Starting in season 3, the writers made sure to spend at least one episode per season advancing the Prophets arc - which, in some ways, matched the Dominion War in importance. This episode continues that arc, while unifying a few other loose ends and propels the story toward the final season.
Along with the "blurred boundaries between good and evil" theme, the Prophets arc did more than any other element of DS9 to break with the traditional, hyperscientific Star Trek universe. By this point, it's not clear whether Sisko's loyalties lie with Starfleet anymore, or even with his family! At its climax, the episode introduces an unusual element that I believe had never appeared in Star Trek before - two effectively supernatural beings battling it out, with humanity and other mortals reduced to mere spectators.
As usual, Louise Fletcher offers a wonderfully textured performance as the villanous Kai Winn.