- Mega meeting with his family in "Future Shock."
"Rush's jetmode doesn't work anymore," Roll told Mega Man regretfully.
- Mega Man and Protoman's heart-to-heart conversation in "Future Shock" on the way to Robo-Island Prison. It's made worse because, due to time travel laws, only Mega will remember it.
- The endgame of "Future Shock". The bad future ends with Roll, Light, and Wily dead and, while Mega Man is able to return to his own time thanks to future!Protoman, present!Protoman takes the password as a sign that Mega knows too much about him and decides to kill him.
- Protoman deliberating whether or not to fire the Lunar Laser at New York.
- Snake Man's situation. Even though he's one of the bad guys, it's hard not to feel sorry for the guy. He's fiercely loyal to his creator but largely ignored by him, he cannot be understood by anyone except Cut Man and is therefore easily dismissed, and his crush hates his guts. On top of that, his experience in Mega Man's body has altered him permanently, and is a constant source of confusion and frustration.
- The fact that Mega Man and Proto Man are genuinely fond of each other, but can't fight on the same side due to their different moral alignments. Nevertheless, they never stop trying to get each other on their side...