The plot takes place on an unnamed island in the Carribean. The player takes control of Randy Mercer, an infamous CIA agent, who arrived on the island to hunt down an unknown arms dealer who has set up his network on the island. However, the landing went awry and he arrived in the middle of the enemy's camp. After trying to escape, Mercer is caught and held captive in the camp by a man named Rico, who works for the arms dealer. After Rico has introduced himself, he leaves. Mercer then attempts to escape, burning down the whole camp. He succesfully escapes, but he turns into a killer.
After Mercer finds another camp full of prisoners, he decides to free them. He liberates the camp and sets free the friendlies, joining their side. One of them, a woman who's called Leah, says that Rico is Raul Vasco's main handler on the island, revealing the unknown arms dealer's name. Vasco has shipment full of weapons going to every war in the world, supplying all fighting sides.
When Mercer returns to the camp after multiple quests for Leah, Rico's gunmen attack the camp. Mercer is knocked out by a grenade blast and is taken to a special building on the island. He wakes up, seeing Rico. Rico lights up a sigarette, but throws it on the ground when he says that he doesn't smoke. He than grabs Mercer CIA files and leaves the building. Rico's men then poor gasoline on the sigarette, making a huge flame. Mercer kicks the gasoline bottle on the man who is set on fire. The other one tries to stop the fire, but his boot also catches on fire. After one drops his knife, Mercer grabs it and cuts himself loose. After he travels back to the camp, he finds it on fire. He then swears that he is going to kill Rico and Vasco.
Mercer searches the whole island for Rico, finding him in his compound in the middle of a lake. After a hard fight to reach Rico, Mercer is knocked out. He wakes up in a big cage, seeing thousends of man yelling at him. Rico stands in front of him with a knife. He says all kinds of things, like how stupid Mercer is by not doing his duty, that he was dishonored, that he wants redemption. But the most weird thing Rico says is that Mercer, can't kill himself. After a heavy struggle, Mercer stabs Rico in his chest. Suddenly, Rico changes into Mercer. Mercer falls on the ground. Mercer who lives looks at his hands, changing into Rico's hands. It is revealed that the player was Rico all along, fighting against Vasco's soldiers, while hunting Mercer for his redemption.
Rico and his loyal PMC's them try to destroy Vasco's organization by multiple search & destroy, sabotage and hijacking missions. However, Rico is hunted by almost every man on the island. When CIA forces enter the island, to find the dead Mercer, Rico joins the CIA to set up the plan to kill Vasco once and for all. Right when the plan starts moving in motion, the CIA betrays Rico, seeing him as a possible target. Driven by rage, Rico goes on an onslaught through the battlefield, finding and killing the CIA commander. After these events, the past of Rico is revealed.
Rico was a hostage of Vasco due a cruise hijacking where Rico worked. Rico was an european, named Rico after joining forces with Vasco for money and drugs. Rico, losing his memories of himself before the island, turns into a cold blooded, die hard operator in Vasco's network. But when Mercer escaped, Vasco held Rico captive and tortured him with waterboarding and other horrible things. Rico managed to escape in the same scene as Mercer did in the first scene, and all the things Mercer did, was actually Rico. His thoughts were so messed up, he saw himself as the enemy and replaced himself with the heroic warrior he thought Mercer was. After his hostile-side was killed, he saw that Mercer was the enemy. He continued his hunt for Vasco, however the CIA was also all qround tht island.
After multiple lone wolf operations, trying to regain grip on the situation, Rico met Hawke. He was a CIA operative and held Rico to his gunpoint. After Rico had declared his motives to Hawke, Hawke decides to go dark before the CIA find out his pact with the enemy. Hawke says that there was an asset in Vasco's network all along, but he can't do a thing. Hawke asks if Rico has knowledge about Vasco's location, but Rico denies. When CIA operators appear, Rico starts running after Hawke insists him to do so. He gave him his channel so they could have contact when he finds out Vasco's location.
After Rico searches the whole island, looking for supplies and weapons, he gets a call from Hawke, saying that Vasco is trying to make his way of the island. Rico them proceeds to the harbor where the CIA is destroying a ship. Rico tries to find Hawke, but he gets under fire of CIA troops. Suddenly, Vasco's shipment explodes, killing almost any soldier in the area.
Rico wakes up in a strange hut. Hawke is standing in front of him. He tells him that Vasco set up a trap and that he can do whatever he wants. Hawke saved Rico by dragging him out of the blast radius when he was knocked out. Hawke says that Vasco now runs all his weapons on this island, using the rivers as transport. Rico has to hijack a ship, trying to enter Vasco's secret safehouse. Rico travels to the riverside, while pursuing a ship. He succesfully hijacks it. He then uses the navigation to enter Vasco's safehouse. He finds the command room, finally finding out Vasco's compound, digged into the volcano. After a rough escape scene which alerts all guards. Hawke picks Rico up in a stolen chopper.
After flying all over the island, Rico mas the machine gun and fires at all troops on ground, emtering Vasco's airspace. They land, but Rico says that only he will step off and that Hawke has to leave. Hawke says that he will return after Vasco is caught, but Rico says that there is no catching him, only killing. Mhawke then reveals the motives of him, saying they want him alive. After Rico steps off, Hawke reminds him of the fact that he wants him alive. Rico fights his way to Vasco's private villa, but when he wants to enter Vasco's room, he is caught and tied to a chair with a bag on his head.
Moments later, the bag is pulled away. Rico is facing a video camera. Vasco and a room full of armed men are watching at him. Vasco tells him that if he wants to say something to his family, he has to do it now, revealing he knows Rico's origins. Rico refuses to, making the guards angry. Vasco laughs and unties Rico from his chair. He then pulls out his knife and cuts a cross in Rico's chest. He synically continues with talking about Rico's origins, saying how he changed into a killing machine. He then picks a little cilinder with a liquid, saying that that little liquid was the only thing to take him to that. He puts it into a nail and gives Rico the liquid via the nail into his blood. Rico goes crazy, entering a strange state like he did when he was Mercer. He hears multiple voices in his head while looking at his hands.
Suddenly, Rico punches a guard. Grabbing his knife stabbing another. After using one as a humanshield, he attacks Vasco. A knife fights between them starts when Rico throws away Vasco's gun. During the fight, guards try to stop them, but Rico kills them. After all guards are dead and Rico defeated Vasco, he gets his normal mind back. He pulls up Vasco, holding the knife against his throat. Suddenly, Hawke enters the room. Hepoints a gun at Rico. He says that if Ruco kills Vasco, he needs to kill Rico. If he doesn't, he can be reunite with his family. Rico can now choose if he kills or spares Vasco.
If he kills him, Hawke fires his gun, but Rico dodges the attack. He then throws the knife into Hawke's neck, killing him. A cutscene start with Rico living on the island, while being hunted by multiple armed forces. But despites that, Rico loves his life there, he says.
If he spares him, he releases grip on Vasco and Hawke walks towards him, saying that that is the right thing. A cutscene starts with Rico narrating his experiences on the island and how he feels now he hpis back in the real world.