As Julian Bashir prepares to go to a conference on Romulus, Luther Sloan shows up in his quarters with a Section 31 assignment.
Bashir boards the USS Bellerophon, where Sloan explains that the assignment is to visually confirm the rumor that Koval, the anti-Federation head of the secretive Tal Shiar Romulan intelligence agency, and a candidate for a seat on a powerful Senate committee (The 'Continuing Committee'), suffers from Tuvan syndrome, a condition that primarily affects Vulcans and Romulans. Bashir discusses the issue with Admiral William Ross. Ross says it would be better if Federation-friendly Senator Cretak gained the empty seat on the continuing committee as she was a patriot and publicly supported the alliance against the Dominion.
Koval deliberately seeks out Bashir at the conference and asks about a disease called "The Quickening" which the Dominion introduced to a planet in the Gamma Quadrant (see The Quickening (Star Trek: Deep Space Nine)) and how that could be induced into a planetary population. Bashir chairs a symposium on the subject at hand and later tells Sloan that he believes he does have Tuvan syndrome although he does express concern that the head of the Tal Shiar is asking so many pertinent questions about "The Quickening". Sloan says he doesn't care about that question but instead asks how the disease could be accelerated. Naturally, Bashir suspects that Sloan wants Koval killed in a way that makes it look like the Romulan's illness took a turn for the worse. Bashir decides to inform Admiral Ross, who plans to have Sloan arrested. Ross muses that Sloan could have an accomplice on Romulus to actually carry out the plan as they are both watching Sloan, and orders Bashir into silence.
The next morning Bashir overhears that Ross has suffered from an aneurysm and spies Sloan looking smug at the next table. With nowhere else to turn, Bashir approaches Senator Cretak and tells her of his suspicions about Sloan. Cretak views the information as appalling at first, but believes Bashir's good intentions enough to help him by giving him classified Tal Shiar information. Bashir tries to delay Sloan's timetable by telling him he needs a tissue sample for confirmation of the diagnosis as said the visual symptoms could be any number of diseases. Sloan has Bashir's hand treated with a micro-adhesive that will serve as a skin sample collector during a handshake.
Bashir is able to shake Koval's hand but is then immediately taken into Romulan custody and tortured. He and Cretak are brought before the Continuing Committee where Koval elaborates on the plot and brings in a tortured Sloan. Koval discloses that the plot as Bashir has described is actually the work of a renegade Starfleet Intelligence operative obsessed with getting revenge for his mentor's (Vice Admiral Fujisaki) death. Koval says he doesn't know whether Bashir was in on the plot or was a tool of Sloan. The Committee decides that by assisting Bashir, Senator Cretak has committed an act of treason and will be sentenced later. Dr. Bashir gets returned to the Bellerophon, and Sloan is handed over to the Tal Shiar for further interrogation. Enraged by this, Sloan grabs a guard's disruptor but Koval fires his weapon vaporizing him.
Back in his quarters on the Bellerophon, Bashir lies in bed and suddenly realises that he has been had. He marches off to meet with Admiral Ross and asks the whereabouts of Sloan, concluding that the man who was described by Koval was not the same man who tried to recruit Bashir into Section 31. They agree to have an off the record conversation and make a point of removing their communication badges.
Ross elaborates that the real mission was to get Koval into the Continuing Committee where he would advocate continuing the alliance with the Federation as opposed to his previous opposition to it. He also admits that Senator Cretak was not the supporter of the alliance the way Bashir thought; that Cretak was a "patriot" and if she thought it in the best interest of the Romulans to abrogate the alliance then she would pursue that avenue. Cretak would definitely be dismissed from the Senate and imprisoned, and probably be executed for her role in the affair. This angers Bashir which causes Ross to utter the quote from Cicero: "Inter arma enim silent leges." Bashir retorts that perhaps the Federation has become "a 24th-century Rome, guided solely by the principle that Caesar can do no wrong!" Ross picks up his communicator and pins it back onto his chest saying that their conversation never happened. Bashir picks up his communicator and briefly looks as if he is willing to throw it back onto the table in disgust before exiting the room.
Back aboard Deep Space Nine, Sloan shows up in Bashir's quarters, explaining that he needed a man of conscience for the operation, that the Federation needs men of conscience. He adds that the Federation also needs men like Sloan to defend men like Bashir before he turns to leave. Bashir initially calls Odo, but decides not to report Sloan's visit, instead reflecting on the words of Section 31's agent.