The newly promoted Captain Sisko and crew head for the Tzenkethi system to quell possible violence from a coup. But things take a turn for the worse when a saboteur begins to interfere. And not just any saboteur. A Changeling.
- The 47 Society: There are 47 people on the Defiant.
- Bait-and-Switch: The first lines are Sisko says are that this is his last entry to his commander's log and how fulfilling the past three years have been, as though leading up to his leaving the station. Then the scene switches to Jake looking solemn and saying that he's been wanting to tell his dad something for a long time. Turns out it's a question of semantics — from now on, Sisko will be dictating a captain's log, and Jake is just stoked to be addressing his dad by that rank.
- Call-Back: To Bashir's engineering extension course.
- The Captain: Sisko officially becomes this after three seasons of Commanding Coolness.
- Captain's Log: Sisko's first entry as Captain.
- Faux Affably Evil: The Founder is rather friendly towards the crew while in his Krajensky persona, up to celebrating Sisko's promotion with the rest of the crew, but he dies trying to spark an interstellar war. The gentle smile he offers right before transforming and jumping into a vent is downright disturbing.
- Foreshadowing: Eddington's desire to be in the captain's chair comes up when he congratulates Sisko on his promotion.
- Gunboat Diplomacy: The idea of the mission, as far as Sisko's told — the Defiant goes on patrol to make sure that the Tzenkethi behave themselves.
- Guns Akimbo: Sisko during a Mexican Standoff with Kira and a paranoid Bolian.
- Kill and Replace: It's implied that Ambassador Krajensky was killed on his way to Risa and the changeling took his place.
- Let's You and Him Fight: The Founders' plan is to make the Federation and the Tzenkethi fight each other, weakening both of them.
- The Main Characters Do Everything: There's absolutely no reason for Deep Space Nine's Chief of Security to come along a routine Starfleet mission, but since Odo is needed for the plot, there he is. The absurdity of the situation is emphasized by the fact that Odo is put in charge of the Defiant's communications, which is hardly his field of specialty.
- Mandatory Line: Quark only appears at the party celebrating Sisko's promotion.
- My God, What Have I Done?: Odo doesn't say it, but it's written all over his face when he kills the changeling.
- No OSHA Compliance: While it does at least have a protective forcefield around it, the warp core of the Defiant emits enough radiation that anyone who comes into contact with the unshielded core will instantly get a lethal dose, and the engineering section will apparently become dangerously radioactive after a prolonged period without the forcefield in place. By contrast, people were able to touch the unshielded warp core of the Enterprise-D several times over on TNG with no ill-effects.
- Non-Standard Character Design: The Bolian in this episode has a far more muscular build than the other, more portly, members of his species seen in Trekdom. Then again, he is a security officer.
- On Three: Sisko and a Red Shirt are about to do this when the changeling attacks and takes out the Red Shirt.
- Paranoia Fuel: A quite unsettling In-Universe example. The end of episode quote sums it up.Odo: You are too late. We are everywhere.
- The Bolian security officer is quite paranoid about whether or not Kira is the changeling. Kira at the same admits to not trusting him either.
- Punctuated! For! Emphasis!: Odo resisting the changeling's attempt to turn him against Starfleet: "I...don't...think...so!"
- Rank Up: Sisko's promotion to captain, though he does admit that it doesn't actually change the dynamics on DS9, as he's still in command no matter what his rank is.
- Scotty Time: After Sisko activates the self-destruct, he asks O'Brien how long it will take to deactivate the changeling's sabotage. When the computer says the ship will explode in seven minutes, the Chief replies "I guess it'll have to be less than seven minutes."
- Self-Destruct Mechanism: Sisko is willing to use it to keep the Founder-controlled Defiant from attacking the Tzenkethi. Fortunately, he aborts it just in time. Complete with a verbal version of a Two-Keyed Lock (voice authorizations from Sisko and Kira).
- Shipper on Deck: Jadzia interrogates Sisko on whether or not he's told Kassidy about his promotion, what he counts as "dates" and where he's taking her next — she also knows more about Kassidy's cargo route than he does.
- Spot the Imposter: Subverted when O'Brien is faced with two Odos, but doesn't bother trying to figure out who's who. Instead, he has his assistant hold them both at gunpoint while he keeps working.
- But also invoked earlier when Sisko, Kira and the Bolian security officer are all pointing weapons at each other. Odo points out that Sisko can't be the changeling because he's bleeding. Any piece of a changeling that is separated reverts back to its original gelatinous form, so off to the infirmary for blood samples.
- Tempting Fate: Odo remarks about how no changeling has ever harmed another and how he's never had to kill anyone. Guess what happens during the climax.
- That's What I Would Do: Eddington encourages Odo to do this regarding the changeling. Unfortunately, Odo's understanding of his own people is too limited to be of much help.
- Trapped with Monster Plot: The DS9 crew is trapped aboard a hijacked Defiant, desperately trying to hunt down a changeling before they have to self-destruct the ship to prevent an interstellar war. The writers said there was something pure about this because of how anti-Star Trek it was. There's no attempt at negotiation or understanding the changeling, just find the changeling and kill it.
- Trust Password: Odo tries this with Chief O'Brien to convince him he is the real Odo. It fails when the Founder proves to be just as knowledgeable about O'Brien.Odo #1: Chief, do you remember the last time you went kayaking on the holosuite? You had lamb stew for lunch.
O'Brien: That's right.
Odo #2: But you forgot to bring a fork. Anyone could've gotten that information.
- We Are Everywhere: The Founder's last words to Odo.
- Wham Episode: No changeling has ever harmed another until this episode, when Odo kills a changeling to protect the Defiant. This will have far-reaching consequences as the series progresses.
- You Have to Believe Me!: Eddington trying to convince everyone else that he's not the Founder. It doesn't work — until two Bashirs show up.