There's a little more of a plot compared to the previous game — this time around, Dr. Wily has used a stolen time machine to travel into the future, and brought back some rebuilt versions of the Robot Masters from the second and third NES games. Along with the Robot Masters, Wily has brought back Mega Man's own future self, who has been corrupted into an evil robot known as Quint, who is armed with the Sakugarne, a deadly cross between a jackhammer and a pogo stick. Yes, really.
This game was released just five months after Dr. Wily's Revenge, and both the rushed development schedule and developer Biox's unfamiliarity with the series are rather apparent in the rather odd storyline and various aspects of the gameplay. Unsurprisingly, this proved to be the only Mega Man game which the company ever worked on.
Aside from all that, the gameplay is much the same as in the NES Mega Man 3, meaning that E Tanks, the slide move, and Rush are introduced for this entry. In addition, despite the game's numerous other flaws, it did introduce what would become the standard format for the three following games, which consists of four full Robot Master levels and fights, followed by another four Robot Master levels and fights (as opposed to the previous game, which just gave you four Robot Masters from Mega Man with corresponding stages, followed by a Boss Bonanza of the Mega Man 2 Robot Masters).
Robot Masters from Mega Man 2:
- DWN-009: Metal Man, gives Metal Blade
- DWN-010: Air Man, gives Air Shooter
- DWN-013: Crash Mannote , gives Crash Bombernote
- DWN-016: Wood Man, gives the Leaf Shield
Robot Masters from Mega Man 3:
- DWN-017: Needle Man, gives Needle Cannon
- DWN-018: Magnet Man, gives Magnet Missile
- DWN-020: Hard Man, gives Hard Knuckle
- DWN-021: Top Man, gives Top Spin
The remaining Robot Masters from 3 NES were held over until the following Game Boy outing.
New for this game:
- ???-???: Quint, gives Sakugarne
- 11th-Hour Superpower: The Sakugarne is only obtained before the final Wily stage and can't be used anywhere else, but is the weakness of the Wily Machine's final form. However, unlike the previous game, it's not necessary to win.
- After Boss Recovery: Starting with the 3 NES Robot Masters, while you'll still get health refills after defeating each Robot Master (and Quint), you'll no longer get weapon energy refills and will have to rely on item drops from the enemies. Many fans actually appreciated this, feeling that it added an element of strategy to an otherwise ridiculously easy game and forced careful management of weapon energy during the second half, and this mechanic would later reappear in Mega Man IV and Mega Man V.
- All There in the Manual: As with the previous (and following) game, the only way to understand the plot is to read the manual. The Japanese manual gives more backstory than the localized Western one; Wily originally intended to use the stolen time machine to go back in time to before the events of the first game and launch a secret attack. However, the time machine was seriously flawed, and even with his modifications, it could only travel to the future and back.
- Astral Finale: Like before, the final stage takes place in outer space, onboard the Wily Station.
- Chain Reaction Destruction: At the end of the game, you shoot down Dr. Wily's escape pod with a giant missile. Wily then explodes repeatedly and crash-lands on Earth in a massive skull-shaped explosion.
- Easy Levels, Hard Bosses: Unusually for a Mega Man game (which usually fall under the opposite trope), the bosses are the only part of the game to present any real challenge.
- Goomba Stomp: The Sakugarne allows Mega Man to damage enemies by jumping onto them. However, he will still take damage if an enemy survives a hit.
- Grandfather Paradox: Ignored, which begs the question of what could happen to Quint if he destroyed his own past self...
- Guide Dang It!: Like Mega Man: Dr. Wily's Revenge, the second set of Robot Masters are accessed from identical teleporters. However, there's no way to tell which teleporter leads where until they're used, making it almost impossible to follow their weakness loop without a guide.
- Hitbox Dissonance: The game's hit detection is notoriously spotty in both directions, meaning that enemies can damage Mega Man despite his not appearing to touch them, while Mega Man's own shots can either no do any damage despite making contact, or destroy an enemy even when his aim seems slightly out. That said, the easy difficulty means this is more of a minor inconvenience than anything else; it only really becomes a problem in the final level (and Crash Man's to a lesser extent), where shooting enemies while on ladders can be difficult.
- My Future Self and Me: Quint is this to Mega Man. Wily gets in on the action too, with the Japanese manual saying he collaborated with his (apparantly reformed) future self to abduct the future Mega Man.
- Obvious Beta: The game had less than a year (possibly even less than five months) of development, and glitchy collision detection, bland level design, a strange plot, and poor sound quality stand as proof of it. It certainly didn't help that the developer had only ever made games for the Master System and Game Gear prior to working on this.
- Oddball in the Series: Despite being one of the Game Boy games where the Robot Masters come from the NES series, this game does not use adaptations of their original stage music.
- The Wily Machine's sprites depict Dr. Wily as much smaller than he's supposed to be, with him looking like a midget next to Mega Man.
- The game's U.S. and European covers both depict Quint in the background. Unfortunately, the artist apparently screwed up and confused him with Proto Man, resulting in him having red-and-white armor instead of the green armor of his official character art, along with slightly odd proportions that make him look more like a Mega Man X character.
- Power-Up Mount: To use the Sakugarne, Mega Man must first summon it and then jump onto it. With it, he can Goomba Stomp enemies and is immune to spikes.
- Rearrange the Song: Zig-zagged. Almost all the music in this game is new, but the "Got a new weapon" theme is a slightly rearranged version of the one from 3 NES.
- Sequel Difficulty Drop: Put it this way — it's like the developers only played Rockman 2 and found it way too difficult, so they imported the Mega Man 2 version just so they could play it on its easy mode... and then decided that was way too difficult! Even without the decidedly easy level designs though, the introduction of Energy Tanks and Rush makes the challenge much more reasonable than in the previous game.
- Sequel Escalation: For the game's many faults, it does at least manage to be larger in scope than Dr. Wily's Revenge, thanks to introducing a second set of Robot Master levels, along with Rush and various other gameplay mechanics.
- Shout-Out: The Wily Station's background features several melting clocks, as seen in the works of Salvador Dalí.
- Spell My Name with an "S": Crash Man's name is spelled as "Clash Man" in this game, which is actually his original Japanese name.
- Time for Plan B: The Japanese manual states Wily initially planned to go back in time to before Mega Man's creation, and launch a surprise attack. When the flawed time machine could only go to the future and back, however, he settled for abducting the future Mega Man and remodeling him into Quint.
- What Happened to the Mouse?: Quint just teleports out after you battle him, and is never seen or mentioned again. Presumably with Wily's plot foiled, either the timeline which led to Quint's creation ceased to exist, or he was changed back to Rock and returned to his own time.
- Your Size May Vary: Dr. Wily especially suffers from this in the final battle, which, on top of having his Wily Machine being smaller than usual, depicts him as smaller than Mega Man himself.