- X's friendship with Zero throughout the series. Whether you view the duo as Bash Brothers, Heterosexual Life-Partners, or something more, you cannot deny that their bond is one of the bright points in a Darker and Edgier universe.
- In X's ending for X4, X asks Zero to terminate him if he ever goes Maverick. Zero's response? "Don't be absurd." The unspoken message there is that Zero doesn't think that X could ever be corrupted by the Maverick Virus.
- Zero's return in X6. The music, and the joy in X's voice when Zero reveals himself really sell the moment.
- In X6's Good Ending for X, he brings back a mortally-wounded Gate for Alia to try and repair, as she used to be his best friend. Really, that whole ending is pretty heartwarming—the rest of the Maverick Hunter team shows up to offer their support in restoring all the damage caused by Sigma's Colony Drop in X5, leading to the most optimistic ending in the series.
- In Zero's X6 ending, when he's sealing himself away to purge the Maverick Virus from his system completely, the scientist in charge of the operation is concerned about what might happen in his absence. Zero calmly replies not to worry about it, as X will always be there to protect the world and calling him the superior hunter. He's got that much faith in his partner.
- X finally warming up to Axl by the time of X8.
- A subtle one from the mini-comic in Mega Man #35. In X's apartment, you can see a picture of him and Dr. Cain looking happy together.
- Towards the end of the flashback of "The Day of Sigma" in Maverick Hunter X, Dr. Light is clearly at the end of his lifespan and preparing to seal X away for the day he is ready in the future. Before he is sealed, X promises his father that he will use his powers to fight for good if needed, leaving Dr. Light to cry with pride for his son.
- In the manga adaptation of X1, X encounters a group of infected former Maverick Hunters who want him to "prove his loyalty" by killing a defenseless human girl. Not only does he stop them and put them down before they can hurt the girl, he carries her to safety, and she clings to him with very visible gratefulness and comfort.
- In the manga adaptation of the Overdrive Ostrich fight, Ostrich was not an infected Maverick, but rather Storm Eagle's kouhai out to avenge his death at X's buster. However, in the progress of the fight, X reminds him so much of Storm Eagle that his will to fight is sapped away; when X tries to stop a (possibly nuclear) missile from launching, just barely failing to reach the missile by dash-walljumping, Overdrive performs a Heroic Sacrifice to stop the missile, having forgiven X as the actual ghost of Storm Eagle shows up. Even X can see the apparition of Storm Eagle as Ostrich makes his last booster-assisted leap to destroy the missile, and he witnesses Eagle and Ostrich enjoy one last happy chat and even a final, audible high five, before he stops the missile by fatally crashing into it.
- In the manga adaptation of the Crush Crawfish fight, X is forced to retreat to a safe distance when Crawfish takes a human hostage and cuts her hair with his claws as a threat, and then stresses hard over his aim as he tightly focuses a charged buster shot into an extremely tight, narrow beam to put the maverick down with a precision headshot. He finds his arms stuck in that position due to stress immediately after making the shot, but then he looks around and notices the extremely pleasant weather, and his arms free themselves as he finally relaxes.
Heartwarming / Mega Man X