Dr. Wily has uncovered an ancient alien supercomputer, Ra Moon, hidden in the ruins of the Amazon. He uses it to revive his Robot Masters from Mega Man 2 and Mega Man 3. The ruins are capable of causing almost all of the machinery and electricity in the world, including robots, to shut down. Roll is quickly affected, so Dr. Light immunizes Mega Man and his brothers and sends them to stop Dr. Wily before it's too late.
It's also notable for being one of the very few times that Dr. Wily isn't the final boss.
This game contains examples of:
- Anti-Villain: Wood Man. He's entirely motivated by the death of his friend Shadow Man, whom Mega Man destroyed beyond repair at the end of Chapter 1, and sets out to avenge him by terminating Mega Man himself.
- Back from the Dead: Ra Moon resurrects Dr. Wily's first and second set of Robot Masters. Then by the end, all of them (including Quick Man and Gemini Man, who got poignant death scenes, and excluding Shadow Man, who was Deader Than Dead) get brought back.
- Beware the Nice Ones: Mega Man has a major moment of this at the end of Chapter 1. After successfully convincing Quick Man of Ra Moon's evil intentions, Shadow Man shows up to try and finish Mega Man off, which leads to Quick Man taking a Shadow Blade to the back to protect Mega Man. Devastated by Quick Man's death, punctuated by Shadow Man cruelly mocking his sacrifice, an enraged Mega Man stops holding back and blasts Shadow Man to literally nothing, destroying him to the point where not even Ra Moon can revive him.
- Big Bad: Wily, who uses the ancient supercomputer Ra Moon to revive his Robot Masters and tries to Take Over the World; except it's actually Ra Moon who is using him.
- Big Damn Heroes: If you lose against some of the Robot Masters, you will be saved and healed by one of the Mega Man Robot Masters, such as Guts Man rescuing Mega Man should he lose to Heat Man/Bubble Man, or Cut Man flying in on Rush Jet to catch Mega Man before he falls into a vat of acid. They also pull Mega's unconscious body out of the temple following Ra-Moon's defeat.
- Canon Discontinuity: This game was disowned by Keiji Inafune and Capcom as a whole, and has never been referenced in any subsequent games.
- Choose Your Own Adventure: Outside of battle, the game plays like this.
- Dangerous Forbidden Technique: The Double Rock Buster, which Wily exclaims will severely overheat Mega if he attempts to use it. It is so powerful that it instantly kills Ra-Moon in a single use, and the worst that happens to Mega is him losing consciousness.
- Darker and Edgier: Roll is in a state of near death for the whole game, several humans and Robot Masters (including Quick Man, Shadow Man and Gemini Man) are shown being outright killed, if you get a standard Game Over Roll does die, and if you lose to the final boss, everyone, even Wily, dies.
- Deader Than Dead: Shadow Man is destroyed by Mega Man — so thoroughly, in fact, that even Ra Moon is seemingly incapable of reviving him (given his absence from the finale).
- Enemy Mine: To defeat Ra-Moon, Wily and his Robot Masters are forced to co-operate with Mega in the game's climax. This includes the Masters donating their last bit of strength to return Mega to full energy after he takes an otherwise-fatal attack from the New Yellow Devil.
- Everybody Laughs Ending: With Mega and the Light Masters.
- First-Person Shooter: The battle scenes are this, similar to Yoshi's Safari.
- Full Motion Video: Unlike most Mega Man games, the game's story is almost entirely told through fully-animated cutscenes.
- HeelFace Turn: Quick Man. By the end of the game, all the Robot Masters pull one to help Mega Man destroy Ra Moon.
- Heroic Sacrifice: Some of the Robot Masters do this, and Mega Man himself nearly does in the finale.
- Ill Girl: Roll, to the point of near-death.
- Kick the Dog: Shadow Man's remorseless reaction to accidentally killing Quick Man when he sacrifices himself to protect Mega Man after being convinced by him that Ra Moon is really planning to destroy the world is a textbook example of this. Needless to say, it backfires horribly for him.Shadow Man: What a show he put on for my blade!
- Killed Off for Real: Shadow Man is thoroughly destroyed by Mega Man, to the point where he can't be rebuilt, not even by Ra Moon. Quick Man, despite getting a burial scene, gets brought back for the final act.
- Nonstandard Game Over: Refusing to fight Wood Man and losing to the final boss give different Game Over scenes.
- OVA: The games acts like this.
- Point of No Continues: Losing to Shadow Man and Gemini Man gives no chance to continue.
- Stay in the Kitchen: The in-game explanation for why Roll was affected by the EMP is because she's a girl. There's a reason the Archie comics version of this game's events has nearly all the robots be affected at the start, ignoring their genders entirely.
- Taking the Bullet: Quick Man takes one of Shadow Man's blades and dies. He gets better, though.
- The Unfought:
- In addition to not being the Final Boss, this is probably the only classic Mega Man game where Dr. Wily appears, yet is never fought at all.
- Either Heat Man or Bubble Man won't be fought if Mega Man traveled up the mountain or down the river. Though Proto Man handles the other.