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  • After Spock compares V'Ger to a child, McCoy replies: "This 'child' is about to wipe out every living thing on Earth. Now, what do you suggest we do, spank it?"
    • A few moments later, when V'Ger is attacking the ship: "Your 'child' is having a tantrum, Mr Spock".
  • McCoy again, after Spock rejoins the crew:
    Spock: On Vulcan, I began sensing a consciousness more powerful than I have ever encountered — thought patterns of exactingly perfect order. I believe they emanate from the intruder. I believe it may hold my answers.
    McCoy: Well, isn't it lucky for you that we're heading your way? [does hitchhiking gesture]
    Kirk: Bones!
  • McCoy again:
    Kirk: Well, for a man who swore he'd never return to Starfleet—
    Bones: Just a moment, Captain, sir. I'll explain what happened. Your revered Admiral Nogura invoked a little-known, seldom-used reserve activation clause. In simpler language, Captain, they drafted me!
    • What really sells it is his hilariously '70s Space Clothes and beard. (He shaves it between scenes later.)
    • For those with a military background, it's appropriately amusing to know that even two hundred and fifty years in the future, Stop-Loss policies and orders still wreak their havoc on poor servicemembers' retirements. To say nothing of the traditional post-separation beard worn by many a veteran finally free of grooming standards.
  • Outtake first seen in the ABC-TV version:
    After the transporter is fixed, an arriving crewman says "Someone wanted to first see 'how it scrambled OUR molecules'".
    Kirk to Transporter Chief Rand: That has a familiar ring to it....note 
    • Given that this happened only a few scenes after Sonak's demise in that very same transporter, it's amazing that Kirk or the audience can find that funny.
  • Uhura explaining (while having a hard time keeping a straight face) that "one" of the extended crew members is refusing to beam aboard and Kirk (with a barely contained straight face himself) saying he will make sure that crew member beams aboard. They both know damn well who it is.
  • Bones patting himself after beaming onboard the Enterprise, to make sure he’s all there, really sells his distrust of the transporter. And it’s funny too.
  • Not intentionally funny, but Bones appearing on the ship in a funky 70s robe-like uniform, full beard and what appears to be the eye piece of the Staff of Ra from Raiders of the Lost Ark around his neck definitely elicits a laugh. His clothing and demeanor combine to give the impression not that Bones was recalled to Starfleet and was standing by to come aboard, but was instead in a retirement home and got beamed up with no warning on the way to the bathroom.
    • Just as a rule, any example of Space Clothes in the original cast films tends towards the hilarious.
  • In a rare aversion of his usual tendency to react in entirely the wrong way to a potentially dangerous situation and get injured as a result, Chekov's reaction when he's ordered not to interfere with the probe—which is clearly pursuing him while he tries (unsuccessfully) to retreat from it—is very funny. It's the look on his face that really sells it, but the way the line is delivered is hilarious too.
    Chekov: Absolutely I will not interfere with it!
  • Ilia reports to Captain Kirk, and almost immediately feels the need to inform him that she's under an oath of celibacy. Your reputation precedes you, Captain Kirk. It's even funnier when you read in the book Ilia is Trolling Kirk! In Gene Roddenberry's original script Kirk directly asked Ilia the question “Have you ever sexed a human?", which means the screenwriters most likely were trolling Gene Roddenberry for writing such a terrible line.
  • In a scene cut from the original but restored for the expanded TV and Director's Cut versions, soon after the above exchange, Sulu becomes flustered in Ilia's presence, even pushing the wrong button on his console. Takes on an additional tone of irony in that the actor is gay.
  • Kirk and Decker discuss the possibility of manipulating the Ilia-probe's imported memories of Ilia's life, friendships, and loyalties, in order to complete their mission...
    Kirk: Commander! Will, we're locked in an alien vessel, six hours from Earth orbit. Our only contact with our captor is that probe. If we could control it, persuade it, use it...
    [Ilia-probe boldly walks directly through the door, leaving a gaping hole in it.]
  • The wormhole scene and all the slowed voices rocks this with Narm.
    • After escaping the wormhole, Chekov reports no casualties, to which McCoy retorts:
    McCoy: Wrong, Mister Chekov, there are casualties. My wits! As in "frightened-out-of", Captain, sir!
  • A little moment, but when Kirk tries to interfere with Decker directly interfacing with V'Ger, the Ilia!Probe nonchalantly pushes him away, making him reel ten feet, as if to say, "Back OFF! That's my MAN."
  • A moment that unfortunately did not make it into the film, but is detailed in Star Trek Movie Memories; Leonard Nimoy did not like Spock's simple declaration that he didn't need to be returned to Vulcan, having already finished his business, so he ad-libbed a line: "Negatory, Captain. If Dr. McCoy is to remain aboard, my presence here will be essential."
  • The closing lines, before the Enterprise embarks on another mission.
    Chief DiFalco: Heading, sir?
    Kirk: (wistfully) Out there... (Beat, then gestures) Thataway.
    • In the Novelization, Spock asks Kirk if that's an appropriate ordinal direction.
    • Has become something of a Never Live It Down moment in the fandom, with many Expanded Universe works poking fun at how, exactly, Sulu carried out that order.
      You no tell me which one you push for "thataway!"
  • When Spock arrives, he's greeted by Chekov:
    Spock: Permission to come aboard?
    Chekov: (delighted) Granted, sir. Gran-
    (Spock walks straight past him)
    Chekov: (confused) ...-ted.
  • The exchange of surprised looks between the Klingon captain and one of his officers when they see in the tactical screen how one of the photon torpedoes fired against V'Ger simply disappears.
  • As the Enterprise is traveling through the awe-inspiring mystery that is V'Ger, Bones is still on form:
    Uhura: It could hold a crew of tens of thousands!
    McCoy: Or a crew of a thousand, ten miles tall...

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