Thunder Cross is a classic horizontal shooter with 7 stages. Players control the Thunder fighter with up to four "options", which arrange up and down vertically and attack at the player's will. Three weapons are selectable ranging from the Vulcan shot to the Laser and the Boomerang shot (which doubles as a ricochet weapon). End-of-level bosses were present and, typical of a Konami shooter, Thunder Cross forced the player to beat the game twice in a harder Loop of the first seven levels.
Taking place in the future of space colonization, the planet Haniamu IV is under attack from a relentless, unknown military force known only as Black Impulse. The strongest Earth ships capable of stopping the total conquering of the planet are the Blue Thunder M-45 (player 1) and its earlier make the Red Thunder M-24 (player 2).