The first two Sigma stages are both remakes of stages from other Mega Man games.

Stage 1 is a remake of Quick Man's stage in Mega Man 2. The boss, Black Devil, could be seen as a remake/redesign of the Yellow Devil from the original Mega Man, as both are weak against electric weapons. Once his health is low enough, the Black Devil will also turn into the Wily Machine 6 from Mega Man 6.

Stage 2 is a remake of Stage 1 of Sigma's Fortress from the original Mega Man X, and the boss is Rangda Bangda from the same game.