In the 20 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: Paul "De Pleur" Harmon (Travis Willingham), who oversees opium production and runs Pagan's torture chambers; Noore (Mylène Dinh-Robic), who runs poaching and prostitution rings and is herself a victim of Pagan's cruelty; and Yuma (Gwendoline Yeo), Min's trusted general who is obsessed with uncovering the secrets of the mystical realm of Shangri-La.
However, the Golden Path's newfound momentum is threatened by deep divisions between its commanders Sabal, who favors traditional values at the expense of some outdated world views; and Amita (Janina Gavankar), who argues for progress, which includes heavily relying on drug trade. Ajay is forced to intervene on several occasions, with his decisions influencing the direction the Golden Path will take. The first governor to fall is De Pleur - Noore helps Ajay find a way to attack De Pleur's stronghold, allowing the rebellion to capture him. Later on, Amita and Sabal task Ajay with confronting and killing Noore. She dies in her fighting arena as a consequence of either Ajay killing her, or suicide upon learning of her family's fate.
As the Golden Path secures Kyrat's southern provinces, Ajay is contacted by Willis Huntley (Alain Goulem), a CIA agent who offers intelligence for the rebels and pages from his father's diary in exchange for killing Yuma's lieutenants. After Ajay kills several of them, Huntley admits they were in fact undercover CIA agents, and that he was sent to clean house, as the CIA did not see Pagan as a threat anymore. Huntley betrays Ajay to Pagan just as the Golden Path prepare to push into northern Kyrat.
Ajay ends up in Yuma's mountain prison, which he manages to escape from. In the process he finds out that Yuma started despising Pagan, mostly because of his affections toward Ajay's late mother. The Golden Path pushes into the north, and while Ajay attends a meeting with the rebels, Pagan's forces arrive, led by the king himself. Ajay chases and kills Pagan, only to find out that the person he killed was a double. A broadcast appears, on which Pagan states he is alive and betrays Yuma's location. Ajay finds and kills Yuma. As the Golden Path moves closer to the Royal Palace, tensions between Amita and Sabal reach new heights, and Ajay is forced to make a final decision as to who will lead the Golden Path. Whichever leader he chooses then sends him to kill the other to prevent them from starting another civil war, and Ajay can choose to kill them as ordered or let them go. With The Golden Path now united under a single leader, Ajay joins them for an attack on Pagan's fortress and pushes on alone to Pagan's palace while the Golden Path holds off the military.
