Set at an undisclosed date somewhere in Malaysia, NATO Operations Commander Cullen Gray arrives at a NATO operations command center at the request of Area Commander James Gorman. A rebel movement calling themselves "Naga" have rallied and taken up arms against the country's government, and have hijacked ships belonging to Clawhammer Security, a private military company that was featured in the previous SOCOM title, Fireteam Bravo 2. Weapons and supplies were seized by Naga rebels, and Clawhammer has decided to withdraw from the region before losing any more assets, limiting the capabilities of NATO forces operating in the area. Under constant attack from Naga, Gray is given command of U.S. Navy SEALs (or other NATO special forces team members depending on which version of the game is being played) Eric Schweitzer and Dion Wells are tasked with aiding NATO in seeking out and destroying the insurgent threat by removing their leader.