Frustrated by the mechanical problems on the space station, O'Brien attempts to fix the food replicators. Little does he know, an Bajoran device planted by the Resistance was intergrated into the replicator's circuitry. For some unknown reason, O'Brien speaks to Kira in gibberish when she approaches him in the Ops center. Bashir examines him and finds no physiological damage, and diagnoses him with an unusual form of aphasia - a dysfunction in the brain that renders him incapable of expressing himself to others. Soon, Dax also falls victim to the mysterious ailment.
Suspicious of the nature of this aphasia, Bashir runs a neuro-synaptic comparison of Dax and O'Brien and finds that they share a common virus. Sisko and Bashir encounter two more afflicted crewmembers, and Sisko establishes a quarantine on Deep Space Nine.
Odo discovers that Quark has illegally accessed crew replicators to fulfill his orders, inadvertently contaminating all of his customers with the strange virus in the command level replicators. On a hunch, Bashir tests an air sample and learns the virus has mutated to an airborne form - meaning the station population may get infected.
Upon close inspection of an access tunnel, Kira encounters the alien device that O'Brien unknowingly triggered to unleash the virus. Kira suspects Cardassian sabotage. All crewmembers agree something must be done soon, due to the epidemic proportions the virus has reached. Not even Dax and Jake could escape contamination.
Bashir then informs Sisko that the virus was probably created by Bajorans, and Sisko assigns Kira the task of investigating this theory. Meanwhile, O'Brien has contracted a high fever and may die if Kira does not quickly find an antidote. Kira manages to locate Surmak Ren, an underground Bajoran scientist who seems to know something about the virus.
Meanwhile Sisko and Odo attempt to prevent Jaheel from breaking quarantine by leaving Deep Space Nine. Jaheel doesn't comply with Sisko's order, and his efforts in breaking away put the docking ring in jeopardy. While trying to rectify the situation, Sisko comes down with the virus, rendering his commands incomprehensible. Odo and Quark take control, and are able to push Jaheel's ship free of the docking port.
At the same time, Kira, determined to find the antidote, orbits Bajor in a runabout and transports Surmak aboard against his will. Surmak eventually agrees to help develop an antidote, and follows Kira to Deep Space Nine. Fortunately for all, Surmak is successful and life on the station resumes a normal pace.