After the death of his mother Ishwari, Ajay Ghale returns to his home country of Kyrat to carry out her final wish by scattering her ashes in a place called Lakshmana. However, his mission is interrupted when his bus is attacked by the Royal Army and he is taken prisoner by Pagan Min, the country's eccentric and violent king who claims to have been romantically involved with Ishwari. Ajay escapes with the aid of Sabal, a commander in The Golden Path, a rebel movement established by Ajay's father Mohan.
In the twenty years since Ishwari and Ajay fled Kyrat, the rebellion has stagnated, with The Golden Path fighting for their very existence. As the son of Mohan Ghale, Ajay becomes a symbol for The Golden Path to rally around, and after freeing a group of hostages and liberating territory held by Pagan, they plan on breaking Pagan's stranglehold on power by targeting his three regional governors: De Pleur, who oversees opium production and runs Min's torture chambers; Noore, who runs poaching and prostitution rings and is herself a victim of Min's cruelty; and Yuma, Min's trusted general who is obsessed with uncovering the secrets of the mystical realm of ShangriLa. However, The Golden Path's newfound momentum is threatened by deep divisions between its commanders Sabal, who favours traditional values; and Amita, who argues for progress. Ajay is forced to intervene on several occasions, with his decisions influencing the direction The Golden Path will take.