O'Brien returns from a security briefing to find everyone on the station acting strangely toward him. Before long, O'Brien suspects a far-reaching conspiracy that encompasses everyone on DS9 and possibly into Starfleet Command. His suspicions continue to mount as he discovers his activities constantly being monitored, his orders changed without his notification, and station security measures consistently shutting him out of the loop with no explanation or apparent reason.
"Whispers" is an original take on the paranoid thriller, with expert scripting by Paul Robert Coyle, who creates unexpected twists, turns, and revelations that manage to plausibly build a sense that O'Brien is the only remaining individual who hasn't been "gotten to." The first-rate direction by Les Landau evokes a sense of altered reality in every scene, where characters seem to be only slightly different from what they should be, but different enough to seem threatening and to arouse our suspicions alongside O'Brien's.
Told in flashback, the carefully constructed narrative relates the crew's inexplicable half-truths and cover-ups strictly through O'Brien's point of view. In one eerily photographed scene, O'Brien finds himself convinced that food his own wife prepared may be poisoned. Colm Meaney brings his usual credibility to the role, with a textured performance that highlights the character's ability to plan ahead, think on his feet, and attempt to set things right—even in the face of such bleak odds. Once O'Brien escapes the station, he finds what promises to unravel the mystery for us, which is when the story drops the unexpected twist on us: O'Brien is the conspirator—unwittingly—a clone who honestly thinks he's O'Brien but has been programmed as an assassin by an alien government.
The uncovering and death of the clone is unexpectedly tragic and moving—the irony of the old adage that "perhaps it's not everyone else who is wrong, but just you" couldn't be more clear. Other than the slightly dialog-heavy final scene, which feels a bit too much like it was written for the audience's benefit, this is a superbly envisioned episode that ranks among the most deftly constructed mysteries on Trek. The way the clues play toward the two different perspectives (both the false O'Brien's and the rest of the crew's) is brilliant.