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Just when people forgot all about Dr. Wily, robots all over the world began going crazy. It soon became apparent that these robots were those created by Dr. Light. As phone calls came pouring in to Light Labs, Dr. Wily interrupted all television programs to announce that these robotic riots were not his doing. He then continued to show video evidence that proved Dr. Light's involvement in the recent violent outbreaks. To make matters worse, Wily gave the account number to his personal bank account and announced that he would accept donations to build his own robot army to counter that of Light. Mega Man quickly volunteered to clear Light's name and was sent out to investigate the source of the problem.
- DLN-065: Concrete Man, weak to Laser Trident, gives Concrete Shot
- DLN-066: Tornado Man, weak to Plug Ball, gives Tornado Blow
- DLN-067: Splash Woman, weak to Hornet Chaser, gives the Laser Trident
- DLN-068: Plug Man, weak to Jewel Satellite, gives Plug Ball
- DLN-069: Jewel Man, weak to Black Hole Bomb, gives Jewel Satellite
- DLN-070: Hornet Man, weak to Magma Bazooka, gives the Hornet Chaser
- DLN-071: Magma Man, weak to Tornado Blow, gives the Magma Bazooka
- DLN-072: Galaxy Man, weak to Concrete Shot, gives the Black Hole Bomb
- American Kirby Is Hardcore: Spoofed here with the virtual box art created in homage to the first two games.
- And Your Reward Is Clothes: The most expensive item in the shop, at 200 screws, is an alternate outfit for Roll (who's not even playable this time), changing her into her Mega Man 8 duds.
- Charged Attack: While the Mega Buster is no longer this, the Magma Bazooka is.
- Chest Monster: The Met-like enemies disguised as 1-Ups.
- Dual Boss: Thought the Yellow/Green Devils from previous games were tough? Enjoy fighting two at the same time...
- No Name Given: for the first time ever, the Fortress Bosses weren't given any official names.
- Overly Long Gag:
- Promoted to Playable: Proto Man, via DLC. Unlike Mega Man, he retains his charged buster and slide ability, and can block projectiles with his shield (while jumping). The tradeoff is that he takes considerably more damage than Mega and has a greater Knockback. He also can't access the store to buy items.
- Self-Imposed Challenge: Several of the achievements are this. Want to try beating the game without using any special weapons? How about without shooting anything except bosses and mini-bosses? Without dying? Without getting hit??
- Tennis Boss: with the first form of the Wily Machine, since the eggs that it "lays" are the only things that can damage it in this form.
- Tyrannosaurus Rex: the Wily Machine this time around is roughly based on one.
- Visual Pun: Tornado Man has a helicopter-Blade Below the Shoulder.
- Utility Weapon: A few in this game:
- What Measure Is a Non-Human?: Part of the plot explores this a little bit. This game reveals to us that, by law, robots are assigned an expiration date, at which time they are to be disposed of and scrapped. Dr. Wily took advantage of this by convincing Dr. Light's recently-expired robots to allow him to "fix" them so they can live on. Despite his ulterior motives, Wily still made a compelling argument.