Guerrilla War follows the adventures of two unnamed rebel commandos (Che Guevara and Fidel Castro in the Japanese version) as they raid an unnamed Caribbean island in order to free it from the rule of an unnamed tyrannical dictator. Along the way, players vanquish hordes of enemy soldiers while attempting to rescue hostages (with large score reductions for any hostages killed in the crossfire), collecting weapons from troopers and operating tanks.