This episode marks Benjamin Sisko's promotion to Captain. Dax is promoted to Lieutenant Commander and Bashir is promoted to Lieutenant.
First appearance of the Defiant's engineering room.
This is the only episode where blood tests are an effective way of screening for changelings. The Founders quickly find a way around this. In the very next episode, the Changeling posing as Martok fakes this test in front of Sisko and Kira, then acts paranoid that they might be changelings, thus completing his disguise.
It is shown that Bolians have blue blood.
Goof: It is stated quite clearly in the episode that the phaser rifles were set to the special phaser setting to combat the changeling, however, after the incident between Kira and the Bolian, near the transporter, the rifles all fired their normal phaser beams.
Nitpick: Why did Odo go on the mission to Tzenkethi space? As far as the crew knew, they were going on a patrol along the Federation-Tzenkethi border, therefore there would have been no need for him to go along. Odo is Station Chief of Security, so he should have remained on the station - Lieutenant Commander Eddington is the Starfleet Chief of Security.
Lt. Commander Eddington announces "Captain on the bridge" when Sisko first boards the Defiant. This appears to be irregular, as nowhere in the history of The Original Series, The Next Generation or Deep Space Nine (until this episode) is a captain given such treatment. previously, this sort of formal honor had been reserved for Ambassadors and Starfleet Admirals. Perhaps he says it just to commemorate Sisko's new rank, though.
Depending on the stardates, the phrase "Captain on the bridge!" is in fact spoken aloud in the Next Generation episode "Chain of Command Part I" to acknowledge the arrival of Captain Jellico onto the bridge. This however may or may not come before the DS9 episode.
In this episode's promotion ceremony, Sisko, Dax and Bashir still have their original rank on their collars and in the credits. The promotions just don't show up on their collars and in the credits in season 4's "The Way Of The Warrior". There is never anything specific said in any episode about when or how the promotions took place.
Odo: Where's the Changeling? I lost him in the conduits.
O'Brien: We haven't seen him.
(another Odo emerges from another access port)
Changeling/Odo: Wait. It's me, Odo.
O'Brien: (looks at both Odo's) You don't say.
Changeling/Odo: Chief, remember the last time we went kayaking in the holosuites? You had lamb stew for lunch.
O'Brien: That's right.
Odo: (to O'Brien) But you forgot to bring a fork. Anyone could have gotten that information.
Computer: Auto destruct in five minutes.
Changeling/Odo: You'd better make a decision. We're running out of time.
O'Brien: Look, I've more important things to do than play 'Choose The Changeling'. (to co-worker) Keep the phaser on both of them.
Changeling: Why are you protecting these solids? You don't belong with them. You belong with us. Let go. Don't you see? You've lost. It's too late for you to help them, but it's not too late to help yourself. Link with me, Odo. We can escape together.
Odo: I don't think so!
Odo: Captain, there's something you need to know. The changeling, before he... died, he whispered something to me.
Sisko: Go on.
Odo: He said... 'You're too late. We're everywhere'.
The search for the changeling through the Jefferies Tubes and firing phaser blasts down them is very reminiscent of the use of flamethrowers in the air ducts in Alien (1979).