Far Cry 3 is a first-person shooter, which also features role-playing game elements including experience points, skill trees, and a crafting system. The player has the ability to take cover behind objects to break enemies' lines of sight and also to peek around and over cover and blindfire. The player also has the ability to perform silent "takedowns" by performing melee attacks from above, below, or close behind. The game's narrative director, Jason Vandenberghe, said that the story mode map is around ten times larger than in the game's previous installments. Players are given the ability to survey and plan out their attacks with stealth takedown combinations and also tag enemies with the camera in order to track their movement once they break the player's line of sight.
Equipment is controlled by a simple system. As missions are completed, new items are unlocked to be purchased or crafted by Jason, using the pelts of various animals around the island. As radio towers are unlocked, this opens areas of the map and unlocks weapons in the shop for free. As outposts of Vaas' pirate group are attacked and retaken, the vicinity around the outpost becomes safer, it also unlocks new side quests for that area.
Skills are collected by gaining experience from completing missions and killing enemies, and are unlocked in three skill trees, which correspond to the Spider, the Heron, and the Shark. Each skill tree upgrades different aspects of Jason's abilities, with the Spider upgrading his stealth takedowns and hunting skills, Shark for assault takedowns and health, with the Heron upgrading his long-range takedowns and mobility. As skills are collected, the tattoo on Jason's forearm grows which is made up of several different tribal designs resembling the three animal skill trees.
The game also includes a variety of side-quests. One such side-quest involves the player hunting the many different wildlife species on the island for upgrading purposes. There are even some rare hunts that the player must undertake to reach the highest level hunt upgrades. The rare hunts feature wildlife not typically found during normal play.
The game starts with a cinematic showing protagonist Jason Brody on vacation with a group of friends in Bangkok celebrating Jason's younger brother Riley on getting a pilot license. Also during the vacation 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 by Vaas 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 the tattoos of a Rakyat warrior. Jason then helps the Rakyat in a number of missions, and ends up finding one of his friends, Daisy, at the house of Dr. Earnhardt. Impressed with Jason's prowess, the Rakyat allow him to be the second outsider to enter their sacred temple (Dennis was the first being born in Liberia) and their leader Citra initiates him into the tribe, after Jason finds the Dragon Knife, a dagger that is a relic for the Rakyat, having seen it in a previous dream of his. He runs a series of missions during which he rescues his captive friends Keith, Oliver and girlfriend Liza while simultaneously helping the Rakyat retake their island, helped at times by Dr. Earnhardt and Willis Huntley, a CIA agent. After a few run-ins with Vaas, Jason discovers that he is employed by Hoyt Volker, a slave trader, and that Vaas is Citra's brother. Throughout the adventure, Jason matures into a fearsome warrior and is revered by the Rakyat, starting to enjoy all the killing, and growing more distant from his friends, especially after receiving the information that Riley is dead. After Citra asks him to stay in the island, Jason returns to Dr. Earnhardt's house, where his friends are hiding and preparing their escape by boat, and tells them that he is staying, completely distant from his friends and family, leaving them disturbed. Meanwhile, Jason has an affair with Citra after she drugs him and has sex with him while he is in a hallination.
After bidding goodbye to his friends, Jason goes to the pirates base where Vaas is. Believing that Jason was dead after a confrontation between the two, Vaas is celebrating Jason's death, but was actually waiting for him. After Jason kills numerous pirates and reaches a warehouse, he and Vaas fight, but Jason enters a delusional state, fighting multiple Vaas in his dream. He reaches to a final Vaas, and after a brief struggle, he impales him through the chest with the Dragon Knife, and collapses right besides him. He wakes up to Citra in the Rakyat's temple, and promises her that he will kill Hoyt for her. After Huntley helps him get into Hoyt's island, Jason infiltrates into Hoyt's personal army with Sam Becker, Huntley's fellow operative. Together, they grow close to Hoyt, who invites them into a poker night. During this time, Jason also finds that Riley is alive, but being a prisoner of Hoyt. After making a plan to kill Volker, Sam and Jason sit to play poker with him, but Sam is stabbed in the throat and killed, with Hoyt that they were both traitors. After Jason gets one of his fingers cut by Hoyt's bodyguard, he and Volker have a knife fight, with Jason emerging victorious and killing Hoyt. Jason then goes to rescue Riley, receiving a call from Liza, but the signal being cut before she can say anything. Jason rescues Riley and the two escape by Helicopter. After passing by Dr. Earnhardt house, they find the house burning, and the doctor lying on the ground. With his last words, he says to them that the house was attacked by the Rakyat, and that they have their friends.
Jason and Riley arrive at the Rakyat Temple. Jason asks Citra why his friends were captured, but she sprays him with a sleep powder, and Jason falls unconscious, while Riley is captured. Citra has fallen in love for Jason, believing him to be a powerful warrior of Rakyat legend, and the she will free him. He starts dreaming of walking a fiery path, with the Dragon Knife, and having Liza as a monster in his dream. He wakes up holding Liza at knife point with the Dragon Knife, and the player has the option to either kill Jason's friends or spare them.
