Origins: The endings of Megaman 3 and The Power Battle tell us that Protoman was Dr. Light’s first attempt at a fully-functioning humanoid robot (hence his name). The exact circumstances are never mentioned, but at one point, Protoman disappeared from Light’s lab (the most popular theory is that a lab accident threw Protoman into a wormhole of some kind, but I don’t think any official explanation was given). Sometime after, Light builds Rock and Roll.
Megaman 3: Protoman’s first appearance in the games is in Megaman 3, but as an enemy. He shows up in Hardman, Magnetman, and Shadowman’s stages to fight you for a while, then beams out after taking a few hits. In Geminiman’s stage, he appears again, but rather than fight you, he opens up the entrance to Geminiman’s inner sanctum. Later, after defeating Doc Robot, he appears again, this time donning a full-face mask and calling himself ‘Breakman’. After all that, he ends up saving Megaman from underneath the rubble of Wily’s collapsed fortress before disappearing once again, making his presence known only with his trademark whistle. The story behind the events of the game is a mystery, since the game itself doesn’t go into it much, and Protoman isn’t even mentioned in the manual. Here’s what I got from it however, based on what I saw: Dr. Wily found Protoman and convinced him to work for him. It probably wasn’t difficult, seeing how Wily was Dr. Light’s partner, and was thus recognized by Protoman. However, Protoman seemed to recognize Megaman as one of Dr. Light’s creations, since their designs were very similar. He never fought very hard when he did battle Megaman, and he assisted Megaman in reaching Geminiman’s lair. When Wily’s fortress collapses, Protoman enters the lab looking for Wily, but finds a battered Megaman instead. I suppose the biggest mystery is the whole ‘Breakman’ deal. I’m not quite sure what prompted him to change his name. My guess is that Wily had him use an alias to make him seem more like he was entirely Wily’s creation, instead of a joint effort by Dr. Light and himself. That may also be why he gave Protoman the full mask later on. There are other theories as well. Mandy Paugh, of the Megaman Homepage, indicated a different theory in her fanfics. There, Breakman was the original name given by Dr. Light, while Protoman was the name Dr. Wily preferred.
Megaman 4: Protoman makes only a brief appearance, but it is an important one, on many levels. The masked marauder interrupts the battle between Megaman and Dr. Cossack, bringing with him Cossack’s daughter Kalinka. She tells Megaman the truth about her father; that she was kidnapped by Dr. Wily and used as a bargaining chip to force Cossack to do Wily’s bidding. Obviously, Protoman had realized that what Wily was doing was wrong and brought her back to her father. Then Wily appears and curses Protoman for betraying him. Protoman has apparently realized Dr. Wily’s evil intentions, and has severed his ties with him.
Megaman 5: As the game begins, it appears that Protoman, although he left Dr. Wily, is still evil and has kidnapped Dr. Light, and unleashed eight new robot masters unto the world. Megaman battles through his fortress and confronts his brother, but he seems reluctant to attack. Until, that is, the real Protoman appears and reveals the imposter as Darkman, one of Dr. Wily’s robots. Megaman defeats Darkman and Dr. Wily, and saves Light, but when the fortress collapses, Protoman once again appears and helps them escape. Then he disappears as quickly as he came. Now seems to be where Protoman begins his usual habit of dropping in unexpectedly to help his brother when in need. He does little real fighting, though. He left immediately after exposing Darkman, and left Megaman to take care of him and Dr. Wily on his own.
Megaman 6: Protoman has almost no role in this game. He only shows up to deliver an Energy Balancer to Megaman.
Megaman 4 & 5 GB: Same as in MM6; Protoman will beam down in a few secret rooms to deliver some power-ups, much like Eddie.
Megaman 7: Protoman also plays no vital role to the story. He’s simply “the helper guy” again. Although he does it a lot more than in MM6. He will appear in a couple of spots to give casual hints to Megaman. The first hint he gives is about using your special weapons to uncover secrets. The second time is to mention the existence of the Rush circuit plates for acquiring the Super Adapter. The third time you meet him, Proto will challenge you to a duel. He doesn’t hold back, though, like he did in MM3. If you win, he’ll loan you his trusty shield.
Megaman 8: Protoman doesn’t appear much, but at least he’s part of the story. The first time we see him is after Megaman’s duel with Duo. He doesn’t say much, except to tell Megaman that Wily’s Tower is nearby and that Duo was heading there. We then see him in the ending FMV. He has a brief conversation with Duo, and relays his word of thanks to Megaman later.
Megaman & Bass: Proto starts to take a larger place in the storyline. The first we see of him is right at the beginning, where he challenges King. He gets beaten up badly, though, and King escapes. Later, he appears again during your battle with King. King is using a seemingly invincible shield, but Protoman unveils a new attack, and destroys the shield, allowing you to finish him off (whether you’re using Megaman or Bass). During Bass’s ending, he shows up once more and destroys Dr. Wily’s blueprints for King II. He then gives Bass a little free advice; that he’ll never defeat Megaman because while Megaman fights to protect people, Bass fights only for his own enjoyment and to satisfy his ego. I heard a rumor stated once that said there was some secret method to unlock Protoman as a playable character in this game. Unfortunately, there’s nothing to that rumor.
Megaman: The Power Battle: Aright! Protoman is finally a playable character! While there’s little plot surrounding him (he doesn’t have much of an ending). It’s nice to be able to play as him for once.
Megaman: The Power Fighters: Once more, Protoman is playable, and he has a more involved ending, albeit a foreboding one. Dr. Light tells Protoman that he’s detected some sort of energy defect in his systems, and unless he fixes it, Protoman will die. Protoman refuses to have Light work on him, however, and once more leaves on his own.
The TV Series: We really can’t consider this canon to the main series, but we san still talk about it nonetheless. Proto’s TV show origins are quite confusing. In the first episode, “The Beginning”, we see Light and Wily working on a red & grey robot that looks a lot like a miniature Protoman, minus the helmet, visor, and scarf. This robot goes out of control, and Light decides to start over from scratch, subtlety blaming the problem on Wily, which he certainly resents. Wily decides to prove he’s the better robot designer, so he steals Dr. Light’s blueprints and sets off on his own. We later see him constructing the final Protoman on his own, but when he left Light’s lab earlier, he wasn’t carrying the “mini Protoman”, just the blueprints.
If that’s the case, Megaman and Protoman really aren’t brothers, since Mega was built exclusively by Light (after Wily already left, using plans he said he’d have to start over on), and Proto was built exclusively by Wily. So, Mega and Proto were not “built from the same plans” as Protoman later said in that episode. To add to the confusion, in “Bro Bots”, season 2, Dr. Light mentions about Protoman, “I used the same ethical program for him that I used in you, Mega.” So now Dr. Light built Protoman?? Confusing, indeed.
Protoman’s behavior in the TV series is totally different from the games as well. The Protoman from the games strikes me as much more mature than the one from the TV show. Not only is Protoman on a different side, he acts incredibly spoiled at times, and calls Megaman by some very juvenile names, such as “dweeb”. Of course, nearly all of the bad guys have called Megaman a “dweeb” at one point or another, but Protoman is the last one who should be calling people names that aren’t even used by 5-year-olds anymore.
So what more is in store for Protoman? As of now, nothing. Capcom still hasn’t continued the original series at all. Until then, I suppose we can only hypothesize, unfortunately, that Protoman is eventually killed by whatever flaw Dr. Light found during The Power Fighters. Such an event would also explain why Protoman isn’t seen nor heard of in the MMX series. Perhaps we’ll see more unfold when and if Megaman 9 ever comes out.