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.
Notably Darker and Edgier than the rest of the classic series, it was disowned by Keiji Inafune and Capcom as a whole. It is perhaps for this reason that the game was never released outside of Japan, or get acknowledged in any official materials until the adaptation in Archie Comics' Mega Man and a small acknowledgment in Super Smash Bros. for Nintendo 3DS and Wii U and Super Smash Bros. Ultimate (If Mega Man uses his Up or Down Smash, he'll stop to vent heat from his busters like what happens after he beats Ra Moon). Translations of the game's cutscene portions are also available online.
The game is also notable for being one of the very few times that Dr. Wily isn't the final boss.
This game contains examples of:
- Adaptational Badass: Gemini Man has more of his copies by his side when he becomes the second episode's final boss.
- Adaptational Villainy: Shadow Man is much worse here than his canon counterpart. He mocks Quick Man for sacrificing himself to protect Mega Man. Needless to say, Shadow Man gets what's coming for him.
- 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.Wood Man: How dare you do this to Shadow Man?! You even destroyed his core! He can't come back now. He was... he was my only friend! I'll avenge him! Fight me!
- Artistic License – Geography: It is stated that the Mayan ruins are in South America; they are actually in Guatemala and Mexico.
- 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 has never been referenced in any subsequent games.
- Dangerous Forbidden Technique: The Double Mega 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.
- Dark Is Evil: Ra Moon's physical form is a black sphere with golden glyphs and a glowing crimson eye. Its creations also bear its colors.
- 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 and Ra Moon kills all life on Earth, both organic and synthetic.
- 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.
- Heel–Face Turn: Quick Man. By the end of the game, all the Wily Numbers 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.
- Kick the Dog: Shadow Man's remorseless reaction to accidentally killing Quick Man when the latter 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: A coward and a traitor.
- 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.
- Non-Linear Sequel: The game came out after 8, but the lack of any appearance by Auto or Bass, suggests this takes before that, likely between 5 and 6, since Beat is present.
- Non-Standard Game Over: Refusing to fight Wood Man and losing to Shadow Man (kills Rock if he defeats him), Gemini Man (Also kills Rock after beating him), Ra Thor and the New Yellow Devil/Ra Devil (Ra Moon kills EVERYONE inside its temple) give different Game Over scenes.
- OVA: The game acts like this.
- Point of No Continues: Losing to Shadow Man and Gemini Man gives no chance to continue.
- Taking the Bullet: Quick Man takes one of Shadow Man's blades and dies. He gets better, though.
- "The Reason You Suck" Speech: Wood Man chews out Mega Man for killing Shadow Man prior to his boss battle.
- 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.
- Ra Moon itself is technically unfought, as its guardian, the New Yellow Devil/Ra Devil is the Final Boss and Rock destroys both of them with the Double Mega Buster.