Dr. Bashir's plans to attend a cushy medical conference are cut short when Director Sloan, an operative supposedly from Starfleet internal affairs, interrogates the senior staff on suspicion of treason. The investigation eventually focuses on Bashir, who is forced to defend himself against accusations that he is a deep cover Dominion spy. Bashir's search for the truth leads to him uncovering the existence of a clandestine organization that has operated in the shadows of the Federation from its very inception.
- All Just a Dream: The whole "internal affairs tries to find a spy on Deep Space Nine" plot turns out to be a simulation Section 31 created to test the loyalty of Bashir.
- Be Careful What You Wish For: Bashir has always engaged in spy fantasies and been fascinated with being a spy. Both Sloan and Odo remind him of this after Sloan makes his offer.
- Bluff The Imposter: How Bashir figures out that O'Brien isn't really O'Brien, and by extension that the rest of the bridge crew are imposters.
Bashir: Your shoulder...it's all right.
O'Brien: Of course it's all right.
Bashir: But you dislocated it yesterday when...you were playing springball.
O'Brien: So? It's better now.
Bashir: You didn't hurt it playing springball. You dislocated it kayaking in the holosuite. You're not Miles.
- Call Back: Sloan makes references to "Hippocratic Oath," "In Purgatory's Shadow," "By Inferno's Light," "Dr. Bashir, I Presume?," and "Statistical Probabilities" while trying to discredit Bashir.
- Chekhov's Gun: O'Brien's dislocated shoulder. Bashir treats it during The Teaser and tells him to take it easy. Later, when it looks like everyone is turning against him, a desperate Bashir grabs that same shoulder and notices when "O'Brien" doesn't flinch.
- The Conspiracy: This episode marks the beginning of the Section 31 storyline.
- Cuffs Off, Rub Wrists: Bashir just before going in the brig. The guard isn't very sympathetic.
- Good Is Not Nice: Section 31 is capable of anything, but all to defend the Federation.
Sloan: We search out and identify potential dangers to the Federation.
Bashir: And once identified?
Sloan: We deal with them.
- He Knows Too Much: Subverted. Sloan tells Bashir a good deal about Section 31, but returns him to the station when it's all over. Bashir threatens to expose him, but Sloan knows he has little reason to worry.
- Holding Your Shoulder Means Injury: O'Brien after yet another holo-kayaking mishap.
- Humans Are Special (or rather The Federation is Special): Part of a DS9 theme of putting a different spin on this to the older TNG style. The Federation is special not because it's the only major power not to have a secretive spy organisation like the Tal Shiar or the Obsidian Order, but because it's the only one whose organisation is so good that 200 years after its founding, its existence is still completely secret.
- Not So Different: Villainous version, for the Federation. Turns out even the good guys have some skeletons in the closet.
- No Such Agency: Section 31, since the birth of The Federation.
- Secret Test: It's implied that one reason why Section 31 puts Bashir through the simulation is to see whether he has the qualities required of their own agents: intelligence, attention to detail, ability to work under stress, etc. So if he turns out not to be a spy for the Dominion, they can try to recruit him themselves.
- Smug Snake: Director Sloan.
- Suspiciously Specific Denial: Sisko reports that Starfleet Command won't acknowledge or deny Section 31's existence.
- Utopia Justifies the Means:
Sloan: We deal with threats to the Federation that jeopardize its very survival. If you knew how many lives we've saved, I think you'd agree that the ends do justify the means. I'm not afraid of bending the rules every once in a while if the situation warrants it, and I don't think you are either.
- Wide-Eyed Idealist: Bashir is stunned that an organization like Section 31 could exist within the Federation.
- You Don't Want to Know: After Bashir asks Sloan what would have happened if he had been a Dominion spy.
Sloan: We wouldn't be standing here having this conversation.
- You Have to Believe Me: Bashir trying to convince the bridge crew that he's not a traitor, until he figures out that they're not really the bridge crew.
- Your Favorite: Weyoun saying "Do you remember the first time I offered you scones back at the camp?" to Bashir.