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In the closing of Mega Man 6, Dr. Wily was finally put in jail. What Mega Man didn't know was that Dr. Wily had robots hidden somewhere is his lab. After six months without Dr. Wily's input, the robots would activate, and search for Dr. Wily.
The Robots gave a city a surprising attack, looking for their master. Mega Man and Dr. Light watch the robots help Dr. Wily escape from a far distance. Mega Man goes out to stop Dr. Wily. Along the way, he encountered Bass, another humanoid robot, and Treble, his mean robotic wolf. They are also trying to stop Dr. Wily. The battle began...
- DWN-049: Freeze Man, weak to Junk Shield/Scorch Wheel, gives Freeze Cracker
- DWN-050: Junk Man, weak to Thunder Bolt, gives Junk Shield
- DWN-051: Burst Man, weak to Scorch Wheel/Freeze Cracker, gives Danger Wrap
- DWN-052: Cloud Man, weak to Danger Wrap, gives Thunder Bolt
- DWN-053: Spring Man, weak to Slash Claw, gives Wild Coil
- DWN-054: Slash Man, weak to Freeze Cracker/Scorch Wheel, gives Slash Claw
- DWN-055: Shade Man, weak to Wild Coil, gives the Noise Crush
- DWN-056: Turbo Man, weak to Noise Crush, gives the Scorch Wheel
On a side note, a fan-made NES style remake of this game can be found online.
- A Winner Is You: In the Anniversary Collection version, the end credits sequence (Mega Man walking away from a burning skull fortress in deep contemplation, a slideshow of the robot masters, and Bass looking out overhead) is replaced by just showing the credits against a plain black background. Apparently, this is because the developers, Atomic Planet, didn't know how to properly emulate the Mode 7 effects used here.
- Big Boo's Haunt: Shade Man's level.
- Bonus Boss: Proto Man, after meeting certain requirements, can be fought in a secret area in Shade Man's level.
- Breaking the Fourth Wall: try using the Freeze Cracker on Freeze Man.
- Bring It: Freeze Man reacts to everything you do. If you do nothing, he defaults to taunting you.
- Call Back: This game makes several references to previous games, but the most apparent is the robot museum stage. Glass tubes with various robot masters on display, with Wily making off with Guts Man (to be remodeled into a fortress boss later), and the music for that stage is a mix of Guts Man, Heat Man, and Snake Man's themes.
- Charged Attack: The Noise Crush is a Collect Type, where Mega Man must bounce it off a wall to catch the ricochet to empower the next blast. The Wild Coil and the Mega Buster are Hold Types.
- Crazy Prepared: Wily apparently built 4 Robot Masters and put a six month watchdog timer just in case he were arrested.
- Deleted Scenes: scenes Dummied Out for the International versions, where either Roll or Auto would replace Dr. Light in giving comments every time Mega Man gets a new weapon.
- Easter Egg: There is a code that allows you to duel Bass in a one on one two-player duel ala Street Fighter.
- Guide Dang It: Freeze Cracker, Wild Coil, and Danger Wrap can be aimed by holding up or down before shooting. Danger Wrap can also be aimed "foward".
- Invisibility Cloak: the Wily Capsule's usual teleporting ability is replaced by this for some reason.
- The Mole: Bass was first introduced as a potential ally to Mega Man, who claimed to also be battling Dr. Wily. When he's discovered injured later, Mega gives him access to Dr. Light's lab to be repaired. Bass ends up ransacking Light's lab and stealing the plans for some new upgrades for Mega Man and Rush, delivering them to his creator, Dr. Wily.
- Monster Clown: Mash, the boss of the robot museum stage.
- Name's the Same: Turbo Man, not to be confused with the superhero in Jingle All the Way.
- Shout-Out: To Ghosts N Goblins; hold the B button while selecting Shade Man's level and it will play the famous first level theme from the series.
- Springs Springs Everywhere: Spring Man's stage, of course!
- Weather Control Machine - Cloud Man's stage involves lots of pushing wind and blinding rain (one of the few games to notice how driving rain will reduce visibility). Cloud Man uses these gimmicks as well when you fight him.
- Why Don't You Just Shoot Him?: This is the first, and so far only, game to get into this. Mega Man seriously considers killing Wily after defeating him for the umpteenth time. Unfortunately (but fortunately for Wily) Mega Man was "Three Laws"-Compliant, leaving him unable to carry out his threat.
- Your Size May Vary: compare the Mad Grinder in the intro to the actual Mad Grinder that Mega Man fights.