Following Commander Benjamin Sisko's promotion to Captain, he learns that a neighboring race may soon engage in war with the Federation. He brings the Defiant and Ambassador Krajensky along to help negotiations. Along the way, oddities occur on the ship and the crew suspects there may be a Changeling infiltrator. It is revealed to be Krajensky, but it is too late; he has already sabotaged the ship to the point it could instigate a war. After hours of searching, the crew tries to find the infiltrator with blood screenings but are unsuccessful. Sisko readies the ship's self-destruct while Chief O'Brien tries to override the Changeling's systems. Odo fights the Changeling in main engineering and ends up killing him (becoming the first changeling to harm another). It is then revealed that Krajensky may have long been dead and this was a Dominion plot to destabilize the Alpha Quadrant. Back at Deep Space Nine, Odo reveals the cryptic message the Changeling said before he died: "You are too late. We are everywhere".
This episode introduces the idea of blood testing to tell who is or isn't a Changeling. At one point Sisko points out that several people in a certain setting could be a Changeling, including himself. But Odo points to a bleeding wound on Sisko's hand. Humanoid blood, once it leaves the body, is dead tissue; "blood" leaving a Changeling's body would revert to shapeshifting jelly. This suggests a simple effective way to test a person suspected of being a Changeling. The idea is reminiscent of John W. Campbell's classic novella, "Who Goes There?", made into two movie versions both called The Thing, in which scientists at an Antarctic weather base devise a similar test to detect who has or hasn't been infected by an alien creature that can perfectly mimic other life forms. Sisko's own father would point out a possible flaw in the test in the episode "Homefront".