On the eve of Dr. Bashir's departure for a conference on the Romulan homeworld, he's visited by Sloan, the director of Section 31, a secret and unsanctioned extremist entity within Starfleet Intelligence.

Sloan asks a reluctant Bashir to gather information on the Romulan leadership. Bashir reports the request to Sisko, who worries that although Starfleet Command has officially condemned Section 31, someone in its membership may actually be protecting the group. After consulting with Admiral Ross, Sisko advises Bashir to play along with Sloan in order to determine Sloan's motivations.

En route to the conference, Bashir and Ross run into Sloan, who is posing under an assumed identity. Later, Sloan gives Bashir the job of diagnosing whether or not Koval, a key Romulan who opposes the Federation Alliance, is suffering from a degenerative disorder. Sloan hopes to use that knowledge to block Koval's assignment to the Romulans' powerful Continuing Committee.

Shortly after arriving on Romulus, Bashir meets Koval. When Sloan queries Bashir about Koval's health, it becomes clear to Bashir and Ross that Sloan plans to assassinate Koval by accelerating his illness. Ross vows to arrest Sloan to prevent the deadly plot from moving forward, but to Bashir's dismay, Ross is apparently felled by an aneurysm before detaining Sloan.

With Ross incapacitated, Bashir shares his suspicions about Sloan's intent to assassinate Koval with Senator Cretak, and presses her to access top secret documents from Koval's database to help thwart the murder. Meanwhile, a wary Koval turns the tables on Bashir by luring him into an interrogation, where he uses painful, but ineffective, tactics to ascertain for whom the doctor is working.

Bashir is brought before the Continuing Committee, where he learns that Cretak was arrested for trying to tap into Koval's database. What's more, Bashir is led to believe that Section 31 is nothing more than an elaborate cover for Sloan's personal desire to avenge the death of his mentor. But after Sloan is vaporized by Koval while trying to escape, Bashir confronts Ross. The admiral admits that Koval is a Romulan "mole" working for the Federation and that Sloan is still alive — and still running Section 31, which "officially" doesn't exist.