* Mathesar's undiminished faith in Nesmith, despite being captured and tortured by Sarris, is so touching.
--> '''Mathesar''': (''Sarris's men bring Jason and the others into the room'') Commander, thank God you're alive. Now you will face justice, Sarris...
* Alexander finally [[http://www.youtube.com/watch?v=r7bo_A6XnUU#t=1m35s uttering his catchphrase on his own accord]], and ''meaning it''.
* Tommy putting so much effort into "re-learning" how to fly the ship, when he's finally convinced that it matters.
* Fred convincing Guy that he's not the [[RedShirt "throw-away extra guy"]].
** And even right before that; Guy's weakening voice and legs show he's still as terrified of his (perceived) fate as before, but Guy [[HeroicSacrifice has decided to accept it to save the rest of the cast and crew]]).
* At the end of the film, the team has had a DynamicEntry into the side of a convention centre, with [[spoiler:Sarris dead]] and the fans ecstatic. Jason goes forward to bow, but then remembers that his team are there and tells them to all come forth, as he feels that they equally deserve the applause. They gladly accept, at which point Jason kisses Gwen. Contrast to the beginning of the film, when they were almost all reluctant to be there, Jason was hogging the limelight and Gwen couldn't stand him at all.
** And as a metatextual heartwarming moment, we have Tim Allen, Alan Rickman, Sigourney Weaver, Tony Shalhoub, Sam Rockwell, and Missi Pyle (Laliari), taking ''their'' bows, which is something film actors rarely get the opportunity to do on-screen.
* Brandon and his friends, and the way the movie treats them. These aren't useless, pathetic geeks wasting their lives in a juvenile fantasy; they're intelligent people with strong interpersonal friendships, who have an incredible amount of passion for a show that has been empirically proven to ''change lives'' and make people (aliens, in this case) believe in friendship, loyalty, courage, and a better future. It's a love letter to Trekkies and their devotion to the show. ''The fans save the day''. And they save it solely because instead of just shrugging the whole thing off as just a stupid TV show, they connected with it on a deeply emotional level and ''created'' something wonderful.
** On a meta level, the exchange between Brandon and Jason just adds to this--because while the events portrayed in the show obviously didn't really happen, the themes and the emotion that went into it were ''real''.
--> '''Brandon''': "I'm not some kind of brain case, okay? Of course I understand that it's all just a TV show, there's no ship--"
--> '''Jason''': Brandon. Brandon! It's all real.
--> '''Brandon''': Oh my God I knew it. I KNEW IT!