Unlike the first two installments of the series, artist and designer Keiji Inafune has considered the creation of Mega Man 3 to be very stressful due to time constraints and his own increased responsibilities during its development.

2-3 months after Mega Man 2, the mad scientist Dr. Wily, having twice had plans for world domination dashed, claims to have reformed and begins work with Dr. Light on a project to build a peace-keeping robot named "Gamma".

[11] Mega Man is called into action, this time with a canine companion named Rush, to retrieve the crystals from the sites.

Once the crystals are retrieved, Wily reverts to his evil ways, steals Gamma, and retreats to his new fortress.

[18] Inafune recalled the final two months of development as particularly turbulent, when he had to take responsibility for assessing and dividing up tasks among the team members who were not meeting deadlines.

Inafune concluded, "I knew that if we had more time to polish it, we could do a lot of things better, make it a better game, but the company said that we needed to release it.

Though Inafune considers the gameplay to have lost some of its simplicity, he felt Mega Man's slide ability was successfully implemented to enhance the player's control while battling enemies.

[2] The design team wanted Proto Man to sport uncovered hair, but they instead opted for an open-faced helmet illustration for both the television commercials and instruction manual.

[20] Proto Man's original Japanese name, Blues, was changed by Capcom's North American division despite Inafune's protests.

[2][23] Harumi Fujita, credited as "Mrs. Tarumi", was the initial composer of the game, but she only completed a few songs before giving birth and having to drop off the project.

Lucas M. Thomas of IGN, Christian Nutt and Justin Speer of GameSpot, Hartley, Patricia, and Kirk Lesser ("The Lessers") of Dragon, Dan Whitehead of Eurogamer, Edward J. Semrad of The Milwaukee Journal and Electronic Gaming Monthly (EGM), and the staff of Nintendo Power all mutually found the game to have impressive graphics, enjoyable music, and challenging gameplay.

[15][28][29][32][33][34] Nutt and Speer summarized Mega Man 3 as a "top-notch game" and Capcom's "pinnacle of NES effort".

[35] Brett Alan Weiss (AllGame) described it as doing what "a great sequel is supposed to do by recapturing the fun, spirit and excitement of its predecessors while adding new levels, characters and challenges.

[29][30][36][37] GamePro contributor McKinley Noble comically stated that actions such as "pulling teeth, lifting a car over your head or performing open-heart surgery" are all significantly easier than beating Mega Man 3.

[37] Whitehead noted, "Leaps must be precise, enemies must be dispatched rapidly and accurately, and there's a constant state of delicious near-panic as you wait to see what vicious demands the next room will place on your platforming skills.

[27] Since its 1990 release, Mega Man 3 has sold over one million copies worldwide, making it the 48th best-selling Capcom game.

[3][46] The NES edition of the game was also part of a North American compilation of ten titles in the series called Mega Man Anniversary Collection, which was released for the PlayStation 2 and GameCube in 2004, and the Xbox in 2005.

These include the characters Proto Man and Rush, the player's ability to slide, and extra stages set between the initial eight Robot Masters and Dr. Wily's fortress.

[60][61] The game was adapted into the Archie Comics Mega Man series over an extended period, with Gamma being introduced and having its power source stolen in the "Redemption" arc while the full adaptation takes place in "Legends of the Blue Bomber" and "The Ultimate Betrayal".

This also results in Shadow Man's ruins of origin being made the Lanfront Ruins of Super Adventure Rockman and connecting his history to that of Ra Moon; a flashback featured in the "Legends of the Blue Bomber" arc reveals that his history is also connected with the mysterious robot who fights Duo in the beginning of Mega Man 8.