of the writers, though. Eddington has never exactly been a comforting presence. He was introduced as Odo's professional rival, and in "The Search, Part II", he was the chief collaborator in the Dominion's fantasy game for the Defiant officers. Admittedly, the latter wasn't really Eddington, but sabotaging the cloaking device in "The Die is Cast" certainly didn't help. As a result of these instances, when his changeling "identity" is revealed, we see it as only natural--maybe he's been one all along? I read somewhere that after watching the episode, people didn't believe that Eddington wasn't a Changeling, even though the real Bashir was shown. That the show's writers were able to cultivate the "Eddington mystique" and then so effectively pull out the rug from under us is what makes the twist in this episode such a good one. Then again, there is a big hint earlier on (when Eddington talks to Odo) that indicates that he isn't, but it's too subtle to catch the first time around.
There are other important events in the episode: the aforementioned promotion, Sisko's realization that blood tests can screen changelings, and Odo's chilling revelation at the end of the episode, which sets up the excellent (and quite relevant) plot of the mid-season two-parter in Season 4.
Of course, you shouldn't get too comfortable with the idea of Eddington as a good guy. His understated scene with Sisko in the episode is full of subtext. He's got secrets, and they eventually come into view--in a big way--in Season 4.