In the story behind the original series, Mega man is an android originally named Rock, created as a lab assistant by the scientist Dr. Light with Dr. Wily as his partner. Following treachery by Dr. Wily in which he reprogrammed most of Dr. Light's robots, Rock volunteered to be converted into a fighting robot to defend the world from Wily's violent robotic threats, thus becoming Mega.

Though all incarnations of Mega feature unique stories, settings, and characters, they share several common features. All main Mega games released prior to 1997 are side-scrolling action platformers. The player character must fight through the levels using Mega Man's "Mega Buster"—a cannon attached to his arm—to shoot the robotic enemies inhabiting his environment. When Mega was released in 1987, the characteristic that made it revolutionary was the choice given to the player of which robot master to attempt first. After defeating a Robot Master—the boss of a level—Mega gains the ability to use that Robot Master's special weapon. Each Robot Master is representative of a specific element or object, with such bosses as Fire Man, Ice Man, Guts Man, Cut Man, Elec Man etc. The weapons Mega gains share the theme of the defeated boss. After defeating all of the Robot Masters, Mega travels to a multi-stage fortress to confront Dr. Wily, the person responsible for the robotic enemies' destructive acts. In the fortress, Mega fights past new bosses, clones of the game's Robot Masters, and Wily himself, who is usually in a large multi-phase war machine.

Enemies are weak to at least one weapon; for instance, Fire Man will take more damage from Ice Man's weapon than from other weapons. This concept draws inspiration from rock-paper-scissors. Robot Master levels can generally be completed in any order, resulting in a strategic hallmark of the series: determining the best order to defeat bosses and earn weapons. Sequels of Mega games contain new enemies alongside familiar ones, new bosses and weapons, and perhaps new gadgets. Later installments of the game give the player the option of commanding other player characters with different abilities, such as Proto Man, Duo, and Bass.