>>141843127It varies
Powered Up outright rewards you for not destroying them with their weapons because it allows them to be repaired making them playable
Super Adventure Rockman has them be your allies who bail you out when you get a game over
The Megamix manga has them repaired and reformed as well
And then you have other games where they're just on display in a museum
(which Flynn justified in-universe later in this comic) or serve as secret bosses with dialogue antagonizing Mega Man
Personally, I really dislike the idea of Light simply abandoning them because they're as much of his kin as Rock and Roll are