Jason Brody on vacation with a group of friends in Bangkok during which they decide to take a skydiving trip. They land on a pirate-infested island, and are taken prisoner by a pirate lord named Vaas. Vaas plans to extort ransom money from their parents, then sell them into slavery. With the help of his older brother Grant, Jason breaks out of captivity, however Grant is killed along with one of Jason's friends, Vincent Salas, in the escape. Jason is rescued by a man named Dennis, who is part of the Rakyat, the island natives who suffer due to the activities of the pirates. Dennis recognizes Jason's potential as a warrior, and gives him special tattoos that permit him to access his abilities. Impressed with Jason's prowess, the Rakyat allow him to be the first outsider to enter their sacred temple and their leader Citra initiates him into the tribe. He runs a series of missions during which he rescues his captive friends one by one (excluding Grant's girlfriend Daisy, who is discovered to have also escaped) while simultaneously helping the Rakyat retake their island, helped at times by Dr. Earnhardt, a man who is an expert on fungi and various native remedies and drugs. Throughout the adventure, Jason matures into a fearsome warrior and is revered by the Rakyat, though his old friends are disturbed by his transformation into a killer, especially when he contemplates staying on the island permanently to stay with Citra and the Rakyat as a warrior.
After Jason tracks down and kills Vaas, he then moves on to the southern island, which is controlled by Hoyt Volker, a slave trader discovered to be Vaas' employer, swearing to Citra that he will kill Hoyt for what he did to both the islanders and her brother. After killing Hoyt and rescuing his younger brother Riley, Jason returns to find Dr. Earnhardt's house on fire. He looks for survivors and finds Dr. Earnhardt lying in a patio mortally wounded. He tells Jason before dying that he tried to save Jason's friends but they were taken by Citra and her warriors back to the temple. He returns to Citra to find that she has taken his friends captive. She has become absolutely enamored with him, seeing him as the reincarnation of the Rakyat's mythical warrior ancestor. After Jason walks through a hallucination, the player must then choose whether to execute his friends and remain with Citra or save them and leave the island.
If the player chooses to join Citra, Jason executes his friends and has sex with Citra, however Citra stabs him, saying that their child will lead the tribe, and that he dies as the warrior he has become. If the player chooses to save Jason's friends, Citra attempts to convince Jason to stay by claiming his friends will move on, and that he should stay in the jungle and become king. Dennis arrives claiming that Citra saved him and the other followers and attempts to kill Jason for betraying her, but she moves in front of him and is stabbed, mortally wounded. Citra begs Jason not to leave as Jason sadly apologizes to her, and she dies. Soon, Jason and his friends leave the island by boat. He narrates that he cannot come back from what he has done, as he believes he is a monster and feels the anger inside him, but he also believes that there is still something inside him that is better than that.
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