In the replimat, knowing Dr. Bashir is preparing for a conference on Romulus, Elim Garak reminisces about his former Romulan assignment as a gardener of sorts in a Cardassian embassy and notes to Bashir how everything on Romulus is grey: the buildings, architecture, the people, even the Romulan heart. He expresses distaste at how dull and unimaginative they are. That night, Bashir wakes to find Section 31 operative Sloan in his quarters. Sloan tells him that he will be called upon to perform an intelligence assignment on Romulus, alluding to Bashir's affection for romanticized spy stories in a holosuite, but providing the dear doctor something real to take up this time. He leaves and Bashir chases after him with a phaser, but only finds Ezri in the corridor. In Sisko's office, the captain explains that he and Vice admiral William Ross want Bashir to pretend to go along with Sloan's assignment.
Bashir boards the USS Bellerophon, an Intrepid-class ship that is transporting the conference delegates to Romulus. He makes conversation with Ross and Senator Cretak before Sloan appears, undercover as a civilian delegate. In private, Sloan shows Bashir a hologram of Koval, the head of the Tal Shiar intelligence agency and a candidate for a vacant seat on the Romulan Senate's powerful Continuing Committee. Koval is suspected in the death of Admiral Fujisaki of Starfleet Intelligence, and is opposed to the Federation-Romulan alliance. Sloan wants Bashir to observe Koval for confirmation of the rumor that he is afflicted with Tuvan Syndrome. Bashir discusses the matter with Ross, who would rather see Cretak fill the vacancy, but expresses reservations about the Federation appearing to meddle in Romulan politics.
At the conference, Koval approaches Bashir and asks him about the Dominion's Quickening virus. Bashir invites him to the presentation on it he will give later. Cretak, who witnesses the encounter, jokes that Bashir should be recruited by Starfleet Intelligence, because Koval rarely speaks to anyone, especially her. She volunteers a few insights into Romulan life and how much the Tal Shiar has permeated their society.
Bashir gives his presentation about the Quickening, and afterwards Koval asks him if he knows how it could be introduced into a population. Back on the Bellerophon, Bashir tells Sloan about the encounter, and that because of certain subtle symptoms, he believes Koval does have Tuvan syndrome. Sloan shows considerable interest in the illness, and asks how it could be accelerated. Bashir explains to Ross his fear that Koval is about to be assassinated, and his suspicion that Sloan has a Romulan accomplice who will carry it out. Ross tells him that Sloan will be arrested. Later, Bashir overhears that Ross collapsed and is unconscious. He is unable to contact DS9, and cannot trust anyone on the Bellerophon, so he goes to Cretak. She is appalled by the assassination plot, but gives in to Bashir's request to access classified information that may reveal Sloan's accomplice and prevent the murder.
In an attempt to delay the assassination, Bashir tells Sloan that he may have been wrong about Koval's diagnosis because he has only studied the disease's effect on Vulcans, and needs a tissue sample to confirm it. Sloan has Bashir's hand treated with a microcellular adhesive that will collect the sample. Bashir approaches Koval and shakes his hand. Koval asks to speak to him in private, and Bashir follows but discovers that he has been brought to an interrogation room.
Koval uses a Romulan mind probe to find out what Bashir knows, but his genetic enhancements allow him to resist. He and Cretak are brought before Praetor Neral and the Continuing Committee. Bashir describes Section 31, Sloan, and the assassination plot. However, Koval brings in a physically abused Sloan and reveals what Bashir does not know: that Section 31 does not exist. Sloan was a Starfleet Intelligence agent and Admiral Fujisaki's protégé, and invented Section 31 so that Starfleet would not be blamed for his personal revenge on Koval. The committee finds Cretak guilty of treason and remands Sloan for further interrogation. Sloan grabs a guard's disruptor but Koval shoots first and vaporizes him.
On their way back home Bashir confronts a recovered Ross and insists that the admiral knows that Sloan is alive. Off the record Ross confirms that Sloan's death was a faked by beaming away before being hit. Section 31 does exist and Koval is a Starfleet agent who will soon be in a more powerful, and informative, position. Ross declares "inter arma enim silent leges." Bashir is disgusted by the comparison of the idealistic Federation with realist Rome. The admiral justifies his cooperation with Section 31 by citing the growing wartime casualties under his command.
Back on DS9, Bashir wakes to find Sloan again. Sloan explains that he chose Bashir for his conscience, which would cause him to try to stop the assassination, and play into the charade. He praises the doctor but explains that other people, who are less ethical, are necessary to protect the idealists. After he leaves, Bashir calls security but, realizing that there's no point, cancels the call.