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The story is centered some time after 2, where Dr. Wily has seemingly reformed after his previous two defeats, and is now working alongside Dr. Light to build a peacekeeping robot called Gamma. However, a batch of robot masters in charge of eight mining operations go berserk and start reaking havoc. Naturally, Mega Man is sent off to stop the rogue machines, this time with the help of his new canine companion, Rush! Along his journies, he encounters a mysterious being called Break Man, who keeps fighting him, as if to test him...
Obviously, it turns out Dr. Wily was behind the whole scheme, tricking Mega Man into defeating the robot masters so he could steal Light's prototype robot and use it for his own evil ends. Oh yes, and "Break Man" turns out to be Proto Man, Mega Man's long lost older brother.
All in all, 3 was another hit in the series, selling over a million copies and receiving excellent critical reception, although not quite on par with 2. The refined gameplay of 2 was expanded upon further, with the "Items" turned into the far more flexible Rush vehicles, no limit on how many E-Tanks you could carry, and a new slide move. On top of that, 3 is the longest game in the entire NES Mega Man series, with a whopping 18 stages total! Unfortunately, Keiji Inafune claimed that 3 was his least favorite Mega Man game, due to the strained development of the game keeping it from reaching its full potential in his eyes, as well as losing the simplicity of the previous two games.
As with 1 and 2, 3 would later recieve a 16-bit upgrade as part of the europe and japan-only Mega Man: The Wily Wars/Rockman Megaworld cartridge for the Sega Genesis . It would also receive a japan-only PS 1 re-release as Rockman 3: Complete Works, complete with remixed music and bonus content. The game would eventually get a major re-release as part of Anniversary Collection for Play Station 2, Game Cube and X Box, and it is now available on Virtual Console.
- All There in the Manual: The only way to learn about the story, since the game's rushed production didn't afford it the luxury of having an intro cutscene.
- Crate Expectations: A form of this appears as canisters with a "?" on them. Shooting them gets you a random item, from a small energy refill to a 1-Up to an Energy Tank. They were exclusive to this game, however the mechanic was modified into Eddie in later games.
- Disc One Final Boss: The Wily Machine. As soon as it's destroyed and Dr. Wily starts begging for mercy, "his" head pops off, revealing that he's a robotic fake.
- Doppelganger Attack: Gemini Man's specialty, along with Frickin' Laser Beams. The Mega Man clones in Wily's fortress are also a variant.
- Eternal Engine: Spark Man's stage.
- Everything Is Better With Spinning: The Top Spin weapon. Subverted, as it's not very effective most of the time (unless you do know how to use it well).
- Final Boss: Gamma.
- Hijacked By Wily: The first instance of many in the series.
- Humongous Mecha: Gamma.
- Instant Awesome, Just Add Ninja: Shadow Man
- Mission Pack Sequel
- Obvious Beta: A much less severe example than most, though there are still some quirks at times (uneven energy use for the Top Spin, all Robot Masters being weak to their own weapons, inaccurate Skull Castle map paths, etc).
- Puzzle Boss: The Hologram Mega Men.
- Recurring Boss: Break Man (aka Proto Man).
- Reflecting Laser: Gemini Laser.
- Rocket Punch: The Hard Knuckle.
- Sequel Hook/The Stinger: Though it seemed Wily had been crushed by the debris from his collapsing fortress, you can see what looks like his saucer floating away in the distance as Mega Man is gazing up at the sky during the ending.
- Spike Shooter: Needle Cannon.
- Spin Attack: Top Spin.
- Updated Rerelease: The Wily Wars remake, and to a lesser degree, the Complete Works PS 1 port.
- Villains Want Mercy: Both the robotic Wily imposter and the real one in the ending.
- Wall Crawl: Search Snakes do this.
- Wasted Song: A few tunes, like the Skull Castle intermission theme and Proto Man's theme in the cast roll, never played in their entirety.
- Weaksauce Weakness: Shadow Man, one of the toughest Robot Masters in the game, is weak to the Top Spin (which requires close contact, no less).
- Aside from being a Sega Channel exclusive for a brief time