Kira believes a Valerian ship is smuggling Dolemite weapons to the Cardassians, but Sisko refuses to detain the vessel unless she has evidence. Before they can resolve their conflict, a damaged Klingon vessel comes through the Wormhole and one of its crew transports aboard Deep Space Nine as the ship explodes. The bloodied man, later discovered to be the ship's first officer, whispers, "Victory!" and dies within seconds. As the vessel was only supposed to be conducting a biological survey, the crew investigates. While inquiring at Quark's, Odo's head splits in two and he collapses.
He awakens in the Infirmary, and while Bashir is unable to find what is wrong with Odo, he hints at potential trouble between Kira and Sisko. When pressed for more information, he says it is "too early to commit oneself either way." By this time, Kira has found evidence of foul play among the Valerians, but when she informs Sisko of her intention to confiscate their cargo; he forbids her from doing so. Meanwhile, Dax and O'Brien travel to the Gamma Quadrant to find the Klingons' mission recorder.
O'Brien mentions the mounting tension during their trip and makes his loyalty to Sisko clear to a complacent Dax. They find the mission recorder and bring it back to the station, where Kira attempts to win Dax's loyalty. While the others form alliances, however, Dax seems lethargic and only seems interested in reminiscing about the past. When Kira finds Quark attempting to eavesdrop, Kira nearly kills him.
Quark comes into Odo's office wearing a neck brace and announces his intention to file charges. When he mentions Kira's attack, Odo is more interested in the alliances that seem to be forming so quickly and decides to talk with Sisko; after he leaves, it is clear that Quark did not need the neck brace.
In Sisko's office, Odo finds O'Brien, who is reviewing the Klingon captain's log. Odo visits Sisko in his quarters and warns of the parallels between the bloody mutiny that apparently occurred on the Klingons' ship and what is now happening on the station, but Sisko has begun meticulously constructing a clock and cannot be bothered. Kira is waiting for Odo when he returns to his own office, and she solicits his help in her plan to eliminate Sisko and O'Brien. She even offers to make Odo her first officer once she is in command. He pretends to go along with her and decides to review the Klingon log further.
Before the Klingons' mutiny began, they discovered a collection of energy spheres with telepathic imprints of an ancient power struggle that destroyed an entire race. While Odo is reviewing the log, the plot thickens as O'Brien informs Sisko that the Valerian captain has agreed to take them with him once O'Brien helps him escape. Odo visits Bashir again and they realize the imprints from the spheres are causing the crew to reenact the aliens' power struggle, with Odo being the only one unaffected due to his non-humanoid brain. Odo manages to trick the possessed Bashir - whose controlling influence wants to wait and see about which side to join - into helping him.
Bashir develops a way of removing the telepathic signals from the crew and Odo uses the fact that both Kira and Sisko trust him to lure both sides into one of the station's cargo bays. There, Odo and Bashir surprise them as they are about to kill one another. Odo activates Bashir's cure. A cloud of purple gas-like material emerges from the crew and they demand to know what is happening. He tells everyone to grab hold of something stable and opens the cargo bay doors, venting the gas into space and removing the telepathic imprint permanently.