The plot of the game centers on an ancient alien supercomputer named "Ra Moon", which was rediscovered by Dr. Wily in the ruins of the Amazon.

Wily also discovers Ra Moon's ability to cease almost all machinery and electricity in the world, as well as causing an invasive virus to spread across all technology.

Mega Man artist and producer Keiji Inafune claimed that Super Adventure Rockman was developed during a time when Capcom was attempting to branch out the series by "selling [it] to the lowest bidder".

Inafune exclaimed, "The ultimate unspoken rule about making a game that is geared towards children is that you simply cannot kill anyone, but here you have military helicopters falling out of the sky and people dying in droves.

"[6] GameSpot writers Christian Nutt and Justin Speer summarized the game as "an intensely boring and unplayable excursion into timed button pressing".

Proto Man—-going by his Mega Man 3 alias of Break Man—-also joins Wily's forces while he is based in the Lanfront Ruins,[9] and is accidentally responsible for damaging Roll prior to the planet-wide blackout.

[11] Worlds Collide (which crossed over into Sonic the Hedgehog) occurred in between the comic's adaptation of SAR, and included a moment of Ra Moon being interested in the blue Chaos Emerald, only for Wily to demand he makes a Met rice cooker.