Bob and George
Thursday, April 20th, 2000 #20
The Beginning of the Story To Learn A Lesson
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According to the more canon sources, when the first eight robots were created (including Proto Man and Mega Man), Dr. Wily installed programming to turn them evil when he began his plans for world domination. The story goes that when the programming was activated, it didn't work with Rock and it may have seriously screwed up Proto Man. This is sometimes used as another explanation for why Proto Man didn't return until Megaman 3. As is shown later in the series, Proto Man is fiercely independent and he may have spent the time repairing himself before presenting himself to Dr. Wily, while pretending to being under his control.

My interpretation is more that Proto Man left Dr. Light to his own devices in an attempt to get him to wise up to Dr. Wily and his evil ways. Like how you let a toddler stick a screwdriver into the light socket just to teach him not to do it again.

And his reappearance in Megaman 3 might've been because Dr. Light clearly didn't learn his lesson about Dr. Wily the first two times.
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