Bashir and O'Brien travel to a lab orbiting T'Lani III in an effort to eliminate the Harvesters — a deadly bio-mechanical weapon used in the centuries-long war between the Kellerun and T'Lani societies. Working with scientists from both races, they finally find a solution, and the Kellerun Ambassador, Sharat, orders the group to destroy the entire remaining supply. However, just as their mission is about to be accomplished, two armed Kellerun soldiers enter the lab and start firing. Bashir and O'Brien manage to kill their assailants, but fail to notice that during the fighting, a small amount of Harvester material spilled onto O'Brien. As more Kellerun soldiers arrive, the pair attempt to transport to their Runabout, but are unable. Instead, they beam to the surface of T'Lani III.
Ambassador Sharat and T'Lani Ambassador E'Tyshra inform Sisko that O'Brien and Bashir were killed when O'Brien accidentally activated a hidden security device that emitted a deadly pulse of radiation. They hail the pair as heroes and give Sisko a video recording of the tragedy. Sisko, Dax, Odo and Kira later view the recording, and, not realizing it has been altered, accept that their crewmates are dead. Back on T'Lani III, however, Bashir and O'Brien are alive, and have set up a base in a deserted military command center in hopes of finding a way to communicate with the space station. O'Brien begins to work to repair an old com-panel, but suddenly feels feverish. Bashir examines him, and reveals that O'Brien has been infected by the Harvesters.
Sisko is saddled with the difficult news of telling Keiko O'Brien of her husband's demise. After viewing the tape, Keiko points out a major inconsistency. The tape shows O'Brien drinking coffee in the late afternoon — something Keiko insists he never does. She believes this indicates the tape has been tampered with, and Sisko travels to T'Lani III with Dax to find out why. Meanwhile, with O'Brien's coaching, Bashir works to repair the companel. O'Brien continues to worsen, and is horrified to discover that he can no longer feel his legs.
Despite his condition, O'Brien is able to help Bashir get the companel up and running, and Bashir sends out a weak distress signal. Sadly, both realize that O'Brien will probably die if the signal is not answered soon — by the right people.
Meanwhile, Dax tells Sisko five minutes have been erased from the computer log on Bashir and O'Brien's Runabout, and that the time of the erasure proves that the pair could have been alive after they were supposedly killed. Soon afterward, E'Tyshra and two T'Lani soldiers arrive at Bashir and O'Brien's hiding place. The pair are thrilled to see them, until Sharat and his soldiers also arrive. Together, the Kellerun and T'Lani officials inform Bashir and O'Brien that they must be killed since they know too much about the Harvesters and could reproduce them.
Just as a soldier prepares to kill them, Bashir and O'Brien are beamed away to their Runabout, where Sisko and Dax are waiting. Bashir immediately injects O'Brien with a hypospray and the group flees the area. However, they soon realize that a T'Lani vessel is pursuing them. The enemy ship fires a warning shot and Sisko hails his assailants, who demand Sisko turn over Bashir and O'Brien. Sisko refuses and sends the Runabout directly toward the T'Lani vessel. Seeing no other choice, E'Tyshra and Sharat blow up the Runabout, only to realize that Sisko, Dax, O'Brien and Bashir transported to a second Runabout and have left the area. The group arrives safely home, and O'Brien is able to recover.