Kira protests when Sisko allows a Valerian ship to dock at the station, because she believes that the Valerians are supplying weapons-grade dolamide to the Cardassians. However, before the Valerian ship even arrives, a Klingon vessel blasts through the wormhole and explodes. One critically injured Klingon from that ship transports to the station, shrouded in a strange violet light, and dies immediately after uttering the word "victory" — a curious declaration since his ship was supposed to be on a scientific mission. Dax and O'Brien are sent in a Runabout to search for the ship's mission recorder. While the Valerian vessel docks, despite Kira's unusual efforts to delay it without Sisko's knowledge. Odo learns from Quark that the Klingon mission involved procurement of something that would "make the enemies of the Klingon Empire tremble." Suddenly, Odo mysteriously becomes paralyzed with pain, his head splits in two, and a panicked Quark calls for Dr. Bashir.
When Odo regains consciousness in Bashir's infirmary, he is struck by the doctor's cold, calculating tone and his sudden interest in Kira, Sisko, and the Valerian situation. Meanwhile, Kira and Sisko have an uncharacteristically angry exchange over the Valerians, while aboard the Runabout, Dax and O'Brien also seem to undergo personality changes, O'Brien turning very cold and suspicious, asking Dax whether her loyalties lie with Sisko or Kira, while Dax becomes dreamy and removed. Kira, taking on a sensually manipulative tone, later tries to convince Odo to go behind Sisko's back and sneak aboard the Valerian ship — Odo refuses.
Dax and O'Brien show a barely-legible recording made by the dead Klingon indicating mutiny aboard his ship, and the presence of some alien energy spheres, but Sisko doesn't seem to care. Soon afterward, Kira approaches Dax and tries to enlist her allegiance against Sisko, attacking Quark when she notices him eavesdropping. Quark complains to Odo and tells him of Kira's plot against Sisko. Noticing the odd behavior developing among the personnel, Odo goes to find Sisko in Ops, and is shocked to see O'Brien sitting in Sisko's chair, settled in like he owns the place, trying to piece together the mission recorder's log entries. O'Brien tells Odo he believes Sisko's life is in danger because of the mutiny Kira is planning. Odo finally locates Sisko in his quarters, telling him that he fears what happened on the Klingon ship may be occurring on the station. Sisko, however, is only concerned with designing a clock. Odo realizes at this point that he's on his own.
When Odo returns to his office, Kira surprises him with news that she has made sure the Valerian ship cannot leave until she lets it. He learns that Kira is about to go after Sisko and O'Brien. Hoping it might provide an explanation, Odo reviews the reconstructed journal of the dead Klingon and finds a mention of telepathic energy spheres, containing an archive which described a power struggle that destroyed an ancient alien race called the Saltah'na. Odo cautiously approaches Bashir for help, making the suspicious doctor believe he's working to benefit whoever seizes control of the station. They theorize that the Klingon ship was destroyed after an energy matrix from the spheres affected the crew's minds, causing them to reenact that struggle. The Klingon apparently brought the matrix to the station inadvertently, and it influenced everyone in Ops but Odo. While Bashir works to eliminate the matrix's effects, one of his allies tries to attack Sisko with a tiny device. Sisko retaliates against the young ensign, sure that Kira put him up to the mutinous action, until Kira herself arrives, pointing a phaser at Sisko.
Before Kira's guards can take Sisko and O'Brien, the pair dematerialize and beam into an airlock, from where they attempt to escape to the Valerian ship, enlisting Odo's help to eliminate the forcefields blocking their path. Odo lures all the affected individuals together, then activates Bashir's matrix interference signal. The violet-colored energy influence is successfully purged long enough for Odo to release it into space. Life returns to normal on the station, and Sisko and Kira bury their differences.