Chapter three, "Metal Heart", at the end where it's revealed that Dr. Light rebuilt the Mother Computer and her "son" as a park control computer, allowing mother and son to be together forever.
The scene of Skull Man's funeral, after being accepted as a member of Cossack's family.
Star Man laughing in boundless glee as he rides the Skull Satellite (carrying the few Robot Masters that will battle the Stardroids) into outer space. Even more endearing: the rest of the Fifth Numbers, on the ground, looking up at the rocket trail with undisguised pride and affection for their brother.
The Light Numbers and all the Wily Numbers helping repair each other like a huge gathering of friends instead of bitter enemies.
Cut Man sacrificing himself to save Rock, and his robot soul giving the latter the final impetus to overcome his Heroic BSOD.
Pluto calls the hallucination of Skull Man a monster, to which Ring Man responds by punching Pluto through the gut hard enough to destroy him. "He's not a MONSTER! He's...my BROTHER!"
Wily and Light collaborating to fix Rock, and Light later reminiscing wistfully about his old college days with Albert.
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