The city is holding a robot expo one day, when Dr. Wily's saucer appears in the sky and transmits a signal that causes all the robots to go nuts. Worse still, Wily has rebuilt eight of his previous Robot Masters, and has decided that the third time's the charm for the Mega Man Killer series, which this time is represented by Ballade. Fortunately for Mega Man, Dr. Light has gotten tired of sitting ineffectually on the sidelines, and has equipped his lab with the ability to produce upgrades and items for Mega Man, so long as he can find enough P-Chips to make the upgrades.
This sequel continued to expand the series, mostly through the shop mechanic, though also adds a greater emphasis on the storyline (which is a little less of an Excuse Plot this time around) and makes the game even longer than in the previous entry. The overall gameplay is broadly similar to that of Mega Man 5, with Beat being introduced, though this game doesn't incorporate 5 NES's "lose your Charge Shot when you get hit" mechanic, instead including a recoil for when you fully charge up your Mega Buster.
Robot Masters from Mega Man 4:
- DWN-025: Bright Man, gives Flash Stopper
- DWN-026: Toad Man, gives Rain Flush
- DWN-028: Pharaoh Man, gives Pharaoh Shot
- DWN-029: Ring Man, gives Ring Boomerang
Robot Masters from Mega Man 5:
- DWN-035: Stone Man, gives Power Stone
- DWN-038: Charge Man, gives the Charge Kick
- DWN-039: Napalm Man, gives the Napalm Bomb
- DWN-040: Crystal Man, gives the Crystal Eye
The remaining Robot Masters from 5 NES... weren't held over for the following outing, which took the Game Boy subseries in a totally different direction.
New for this game:
- MKN-003: Ballade, gives the Ballade Cracker
- After Boss Recovery: This game brings back one of the few aspects of Mega Man II that was generally well-liked, namely only providing full energy weapon refills after the Mega Man 4 bosses. This forces you to carefully manage your weapons energy while taking on the Mega Man 5 bosses — or just pay for Dr. Light to replenish your weapons, if you have the P-Chips to spare.
- All There in the Manual: Averted. This time around, the only detail not explained in the game is that Wily is attacking a Robot Expo. Everything else is explained in the cutscenes that this game introduces to the series.
- All Your Powers Combined: Aside from Mega Man himself, an unnamed boss on the outside of the Wily Battleship will use the Ring Boomerang, Napalm Bomb, Power Stone and Ballade Cracker as attacks.
- Anti-Frustration Features: If one gets enough Game Overs, Dr. Light will upgrade the Mega Buster to let it charge up quicker.
- The Battle Didn't Count: The first time Ballade is fought, he will always survive with one point of health before fleeing. The second time you fight him, it's for real (not that he doesn't inexplicably turn up in a badly damaged state despite exploding later on).
- Boss Rush: For the first time in the Game Boy sub-series, you have to face off against all eight Robot Masters before you can fight Wily.
- Collapsing Lair: Twice. Firstly, the Wily Station, the lair of the Mega Man 5 Robot Masters, starts blowing up after the second battle with Ballade, forcing you to escape. Then, the Wily Battleship starts to explode after the final battle, though this time Mega Man escapes in a cutscene.
- Collection Sidequest: The first four stages have an optional sidequest to collect the letters "B E A T" to gain access to Beat. With the Wily Station stages however, collecting the letters "W I L Y" is required in order to access the second battle with Ballade.
- Cool Spaceship: The Wily Battleship.
- Degraded Boss: Press'n, miniature versions of the Wily Machine from the previous Game Boy game, appear in the final stage as a Smash Mook-type enemy.
- Escape Sequence: After defeating Ballade for the second time, the Wily Station begins to collapse, prompting one of these to happen.
- Hailfire Peaks: The final four Robot Master stages combine elements from their NES stages and Fortress levels.
- HeelFace Turn: Ballade realises he was wrong to fight Mega Man, and sacrifices himself to save him. But if later games are any indication, it doesn't stick.note
- Heroic Sacrifice: Ballade comes to repent working for Dr. Wily, and blows himself up in the game's climax to allow Mega Man to escape Wily's exploding spaceship.
- Humongous Mecha: Instead of a Wily Machine, Wily fights you using the "Wily Robo Iron Golem", one of these; built in his own image, of course. In contrast to the Wily Machines on the Game Boy games before it, it not only completely dwarfs Mega Man, but it's so tall (for Game Boy standards at least) that beating it requires two phases — one to knock it down to a lower height, and another to destroy its head and fully defeat it.
- Law of Inverse Recoil: The Super Mega Buster averts this - unlike in Mega Man 5 (or indeed any past or future game with a chargeable Mega Buster), firing off a Charge Shot in IV will push Mega Man back a few pixels, making it somewhat riskier to use.
- Me's a Crowd: The two Hunters onboard the Wily Battleship have the ability to create more of themselves (but in the first one's case, the copies are far weaker).
- Oh, Crap!: Mega Man has this reaction to the Wily Robo Iron Golem in its accompanying cutscene, looking up in absolute horror as it rises into view and looms over him.
- One-Winged Angel: Ballade uses a transformation in his second battle, granting him upturned horns and Cool Shades. He also starts using the Ballade Cracker with it.
- Rearrange the Song: As per tradition, the Robot Master stages and boss fights use rearranged versions of the corresponding music from their games (though the Mega Man 4 boss theme is heavily rearranged and barely recognisible). Unlike the previous three gamesnote however, Ballade and Dr. Wily have their own boss battle themes.
- Sean Connery Is About to Shoot You: At the end of the intro cutscene, Mega Man charges up his Mega Buster and fires directly at the camera.
- Sequel Escalation: In a pretty big way. There's more of an emphasis on storyline, purchasable upgrades, cutscenes, many more levels, the series' traditional teleporter room Boss Rush, Beat, and even Proto Man makes an appearance. This is especially notable as the main console games didn't have most of these until Mega Man 7, released around two years later.
- Tank Goodness: The Wily Station makes a fourth appearance, though this time it is now a giant mobile tank.
- Unexplained Recovery: Ballade appears onboard the Wily Battleship— heavily damaged, but alive. Bear in mind that he had completely exploded before then.
- Video Game Settings:
- Absurdly Spacious Sewer: Toad Man's stage.
- Blackout Basement: Bright Man's stage.
- Build Like an Egyptian: Pharaoh Man's stage.
- Disc-One Final Dungeon: Wily Station. Twice, in fact.
- Eternal Engine: The Wily Station and Wily Battleship levels. The Mega Man 5 Robot Master levels, due to being located in the Wily Station, also count.
- Locomotive Level: Charge Man's stage.
- Space Zone: The Wily Battleship.
- Utility Weapon: A few weapons have upgraded utility from their original NES appearances. The Ring Boomerang, for instance, can grab items for Mega Man, and the Rain Flush can freeze the quicksand in Pharaoh Man's stage and put out lethal fires in Napalm Man's stage.