Tommy panicking at his dog Sunkist being threatened by a firing squad of turrets. Downplayed because the dog turns out to be immortal and thus immune to bullets, but still.
Tommy: WAAH- LET SUNKIST GOOOOO!!! *sob*
Right before the final battle, Coomer takes Gordon aside for a moment to talk to him about video games. Coomer admits to not being the biggest game fan but fondly regales how growing up his favorite game was Super Punch-Out!! because of its story being about a boxer facing impossible odds to become the champion, asking Gordon what game he'd like to live in before stating he'd like to be in Super Punch-Out!!. Gordon, confused, asks why Coomer is bringing the topic up before getting this heartbreaker.
When he talks to Dr. Coomer from the past, he tries to remind him of their adventures together. While it does work and Coomer gladly cooperates to help him return to the future, his first emotion after "waking back up" so to speak is... resignation.
Dr. Coomer: H-...H-...H-H... I remember.
Tommy and Benrey's relationship decaying. At the start of the series, Benrey is at least on good terms with Tommy, calling out to him like an old friend when he hears him yelling into the test chamber. He seems to be Tommy's only acquaintance at first, with Gordon initially decrying Tommy as a freak and the other scientists talking to him like he's a baby thanks to his Manchild mannerisms. But as Benrey grows crazier and more depraved, and Tommy cements himself as Gordon's ally, the two stop speaking. It all culminates in Benrey's skeletons attacking Tommy during the final battle and Benrey coolly trying to persuade the Science Team to, "Let Tommy go."
Dr. Coomer's message after the credits.
Dr. Coomer: Hello? Testing, testing... Is... Is this thing on? Ah! Hello Gordon!... I'm... a-assuming that's your real name. You wouldn't lie to us. Would you? Well.. You finally did it! You survived the resonance cascade! You brought us all to hell and back, alive! You made it to the ultimate birthday bash at the end of the world! You beat the video game! And... now I imagine you'll... shut it down. Move on with your life. Onwards and upwards ay, Gordon? I don't... know... how much longer I have to send this to you so I'll try to keep it brief. Not my specialty. Perhaps this is presumptuous of me but... Must this really be the end of our time together? Perhaps you could take the science team's data, transfer us somewhere else, hmm? Now... It doesn't have to be Super Punch-Out™ for the Super Nintendo Entertainment System™. Maybe a USB drive, or a... spare floppy disk. You could take us with you! We could see the world! We could... *throat clearing* I'm... getting ahead of myself, surely. Welp! The option's always there! You changed our lives, Gordon. I'd like to think it was for the better. And I don't know what's going to happen to us once you exit the game for good. But I know we'll never forget you. I hope you won't forget us. Well... This is where I get off... Goodbye Gordon!
The Youtube upload of the Act 3 commentary shows Gordon is completely frazzled from the entire experience.
Gordon: Man, if I had any preconceived notions of what my future would be like after Black Mesa and what I would do with my degree, they're out the window.
While talking to Benrey in the movie theatre bathroom, Gordon refers to himself as "barely human".
