- This remark from K to J near the end:K: I've just been down the gullet of an interstellar cockroach, kid. That's one of a hundred memories that I don't want.
- Before that, K wistfully says of the stars in the sky, "They really are beautiful, aren't they?" - obviously pining for a day that the stars were just that, stars and nothing more.
- Then there's the very sad way J and K say goodbye.K: See you around, kid.J: No. (braces himself and readies the neuralyzer) You won't.
- Orion the Cat. Before Rosenberg was murdered, he really seemed to love and spoil his pet. After Rosenberg's death, Orion even travels with him to the morgue, and hisses at Edgar, evidently able to recognize him as Rosenberg's killer.
- Dee's neuralization. He just looks so heartbroken in the moments leading up to it.
- This little exchange:J: You know what they say. Better to have loved and lost then never to have loved at all.K: Try it.
- When introducing MIB to J, K says there was "one kid who got lost in the wrong back alley". Later on, we find out that K was that kid and that he left his former girlfriend to join the agency. The script makes it clear that unlike later recruits like J, K had no choice in the matter. He was forced to join just for being in the wrong place at the wrong time.
Tear Jerker / Men in Black