Aboard Deep Space 9, Chief O’Brien is feeling both overworked and underappreciated. While he and his crew are in the docking pylon, trying to free several crew members stuck in a jammed airlock, a Boslic freighter captain, Jaheel, complains that O’Brien hasn’t yet fixed his ship’s antimatter flow converter; if his ship is left in dock for too long, the perishable goods aboard will be useless. After Jaheel exits with a rude comment, O’Brien is summoned to Lieutenant Jadzia Dax‘s science lab, where an incessant whine has been coming from her equipment. After fixing this, he rushes to Ops, to repair a conduit near Major Kira‘s terminal. Just as he’s thought he’s earned a breather, Commander Sisko gags on a mug of coffee delivered by the Ops replicator and asks the chief why it hasn’t been fixed yet. O’Brien grumpily makes his way down to the command level. “Can’t have the operations chief sitting around daydreaming when there’s work to be done, can we? Oh, ho, ho, I’ll get right on it!“, he says while leaving, causing Sisko and Kira to exchange looks.
After fixing the replicators, O’Brien asks for a cup of hot coffee, black, double sweet as a test. It tastes fine, but behind the panel, a long-hidden electronic device activates and starts sending a signal into the replicator.
In Quark’s, an angry Markalian customer, Asoth, complains to Quark about his terrible Kohlanese stew, forcing Quark to eat it. Odo recommends Quark ask O’Brien to fix his replicators, but warns wryly that O’Brien is a very busy man. After Odo leaves the bar, Quark breaks into the Cardassian computer system to find the location of a replicator on the station that isn’t broken.
Jadzia Dax, walking along the Promenade with Major Kira, discusses how odd it feels – being female for the first time in eighty years, she clarifies when Kira is confused. They notice Quark’s is busy as they pass, and Quark himself greets them to say that they’re having “a little party” to celebrate his replicators being fixed, and invites them to join in. Kira quickly excuses herself and tells Dax to go in if she wants. Dax is left flustered for a moment, before catching herself and smiling at Quark.
Back in Ops, Sisko thanks O’Brien for fixing the replicator; he also compliments the chief’s wife, Keiko, on being a good teacher to his son Jake in the station’s new school, which she recently opened. When Major Kira is speaking with O’Brien a moment later, his talk turns to gibberish, which no one can understand. He appears similarly unable to comprehend anything said by anyone else.
Dr. Bashir diagnoses the chief as suffering from aphasia: in effect, the connections in his brain between words and their meanings are scrambled. O’Brien tries communicating by writing on a PADD, but produces the same gibberish. As the senior staff discuss his condition in Ops, Lieutenant Dax is suddenly stricken with aphasia as well, unable to communicate with the people around her. In the infirmary, Bashir discovers that a virus has infected the brain’s synapses; as other crew members are afflicted, Sisko orders DS9 to be placed in quarantine immediately.
Odo notices that business is booming in Quark’s. When questioned, Quark lies and says his replicators were fixed by Rom; in fact, Quark is surreptitiously using the replicator of a quarantined crew member. Odo, disguised as a piece of furniture, catches Quark in the act soon after this.
Sisko finds his son Jake standing at the upper level on the Promenade after having been playing with classmate Nog. The concerned father orders his son back to their quarters. Sisko is now confronted by Jaheel, the impatient freighter captain, who is told to stay put.
Back in Ops, Sisko begins to suspect the replicators are spreading the virus. When Odo informs them that Quark has been supplying his entire menu with an infected replicator from vacant quarters on the command level, Bashir checks the station’s air, and determines that the virus has mutated into an airborne pathogen. They are now all infected; however, the virus has different incubation periods in different people.
While searching with a tricorder, Kira finds the device hidden in the replicator’s pattern generator. By now, 60 percent of the station population is showing signs of the virus. The replicators have been creating the virus (at the molecular level) within the food they have been producing.
While Kira initially suspects Cardassians are to blame, Doctor Bashir determines that the virus is actually Bajoran in origin; and the device is 18 years old, the same age as DS9 itself, built in 2351. Presumably it was made and placed aboard the station by the Bajoran Resistance, but never activated to carry out their attack against the Cardassians.
As Sisko takes Jake, recently afflicted, to crew quarters converted into a hospital ward, he tries to console Dax and O’Brien, but they still can’t comprehend one another. The situation soon worsens, as O’Brien is found unconscious in his hospital bed. The virus has attacked O’Brien’s autonomic nervous system, threatening his life. Bashir tells Sisko that O’Brien will be dead in twelve hours.
Using her old contacts in the Bajoran Resistance, Kira tries to discover the creator of the virus. Her search leads her to a Dekon Elig, a Bajoran Resistance member, but he is deceased. Through his death certificate she locates his assistant Surmak Ren, who was also a member of the underground. Surmak has now been repatriated to Bajor and is currently a medical administrator at the Ilvian Medical Complex. When Kira contacts him about the aphasia virus, he rudely terminates the connection.
Quark is still unaffected, for which he credits his Ferengi immune system. Odo warns him that, with DS9’s current skeleton staff, Quark will be held accountable for any thefts occurring during the quarantine. In the infirmary, as Dr. Bashir continues searching for a cure to no avail, he too is overcome by the virus, suddenly speaking gibberish to the medical computer and is forced to abandon his research.
Sisko allows Kira to pilot a runabout to Bajor to confront the uncooperative Surmak Ren; she assures Sisko she will not set foot on the planet (so as not to spread the virus). She abducts Surmak by beaming him onto the runabout without his permission. At first, Surmak protests that his involvement with the Resistance was minimal, and he is not to blame for the station’s current troubles. Kira snaps that she is not interested in assigning blame, just the cure for the virus. Surmak says he doesn’t know if Dekon even created a cure – for all he knows, a cure doesn’t exist. Kira informs him that she is infected with the virus, and now he has been exposed as well, so anything he knows about Dekon’s work had better be put to use, and quickly. They return to DS9 to help with the cure.
On DS9, Jaheel, the impatient and frightened freighter captain, decides to leave the station without permission. However, Sisko refuses to open the docking clamps mooring his vessel to the space station. As Jaheel increases power to his engines, the clamps become stuck in place. The freighter’s engine begins to overheat, threatening to explode – and take half the docking ring with it.
Odo suggests they explode the clamps to blow the ship clear of the station, but finds himself soon working alone, as Sisko now succumbs to the sickness.
When Odo broadcasts a call for help throughout the entire station, help arrives in the form of Quark, one of the few people left unaffected. After smugly advising Odo that they can discuss his compensation later, Quark assumes control of Ops, beaming Odo directly to the docking ring; Kira is stunned to find Quark answering her hail as she returns to the station. After boarding and showing Surmak to medical, however, she becomes the virus’s latest unintelligible victim.
Odo rescues the babbling freighter captain and jettisons the doomed ship just in time before it explodes. Surmak Ren, whose memory is refreshed about the virus once he looks at Doctor Bashir’s notes, quickly develops an antidote for the virus, curing everyone.
As things begin to return to normal, Sisko welcomes O’Brien back to Ops – only to find a moment later that the replicators are faulty once more.