Internal Affairs Officer Sloan arrives on the station, announcing that there has been a possible security breach. He believes an officer may be passing information to the Dominion and promptly confines the senior staff to quarters. Later, Sloan summons Bashir for a brief interview, which appears to go well. Back in his room, however, the doctor learns that O'Brien was interrogated for two hours — about him. Just then, Bashir is taken to a second meeting with Sloan.

Sloan questions Bashir about his time as a Dominion prisoner and picks apart the story of his incarceration and escape. He tells the doctor that because of his superior, genetically engineered mind, the Dominion may be using him as a spy without his conscious knowledge. Bashir doesn't buy the story, and Sloan angrily drags him to a holding cell.

When Sisko sits in on the next interrogation, Sloan reminds him that Bashir recently advised on surrendering to the Dominion, and that he lied about being genetically engineered. In a private meeting, Sisko asks Bashir if Sloan's theory is medically possible, and Bashir realizes that Sisko doubts his innocence. Later that night, Sloan arrives in Bashir's cell to take him to a starbase for further questioning, but the doctor is suddenly transported onto a Cardassian ship.

He is welcomed by Weyoun, who asserts that Bashir was indeed "broken" by the Dominion. Since he has no memory of being a spy, Bashir decides that Weyoun and Sloan must be working together to concoct the story. Just then, the Defiant attacks, and Kira and Worf take him back to their ship. As his fellow officers unite against him, Bashir notices something is wrong — O'Brien suffered a recent shoulder injury but shows no symptoms. Suddenly, everything fades away. He was in a Federation holographic simulation. Now, he faces the real Sloan.

Sloan explains that he works for a secret division of Starfleet Intelligence — Section 31 — that eliminates dangers to the Federation without answering to anyone. They secretly took Bashir from the station and put him through a series of tests, which he passed. Bashir is horrified when Sloan invites him to join their group, then turns him down. Later, when he tells his story to Sisko, who thought the doctor was at a medical conference, Bashir gets an unwelcome assignment. Sisko surmises that Sloan will not give up hope of recruiting Bashir, and that when he returns, Bashir must join the secret unit — as a spy for the captain.