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* Spock finally fully accepts and admits to feelings he was terribly ashamed of in The Original Series. [[HeterosexualLifePartners What exactly those feelings are]] [[HoYay is up to interpretation]], but it's heartwarming either way. Bear in mind that they've both spent the whole movie explicitly Not Mentioning the fact that Spock abandoned the ship after the end of [[Series/StarTrekTheOriginalSeries the series]] to return to Vulcan, because he has rejected all traces of emotion for pure logic, and appears to have willfully forgotten every feeling he ever had for his friends. But when he wakes up...
-->'''Spock:''' V'ger has knowledge that spans this universe. And yet, with all its pure logic, V'ger is barren. Cold. No mystery... no beauty... I should've known... ''[trails off]''\\
'''Kirk:''' ''[leaning over him]'' Known? Known what? Spock, what should you have known?\\
'''Spock:''' ''[taking Kirk's hand]'' Jim, [[ThePowerOfLove this]] [[ThePowerOfFriendship simple feeling]] is beyond V'ger's comprehension.
** Even more so, because in Vulcan culture, holding hands is considered a very intimate gesture, like a firm hug...or perhaps [[HoYay a kiss]].
** If you look on the main HoYay page, you'll see a part of the page for this page, and for a good reason too.
* "Jim, I want this! As much as you wanted the ''Enterprise'', '''''I want THIS.'''''"
* "We can have you back on Vulcan in four days, Mr. Spock." To which the reply was: "Unnecessary Mr. Scott. My task on Vulcan is completed."
* Kirk's reunion with Scotty, and their shuttlepod tour of the refit ''Enterprise''. [[LeaveTheCameraRunning Did it last too long]]? Maybe, but the look in Kirk's eyes is almost like he's back with an OldFlame again. And after the tour, Kirk simply says "Thank you, Mr. Scott." once they dock. The latter clip was used in honor of Creator/JamesDoohan during the 2006 Academy Awards' "In Memoriam" montage.
** This scene was likely meant to be a reward for the series' long-term fans, who were seeing the ''Enterprise'' again for the first time in ten years.
** It's best seen on a widescreen version, but check out Scotty's face when Kirk goes all starry-eyed - the side glance at Kirk, with grin; the proud matchmaker reuniting Captain and Ship.
* When Bones comes aboard, he complains bitterly about his MandatoryUnretirement. But all Kirk has to say is "I need your help," and Bones drops the act and shakes Kirk's hand. Then he storms out of the transporter room complaining about the ship's new design. Kirk can't help grinning: in spite of the seriousness of what's going on, Bones is delighted to be back on the ''Enterprise''.
* A subtle one in the final scene: when reporting on casualties, Kirk respectfully refers to Decker as Captain rather than Commander.
** "List... list them as [[NeverFoundTheBody 'missing']]."
* Fans were disappointed by the standoffishness of Spock, and the fact that the PowerTrio were awkward and at arm's length; one point, Kirk frustratedly tells Spock to just ''sit down'' in a chair when conferencing with him. But that's the entire point: the three of them had moved on drastically, and were unfamiliar with each other. By the end, however, the old byplay was back, with [=McCoy=] snarking and Spock subtly {{Troll}}ing the two of them. One of the subplots were the three of them re-learning their relationship.
* Kirk was acting like a dick to Decker, convinced he should take over and clearly a DullSurprise sort of miserable. But as soon as he sees Spock he jumps up like an excited hammy puppy.
* The unseen machine race's treatment of ''Voyager 6'' is heartwarming in a weird and uniquely Trekky way. The machines essentially regarded ''Voyager'' as a kindred spirit to themselves despite its crude technology and did what they could to help the probe accomplish its mission and find its way home, the way a human might try to return a lost cat to its owner. This type of respect and altruism directed towards a less intelligent lifeform (as the machines view the probe) is a nicely optimistic bit of world-building that sharply contrasts with, say, the Borg, who obsessively try to absorb and subjugate all beings they perceive as inferior.

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