- The alien birth scene, in its own sort of way.
K: Congratulations Reg, it's a... squid.
- Although it being retconned to hell and back in the sequels sort of ruined it, the final scene where the newspaper showed the Agent K was reunited with his lost love and Agent J's simple smile at it.
- YMMV, but in an odd way, the memory J thinks up for Edgar's wife after she's been neuralyzed is kind of heartwarming. K makes up that Edgar ran off, and she'll decide she's better off, then J adds that she threw Edgar out because he never appreciated her anyway and now she's going to make a fresh start. Considering what little we see, it seemed like an abusive relationship, and the altered memory that she took charge and ended may end up empowering her in the future.
- The animated series has a Christmas Special in which Agent K receives the first edition of Charles Dickens' A Christmas Carol. He cracks a smile, and looks like he's about to tear up for the first time in ages.
- At the end of the series, J says "I'd make that Medal of Honor look good" after MIB works with the President to save the world from the Ixions. K answers "I know you would."
- "The Sonic Boom Syndrome" has a Cold Opening in which J and K are running through a dark sewer, apparently chasing some beastie. Turns out they were the ringbearers for an alien wedding. Awwwwwww.
- The one time K actually calls J by his name is very heartwarming. Especially J's reaction.
- The episode "The Head-Trip Syndrome" has J mess up using alien technology to become super smart, but his brain will blow up. K and MIB try to find a way to save him, when it turns out someone is using time travel to erase the MIB. K suggests with them gone J will be healed and back in the NYPD. J only needs a second to think about it before saying that's not an option.
- In "The Little Big Man Syndrome", when an Arquillian was brought to MIB headquarters, they go to the kitchen for some coffee, but when he asks for decaf, the Worm Guys mock him. But later, when it looks like Arquillia is about to be destroyed, the Worm Guys bring a cup of decaf coffee.
Worm 1: It's decaf...Worm 2: Just the way you like it...
- Towards the end of "The Neuralyzer Syndrome", an accidentally neuralyzed Kay goes to his boyhood home, giving a proper farewell to his father before returning to the MIB.
- This may be heavy on the Fridge Logic, but hang with This Troper. In "The Dog Eat Dog Syndrome", the MIB are about to torch a diner that a spaceship had crashed into, presumably to remove any evidence of aliens or residue from the crash. But when the owners - an elderly couple - mention that the diner is all they own, K calls for a "Code 2" and instead they Neuralize the couple, covering up the crash as a new facade for the diner. This is Heartwarming not just because the MIB are willing to help the couple like that, but when you think about it they may well have left bits of evidence or items that may have blown the whole Masquerade wide open. And that's assuming they closed up the hole Drekk melted to get out of the crashed ship, as seen when J and K check up on Elle. And the fact that K referred to the procedure as a "Code 2" implies that the MIB do this often enough that it's a standardized practice.
- The aliens in "The I Married an Alien Syndrome" try to increase Earth's temperature to make it more habitable for them. They inserted deep cover agents as part of their plot, but one fell in love with a woman and married her. He helps MIB save the world, but when it's all over, he knows he has to confess the truth to his wife and fears how she'll react. The scene then cuts to a hot sheet headline: "He's an alien, and I love him."