Just Cause begins with Rico Rodriguez, an operative for an organization known as the Agency, being dropped into a tropical island called San Esperito, after being called there by his commanding officer, Tom Sheldon, to help overthrow San Esperito's , Salvador Mendoza, whom the Agency believes to be in possession of equipment After his arrival, Rico meets up with Sheldon and fellow agent Maria Kane, and they ally themselves with a group staging a rebellion against the regime and the Rioja , another enemy of the government. Rico assists them in their civil war against Mendoza's corrupt officials; Black Hand mercenaries and the Montano cartel. Rico can also assist in the liberation of various territories to further destabilize the government's rule over the island.
Eventually, Sheldon discovers that Mendoza does, indeed, have control of WMDs, and with San Esperito so politically unstable and with the guerrillas having the upper hand, the president is forced to retreat to his private presidential island just off the mainland. Sheldon and Kane fly Rico to the island to kill Mendoza, but he attempts to escape via jet. However, Rico boards the jet and kills Mendoza and his remaining bodyguards, ending his reign over the islands
- The core gameplay consists of elements of a third-person shooter and a driving game, with a large, environment in which to move
- On foot, the player's character is capable of walking, swimming, and jumping, as well as utilizing equipment and basic hand-to-hand combat
- Players can take control of a variety of vehicles, including , , , , and .
- Players can also perform stunts with their cars in which they can stand on the roof and jump to another car, or choose to open their while still in motion on the roof.