Proto Man is the Blue Bomber’s older, cooler brother otherwise known as “Blues” in the japanese version. In fact his original name in Mega Man 3 was Break Man since he would destroy the objects in your way to help you progress further into a level. Whenever this ambiguous character would make his appearance a distinct whistle would always be heard before he entered the room. The whistle was without doubt supposed to be a blues/ jazzy sounding tune to go with character’s original japanese name.
When Proto Man first showed up in Mega Man 3 he wasn’t known to be anyone significant, just another robot who seemed to have a good side. However once the player reached the end of the game a startling revelation would be told you. Dr. Light revealed to Mega Man that Proto Man was in truth your older brother. The American cartoon that began playing in the early 90′s also had a explanation and a backstory to Proto Man’s creation. As the cartoon tells it Dr. Wily and Dr. Light were two scientists who has teamed up to create the world’s first robot. As time went on the two eventually built Proto Man, but Dr. Wily’s intentions became corrupted and so he stole Proto Man and began to create his own brand of robots to conquer the world. With what designs Dr. Light still had he created Mega Man to stop Dr. Wily’s insane plot, now bringing into full circle why Mega Man was altered to fight. There are some plot holes in the cartoon so it shouldn’t be taken as canon, but it’s interesting view into the story.
Proto Man eventually became a villian in Mega Man 5, but later was discovered to be framed by another robot. At the end of the classic series there were two arcade style fighting games released in Japan named “Mega Man: The Power Battle” and “Mega Man: The Power Fighters”. These games were actually pretty fun but also very simple. You could choose to play Mega Man, Proto Man, or Bass and each character would have their own individual ending. The ending to Proto Man’s story revealed that he was suffering from a fatal defect in his system and his life span was being cut short because of it. At the end Proto Man simply vanishes rather than have Dr. Light try to fix him, saying he’d rather find his own way. Nothing else is much known about Proto Man after his disappearance.
Some say that Proto Man was eventually created into Zero from the Mega Man X series, but this is also explained in Mega Man: The Power Fighters. If you choose to play as Bass his ending reveals Dr. Wily working on a new robot to battle Mega Man, since he feels Bass is no longer strong enough. The player is shown a silhouette of whom is undoubtedly Zero, at which Bass calls it a “Girly” looking robot. Wily scoffs saying that this is the most advanced and strongest robot known to man and won’t be ready for some time. This explained Zero’s beginnings but still didn’t reveal much about Proto Man’s future. Players wouldn’t find him in the X series, Zero series, or even ZX series – His existence ended in the classic series but he made a grand return in the Battle Network games and Anime series as well (where he looked a lot like Zero).