The Bydo are back and are out for revenge! After halting their assaults in the previous three R-Type games (R-Type, R-Type 2 and R-Type Leo), they have hidden in another dimension and recuperated their powers and resources, and have returned, stronger than ever, and are ready to destroy mankind.
They, however, have underestimated the human race, and while they Bydo were recuperating, the Earth Defence Force have spent valuable time improving the R-9, and have developed new Force Devices to aid the battle.