When the hi-jacking Eldritch Abomination possesses the ship, almost all warning lights on the Bridge consoles light up, indicating the areas under it's control. Kirk notices that even the galley lights are glowing red.
Kirk: What the hell would that thing want in the galley?
Spock: (bemused) Sir?
Kirk is making a shipwide announcement after the entity beamed aboard with them, informing the crew what is going on and asking them to remain on alert. A very professional and captainly announcement, till...
Kirk: All personnel shall wear..(About to say 'sidearms', then realizes that with the incorporeal creature, there's nothing to shoot at, changes tracks mid sentence) ..All personnel shall wear clothes.
Scotty trying (and failing) to explain idioms to Spock...
Scotty(to a grinning Kirk): I've an easier time communicatin' with a number-four automatic welder!
Drumming his fingers on the armrest of his command chair is one of Kirk's tics when thinking - this time, he's drumming the tune to an obscene ditty. While Sulu is trying to figure out what that tune is.
Spock: It is very easy to tell when you are joking, Doctor— which is most of the time. It is when your statements make absolutely no sense—which is most of the time.
In a Call-Back to this, later (when the doctor has got Spock back on his feet after the entity went at him with an Agony Beam):
Spock(still slightly groggy): A fine, professional job, Doctor. Fortunately, your medicine is more effective than your jokes.
When Spock gets a bit too Literal-Minded in answering a rhetorical question
Kirk: Now you're acting unnecessarily rational, Spock.
Spock: To me, Captain, that's a contradiction in terms.
Kirk: Shock? What do you mean, shock? I'm not in shock, Spock. And nothing you slipped me, Bones, is going to make me go un . . .
Yesteryear
Kirk keeps getting interrupted as he is recording the Captain's Log.
Kirk: Quiet, Mr. Spock. I'm recording. Or trying to. (Hits the unlucky Pause Button again) Erase that last.
While having tea on the Planet Surface research station, one of the alien researchers (of Avian ancestry) gets impatient and starts flapping his wings about. Kirk, who is having an interesting discussion with another (very pretty) researcher wouldn't have minded, if the flapping wasn't sending feathers into everyone's tea.
Spock: I beg your pardon, Captain, but what exactly is happening?
Historian: We're going to decide which one of us goes and which two stay behind, Commander.
Spock: I see- no, I do not see.
Kirk(trying not to laugh): I'll explain it all to you later, Mr Spock.
One Of Our Planets Is Missing
Kirk's irritation at being assigned a difficult mission right after an arduous trip.
The Mantillian government had shouted loud enough for Starfleet Command to hear, and Starfleet Command had shouted for the Enterprise. And Kirk—Kirk could only shout at the gods of coincidence and bad timing. At least they didn't shout back, they only snickered.
McCoy's dramatic declaration is undercut by Kirk's calm response.
McCoy: If we can't stop it, Jim, millions will die. Kirk(looks back, not having noticed McCoy was on the Bridge): Hello, Bones. I know.
The approaching cloud has just broken down a planet as they watched. When Kirk asks Spock whether the cloud-thing could be eating planets-
Spock: Captain, I believe that your question is unnecessarily replete with emotional overtones. Kirk(glaring at him and the cloud in turns): This whole situation is unnecessarily replete with emotional overtones, Mr. Spock. Please answer the question.
The Enterprise is trying to reach the entity's "central core". Sulu finally finds a possible entrance to it, but it's closed.
McCoy: Do we knock?
When faced with the imminent self-destruction of the Enterprise (and themselves) as the only option to destroy the entity, the human Bridge crew resorts to Black Comedy, much to Spock's bafflement.
McCoy: Well, gentlemen, that's one decision you won't have to live with.
Kirk: Wait till you hear the next one, Bones. It'll kill you.
Spock(Clearly wondering whether his teammates have lost their minds): What on Vulcan is the matter with you two?
McCoy: Nothing, Spock. You're right as usual. As a comedy act, we're dying.
Kirk(grinning even wider): Stop it, Bones. You're killing me.
