Dr. Bashir and Chief O'Brien have spent the past two weeks helping two races, the T'Lani and the Kellerun, dismantle deadly biological weapons known as "Harvesters" which were used by both sides in a centuries-long war. When Bashir finds the correct level of radiation to destroy a Harvester sample, everyone is speechless. The T'Lani and Kellerun ambassadors enter to see for themselves and O'Brien assures them that all files related to the Harvesters have been destroyed so as to prevent them from ever being created again. This means the two races can finally put the war behind them. He and Bashir then inform Commander Sisko that they plan to stay for a celebration once they finish destroying the remaining stockpiles of Harvesters and will return to Deep Space Nine in two days.
When the moment comes to destroy the final Harvester tube, Bashir ceremoniously places it in the machine so it can be destroyed. However, as the Harvester is being destroyed, two Kellerun soldiers enter the laboratory and begin shooting the scientists, T'Lani and Kellerun alike. Bashir and O'Brien manage to overpower the guards in the frenzy that ensues, but a drop of the Harvester liquid falls on O'Brien's skin. The doors locked and communications with their runabout jammed, they are forced to beam down to the surface of a planet whose population was devastated by Harvesters.
The T'Lani and Kellerun ambassadors inform Sisko that O'Brien and Bashir died in an accident and provide a video supposedly showing the officers' deaths. Meanwhile, Bashir and O'Brien are stranded in a ghost town. Taking refuge in one of the buildings, they decide to try to find a way of contacting the T'Lani to inform them of the Kelleruns' betrayal. Back on the station, the entire crew watches the video of the "accident," in which Bashir, O'Brien, and the scientists are vaporized instantly. They presume the men dead, and begin grieving them.
At O'Brien's suggestion, he and Bashir stay in the building where they have taken refuge in order to minimize the prospect of the Kellerun finding them. Small talk runs out and an irritable O'Brien appears to have a fever. Bashir looks at O'Brien's arm and realizes he has been infected by the Harvester. As O'Brien begins to lose coherence, Bashir takes over and works on their would-be communications device.
Sisko has the grim duty of informing Keiko O'Brien of the accident, and she can tell before he says a word. Dax tells Kira she has Bashir's medical diaries, which he gave to her some time ago to "help her understand him," and feels guilty because she never even read them. Even Quark mourns the officers' deaths, offering Kira and Dax each a free drink, a gesture that Kira notes is almost unbelievable. The crew resolve to go on without their two dead crewmates. However, Keiko brings the recording of the "accident" to Sisko's office and shows him that, according to the recording, her husband was drinking coffee in the afternoon - something she is certain he would never do. Sisko decides to investigate.
Back on the planet, O'Brien's condition deteriorates quickly.
Sisko and Dax visit the T'Lani ambassador, who allows Sisko to view the site of the "accident." While he is gone, Dax investigates O'Brien and Bashir's runabout and finds evidence of foul play. In the meantime, Bashir manages to get a signal to the T'Lani, but when the Kellerun show up as well, the ambassadors reveal that the "accident" was a joint endeavor meant to erase any knowledge that could potentially be used to make Harvesters. Sisko and Dax manage to transport Bashir and O'Brien to their runabout. The T'Lani and Kellerun destroy the runabout, only to discover that the crew beamed to the other runabout and escaped.
As Chief O'Brien recovers from the Harvester poisoning in sick bay, Keiko is stunned to discover that he does drink coffee in the afternoon, meaning the entire operation was done by accident.