Choose from among seven high-powered fighters (including the Raiden MkII and Judge Spear from Viper Phase 1) and take to the skies in three dangerous missions. The first two missions are comprised of three stages each, the first two of which may appear in either order. Stage 1-3, Stage 2-3, and the final mission are all the same.

Raiden Fighters' plot is not directly apparent in and of itself. The opening prologue of Raiden Fighters 2 hints at a plot from its predecessor, which the sequel follows. The protagonist squadron must quell a massive guerrilla uprising headed by a ruthless dictator. The setting of this conflict appears to take place in eastern Asia, as the briefings for each "Mission" include a war plan superimposed over a map depicting the countries of China and Japan.