The fictional Rook Islands are familiar to fans of Far Cry 3, though what happened to the islands after the events of the game is never detailed. The final decision of Far Cry 3 determines the fate of Jason Brody and his friends but doesn't seem to directly concern the fate of the islands. With limited new information, speculation on the events that occurred on the Rook Islands continues.
The Rook Islands and the native Rakyat have a past filled with war and turmoil, having been conquered numerous times before the events of Far Cry 3. Several different invading armies controlled the islands throughout its history, though all were inevitably expelled. The Rook Islands enjoyed an economic boom in the 1980s due to mining efforts and began forming its own organized government.
The native inhabitants of the Rook Islands were enjoying these prosperous years when Hoyt Volker and his band of privateers moved in sometime before 2012 and eventually convinced Vaas to join them. Hoyt was a known human trafficker and drug lord looking to expand his empire. He brought anarchy and crime with him to the Rook Islands and took control from the native Rakyat. These dark times are the setting for Jason Brody's arrival and the events and ending of Far Cry 3.
The Rook Islands After Far Cry 3's Ending
During Far Cry 3, Jason Brody kills Hoyt Volker and at the time was assumed to have killed Vaas as well. Depending on the final choice the player made, Jason may have also killed Citra as she threatened the lives of his friends. With the threat of Hoyt Volker removed, it can be safely assumed the previous government installed by the natives of the island was restored. If Citra wasn't killed following the events of Far Cry 3, her child from Jason Brody most likely became the new leader of the Rook Islands as she foretold.
Prior to Hoyt's arrival, similar to other Far Cry title's large maps, the Rook Islands were well known for their dense jungles rumored to be filled with hidden treasures from past invaders and perilous terrain that required true skill to traverse. As the island inhabitants learn the danger Hoyt posed has passed, life will slowly return to peace. With its untamed natural beauty and apparent value as a mining operation, the Rook Islands were set to recover from the recent political turmoil.
Vaas is revealed to be alive through the DLC Vaas: Insanity and seems to still live on the Rook Islands working as a smuggler. During the DLC, Vaas fights against Citra's negative influence on his life and comes to the conclusion he doesn't need her anymore, which may have helped him live through the ending of Far Cry 3. This turn to a relatively peaceful life Vaas chose for himself could be seen as a metaphor for the Rook Islands themselves.