Set in the 1990s, the Geldra organization, thought to have been eliminated during the first game, returns and is destroying several of the world's satellites in outer space. As in the original Rolling Thunder, the players must take control of a member of the WCPO's Rolling Thunder task force.

Two players can now play simultaneously, with Player 1 as female agent Leila and Player 2 as male agent Albatross. Even though they possess different external appearances, including different handguns, the two characters have identical abilities (much like Yūichirō Tomari and Sunday Chin from Namco's own Ordyne, which was released two years earlier and is also a Namco System 2 game). As with the original game, both Leila and Albatross can only take two physical hits from the enemies - and a hit from a bullet or other projectile such as a laser will result in an immediate death. Both are armed with a default pistol that has only limited ammunition; when bullets run out, their guns fire a slow "chaser" bullet instead. Players can also upgrade to a submachine gun (based on a Walther MP from the artwork) by entering marked doors - and when entering one of these marked doors, a counter appears indicating the number of remaining bullets left to be picked up, allowing one player to leave ammo for the other.