A mysterious alien race called the Bydo have begun a war with mankind and after losing waves after waves of enemy fighters in Bydo territory, Earth has sent a lone commander leading a small armada into the heart of the Bydo Empire to end the war.

R-Type Command is a turn-based strategy re-make of the side-scrolling shooter, R-Type series. This version still has the side-scrolling view, but uses hexagonal grid to move. Players have over 100 units to use as well as many weapons to unlock and use against enemy ships. After each mission, upgrades, weapons and ships are able to be purchased and used in later missions.

Players now choose which grid they want to attack and which ship and weapons they wish to use. At the end of each level the player will engage in giant boss battles using all their ships and weapons at their disposal. Players can not only play as Earth Forces, but can also choose the Bydo's in the assault on Earth. There is also online capabilities using the Ad-Hoc that lets human opponents go head-to-head in battle.