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.
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, it introduced what would become the standard format for the rest of the Game Boy installments, with an additional set of four full Robot Master levels and fights following the first set (as opposed to the previous game, where the second set of Robot Masters are all fought in a Boss Bonanza with no additional stages).
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 in Dr. Wily's Revenge, the final stage takes place in outer space, onboard the Wily Station.
- Chicken Walker: The first form of the Wily Machine is Wily's spaceship attached to a pair of backwards bending legs. In this form, it can jump toward Mega Man.
- 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.
- Early-Installment Weirdness:
- Considering the later Mega Man sequel series that take place across the coming centuries, it's pretty bizarre to see Wily just casually going to the future and back.
- This is the first Game Boy game where the second set of Robot Masters have dedicated stages, but they are accessed through a teleporter room instead of a level select, with no indicator of which Robot Master is in each teleporter.
- Enemy Roll Call: After the game is completed, Mega Man looks out into space, while all of the enemies and Robot Masters in the game fly by with their names displayed.
- 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. The only saving grace is you're given a level to play through to get yourself a chance to heal up, stock up on weapon energy, and earn bonuses before the boss.
- 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.
- Quint can be damaged by firing at the area above his head for a few early hits before he even calls his Sakugarne in and starts attacking.
- Needle Man's hammer attack has a smaller hitbox than its animation would suggest, so it often appears to go right through Mega Man without dealing damage.
- Improbable Weapon User: Quint's signature weapon is the Sakugarne, a robot resembling a jackhammer crossed with a pogo stick that he uses to jump around and spread debris.
- Inconsistent Spelling: Crash Man's name is spelled as "Clash Man" in this game, which is actually his original Japanese name.
- My Future Self and Me:
- Quint is Mega Man from the future, whom Wily brings back in time to fight his past self.
- The Japanese manual says that Wily collaborated with his (apparently reformed) future self to abduct the future Mega Man.
- 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.
- Post-Defeat Explosion Chain: 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.
- 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 Escalation: This game is larger in scope than Dr. Wily's Revenge, thanks to introducing a second set of Robot Master levels along with Rush and the Slide maneuver from Mega Man 3.
- Sequential Boss: The Wily Machine has three forms. After each form is destroyed, Wily's spaceship will detach from the previous form before flying away and coming back with a new attachment. The first form has his ship attached to a pair of legs, the second is attached to tank treads, and the final form is a dinosaur-like robot.
- Shout-Out: The Wily Station's background features several melting clocks, as seen in the works of Salvador Dalí.
- 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.
- Unending End Card: The game lingers on the "Presented by CAPCOM" screen until the Game Boy is turned off. Not even the soft reset code works.
- Unique Enemy: Only one Bikky appears in the entire game, right before the boss door leading to Needle Man.
- 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: While Dr. Wily appears in his normal size while outside of the Wily Machine, during the final battle, his Wily Machine is smaller than usual, which has the added effect of Wily being depicted as smaller than Mega Man himself.