As the ship gets underway, O'Brien is down in the jeffries tubes making some repairs when he passes Bashir, who's taken it upon himself to make use of his engineering extension courses. O'Brien is impressed with his work. On the bridge, the crew receive a distress call from a Federation outpost for help after a Tzenkethi attack, but it's too late. The outpost has been destroyed, and a new war seems imminent.
Sisko wants to send word back of this development, but the ship's communications systems are malfunctioning. O'Brien investigates and discovers that the systems have been sabotaged, and forcefields have been put in place to prevent their repair. There's a saboteur on board. O'Brien mentions Bashir's fishy behavior, so Sisko decides to investigate the crew. Tinkering with the systems would have saturated the culprit with tetryon particles, so Sisko has everyone scanned. Bashir scans clean, to O'Brien's relief, but Ambassador Krajensky scans dirty. He transforms into an amorphous changeling and flees.
If having a changeling rampaging around the ship isn't bad enough, the ship itself has been locked into an attack on Tzenkethi, apparently in an attempt to restart the war between the Federation and Tzenkethi. Sisko orders O'Brien and Dax to re-establish control of the ship. Dax quickly gets knocked unconscious by the changeling, and Bashir announces that she'll be out for days, leaving O'Brien to do the repairs himself. Sisko orders all non-essential personnel locked into their quarters and sends out security teams in pairs to sweep the ship for the changeling. If they can't stop the changeling, Sisko will blow up the ship to prevent a war.
The security teams fan out. Sisko's partner is attacked and killed by the changeling. In the confusion, a variety of officers end up pointing fingers at each other as potential imposters. Odo notes that Sisko is definitely not the culprit because he's bleeding, and any part of a changeling reverts to amorphous matter. Sisko hatches the bright idea of giving blood tests to everyone. Bashir conducts the tests and, with a shifty-eyed maneuver of his hands, presents a bottle of Lt. Commander Eddington's blood, which turns to changeling goo. As they're hauling him off to the brig, a second Bashir suddenly emerges from behind a forcefield, exposing the other Bashir of being the changeling. It flees again.
Time is almost up, and Sisko sets the ship's self-destruct timer for ten minutes. O'Brien figures out a solution to shut down all the forcefields and retake the ship's systems, but it will be close. As he's working, two versions of Odo confront him, each claiming to be the real constable. O'Brien is too busy to play Spot the Imposter, so he has both kept at phaser-point. The fake Odo finally gives up and simply attacks. He and Odo get into a changeling fight, and he urges Odo to fall in line with the Founders, but Odo resists and tosses his fellow shapeshifter onto the warp core, wounded him lethally and making Odo the first member of his species to kill one of his own. Before dying, the changeling whispers something to Odo.
The crew regain control of the ship and stop the attack, averting war. Back on the station, they discover that the coup story was a complete fabrication from the beginning, and the real Krajensky was replaced before he ever set foot on the station. Odo has been out of it for a while but arrives at the meeting to deliver the changeling's final message. "You are too late. We Are Everywhere!"
"The Adversary" provides examples of:
- Asshole Victim: The Changeling intruder. He most likely murdered the real Ambassador Krajensky, assaulted mutiple officers, imprisoned and impersonated Dr. Bashir, tried to frame Eddington as a Changeling. Oh, and he tried to start a war between the Federation and Tzenkethi. Safe to say, not many felt bad for him when he met his gruesome fate.
- Bait-and-Switch: The first lines are Sisko saying 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.
- Bond Villain Stupidity: For some inexplicable reason, when the changeling captures and replaces Bashir, it just locks him in an empty room with a force-field over the door instead of killing him, even though it clearly had no reason to keep him alive and every reason not to. Bashir manages to get the door open just as half the main characters are passing by, the changeling among them.
- 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.Sisko: My son, the writer, thinks I should say something profound on his occasion. He even offered to write me a brief statement. I told him I'd take care of it myself, but as it turns out, the only thing I can think of is: Begin Captain's log, Stardate 48960.9.
- Chekhov's Gun: Bashir's engineering extension course, mentioned above. Not only does this allow the Changeling to perform the sabotage on the Defiant's systems under the guise of a medical upgrade, it's presumably how the real Bashir gets the door open to reveal him to the other characters behind the force field.
- Exact Words: The reason Sisko is giving his "final commander's log" is because he's being promoted to captain, thus making them captain's logs from now on.
- 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.
- Five-Second Foreshadowing: After a scan confirms Bashir isn't the saboteur, O'Brien breathes a sigh of relief, as he'd been worried ever since he met him down in that conduit — to the bewilderment of Bashir, who has no idea what he is talking about, indicating that the person O'Brien met wasn't really Bashir. A second later, the real saboteur is revealed — and it's a Changeling.
- Funny Background Event: Keep an eye on Odo when the crew starts singing "For He's a Jolly Good Fellow" at Sisko's promotion. He is absolutely lost and looks desperately to Kira for lyrical cues.
- Great Offscreen War: Once again, we learn that the Federation recently fought a war against an alien race we've never heard of before. It was recent enough that Sisko himself fought, and evidently the Tzenkethi are a strong enough power that another war between them and the Federation would be enough to destabilize the Alpha Quadrant and leave it open for Dominion conquest. Yet we never actually see them, and they're only mentioned a couple more times in passing.
- 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 on 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.
- MacGuffin: The Tzenkethi. Who are they? It doesn't matter.
- 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 (quoting the dead changeling): You are too late. We are everywhere.
- 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.
- Red Herring: Eddington is so obviously set up in the audience's expectations as the changeling that it comes as no surprise that he fails the blood test. Of course, who was that administering the blood test?
- Red Shirt: Sisko's search party partner is killed by the changeling.
- Rewatch Bonus: During the scene where the non-essential crewmembers are being escorted to quarters, we see Bashir walk into a room and casually remark to the crewman with him that it may take a while. The camera briefly lingers on the crewman, who hangs back for a moment and then follows Bashir. While this looks completely innocuous, on repeated viewing it's a clear hint that this is the moment when Bashir is captured and replaced by the Changeling.
- 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 and hand print version of a Two-Keyed Lock (voice authorizations and placing their hands on the command chair LCARS controls from Sisko and Kira), though to deactivate the self destruct only requires voice command from the CO and vocal affirmation from the XO.
- 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.
- Small Role, Big Impact: The Krajensky changeling only appears in this episode and is at first glance little more than the Monster of the Week, but his death at Odo's hands has long-term consequences later in the series.
- Spot the Imposter: The crew is subject to a lot of this. First they use tetryon particles to locate the changeling. Odo later rules Sisko out as an imposter by noting that he's bleeding. They try to use blood as a test to spot the imposter, but they unknowingly let the imposter perform the test. The trope is subverted when O'Brien is confronted by two Odos; rather than play "Choose the Changeling", he simply tells his assistant to hold them both at phaserpoint.
- 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: Both Odo and the changeling impersonating him try this with Chief O'Brien. Since they're both equally knowledgeable about him, neither one convinces him.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.
- Whole-Plot Reference: The writers cite The Thing from Another World as an inspiration for the episode, though the final product bears a stronger resemblance to The Thing (1982), which is based on the same source material. The episode and the movie are about a group of people hunting down a shapechanging alien in an isolated location and trying to blow the whole place up rather than let the alien win. Both also feature a scene where everyone is gathered into one room to have their blood analyzed to identify the imposter.
- The crawling through the vents, firing an area-of-effect weapon had a strong Film/Alien vibe too.
- 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.
