Deep in the South Pacific, the waterways vital to international commerce have become lawless and riddled with modern-day pirates. To combat this ever-growing threat, a team of mercenaries called the Pilgrims have set up business, selling their expertise and protection to whoever needs it.

Their newest recruit is Eddie Jackson, a former US Navy SEAL whose wife was aboard a cruise ship hijacked by unknown forces. No reason has been given for the attack, and no ransom demands have been made.

The Player takes on the role of Eddie, as he comes out of retirement on his desperate search to find and free the woman he loves. The game follows his quest as he fights alongside the Pilgrims against the many different pirate and terrorist factions that populate the area, slowly uncovering clues that lead him to his beloved, and the earth-shattering secret behind her disappearance.