Some time after the events of Syphon Filter: Dark Mirror, Gabriel Logan receives an assignment from a bureaucrat named Robert Cordell. A United States Naval supply ship, the U.S.S. Mt. St. Helens, has been boarded by Somali "pirates" in the Indian Ocean and is being led by a Syrian, Ghassan al-Bitar. Logan is supposed to secure the classified contents of Hold Five. Cordell explains to Gabe that he is the only option because he cannot expect special operations to keep any secrets. Despite Teresa Lipan's protests, Gabe accepts the assignment to tie up loose ends with Bitar. Upon arrival by helicopter, Gabe's pilot, Alima Haddad, tells Gabe that a distress signal coming from U.S. special operations has been broadcasting for hours. Gabe realizes that Cordell was lying to him. After fighting the pirates on deck, he learns from a dying special operations soldier that the squad's missions failed due to poor intelligence from Cordell. Gabe surmised that the attack was complex enough that Bitar's terrorist group, Al-Jamil, was behind it. Gabe fights his way to the cargo hold, with Alima being killed by anti-aircraft fire. Gabe makes it to Hold Five, only to find the cargo stolen. Gabe attempts to shoot down Bitar but misses. Cruise missiles were fired at the ship, with the missiles impacting before Teresa's warning was finished. Gabe kills Fahid, the commander of the piracy operation and escapes when a cruise missile hits the bridge. Upon returning to headquarters, Gabe finds out that Cordell accused Lian Xing of being a double agent, while presenting photos of her and a man in Cyprus. Gabe learns of the identity of the man in the photo, a Chinese scientist named Shen Rei, Lian's former husband. Shen was wanted by Cordell, the British and Chinese governments, as well as Bitar for a weaponized device called X-Z-2. Gabe also learns that Lian only went rogue to protect Shen. Gabe finds incriminating evidence on Cordell wanting the weapon and exposes him to the government while neutralizing Bitar and his plans. However, after Gabe destroys the weaponized devices and kills Bitar, Shen commits suicide to avoid capture by Chinese CSS agent Trinidad. After the ordeal, Gabe tells Lian that he is considering retiring due to the nature of their work. However, they find Lawrence Mujari dead and Teresa wounded by Trinidad. While protecting Lian, Gabe is shot four times in the chest by Trinidad. After Gabe kills Trinidad, Lian administers CPR to him, leaving the fates of Gabe and Teresa unknown.