When the al-Jamil terrorist group attacks the USS Mt St Helens, the National Intelligence Oversight Committee must rely on the Agency to secure the classified material within a cargo hold before the antagonists acquire it. NIOC Director Robert Cordell convinces Gabe Logan that he is their only option, but Teresa Lipan counters that this is an assignment outside of Agency jurisdiction. Gabe agrees to go anyway, for a chance at stopping terrorist leader Ghassan al-Bitar, a Syrian he almost caught a year ago.
With his partner Lian Xing on vacation in Cyprus, Gabe flies to the Indian Ocean where a clan of Somali pirates called the Warsingala Protectors have invaded the ship. Bitar is leading them, and Gabe suspects this assault involves more than simply pirating. Intercepting Spec Ops communications, pilot Alima Haddad warns Gabe that Cordell did not tell him everything, and Logan realises the contents of Hold Five, a secret even to the Navy, are Bitar's primary target.
Establishing a link to the St Helens' communications dish, Alima attempts to extract Logan, but her helicopter is shot down. Gabe rushes to rescue her but she dies. Motivated to stop the Warsingala, he destroys several pirate boats carrying stolen goods from the St Helens and re-enters the ship via the main hull. However, Bitar has already stolen the cargo inside Hold Five, which NIOC couriers ship.
When Gabe reaches the upper decks, the Navy has already begun launching cruise missiles to scuttle their own ship. He tries to stop Bitar from escaping, but terrorist Fahid Tamer distracts him. Gabe kills Fahid and escapes from the ship before it sinks. His return to the Agency brings more complications when Cordell mentions Lian was never in Cyprus, and produces pictures of her with a Chinese man, both in a foreign land. From Cordell's point of view, Lian being a defector or a double agent, the Agency would be compromised, and the NIOC suspends the IPCA.
Gabe and marine salvage expert Dane Bishop explore the sunken St Helens for NIOC courier files that could have the information of where Lian was when she was photographed. The duo find Spetsnaz divers are searching for evidence. Gabe realises they work for Surgei Kudrenko, another man he failed to kill during a mission years earlier. Bishop cuts a hole inside the ship, sucking Logan into the hull, and Gabe follows his advise on destroying the engine turbines. When they rendezvous, the pair stop the ship's nuclear reactor from melting down and kill Kudrenko's lieutenant, Surgeyev, before the enemy can escape with the courier codes.
The decoded microfiles show pictures captured by MI6 in Azerbaijan. Lian and the Chinese male are hostages, but the Spetsnaz are also looking for them, suggesting they found out about the St Helens through their intelligence resources. Gabe teams up with Maggie Powers, who claims to be in the same region to track smugglers, to find out who captured Lian. While searching a hotel room shared by Lian and her accomplice, Gabe encounters a Chinese Secret Service agent, codenamed Trinidad. The two fight and kill Spetsnaz forces, but Trinidad leaves Logan to find Maggie on his own. He rescues her from interrogators, but Kudrenko captures them after they destroy a Russian gunship.
Inside Kudrenko's gulag, Trinidad confronts Gabe, the Chinese confessing that she was Lian's instructor in the CSS; but Xing defected when Gabe recruited her into the Agency. According to Trinidad, her student used to be married to the man seen in the pictures, Shen Rei. China wants him back because he is the inventor of the device stolen from the St Helens, and Trinidad helps free Gabe from custody so he can find them. Logan wonders about the significance of the device, such that America, Russia and China all want it. He begins to suspect Maggie is after it as well, and does not know who to trust.
Gabe kills Kudrenko during an aeroplane firefight, but Cordell arrests Maggie and tells Logan he has shut down the agency; because the NIOC's point of view is that Shen and Lian work for Bitar. Cordell had used Gabe from the very start to locate them. The NIOC now knows where al-Jamil's desert stronghold is, but Logan is forced to accept early retirement. Before he can believe Cordell is right, Teresa informs Gabe that Lian is in love with him, and must be Bitar's prisoner if none of the world powers have Shen. Gabe realises that Cordell will bomb al-Jamil's base, and it will kill Lian.
He assists several Army Rangers in the assault on al-Jamil, but Gabe must enter the bunker on his own in search of Bitar. He finds Lian alive, and the two study Shen's device, the X-Z-2. It is an energy source that Shen intended for peaceful purposes, but China wanted to make it a bomb, so he defected with Lian's help and fled to Pakistan. Gabe finds information proving that Cordell hired Bitar as a means to bring Shen to NIOC couriers. Cordell was desperate to retrieve the X-Z-2 before competing nations could, but Bitar decided to steal the device and use Shen to make bombs that would destroy oil sources and drive Western influence from the Middle East.
Everything Cordell did since then was a cover-up, and Gabe has him taken away by soldiers to endure his own early retirement. Lian has difficulty talking to Gabe about Shen, and Gabe focuses on stopping al-Jamil at a Syrian dam. Bitar will use it to charge the last of the X-Z-2 devices for future attacks on the West. During the mission, Lian becomes distracted with saving Shen, and goes to find him. Gabe reaches Shen first, and the two disable most of the X-Z-2 bombs before going after Bitar. The terrorist leader tries to escape with the final bomb, but Shen has rigged it. Gabe shoots the device to destroy the terrorists and end the threat.
He finds Lian and Shen outside the dam, but Trinidad also appears. She has shadowed Gabe the entire time, from Azerbaijan and the Russian gulag to Virginia and the dam. On several occasions, Trinidad murdered al-Jamil operatives to keep Gabe alive just so he could lead her to Shen. Shen will not allow his device to become a weapon, and he commits suicide in front of Lian.
Some time later, Gabe and Lian return to the gym in Langley where Teresa had set up the remote command center during the Agency's shutdown. Gabe has decided he will retire, thinking there are too many secrets in his work. Instead, he will look for Addison and Blake while trying a new life. They walk inside to find Mujari lying on the floor, shot, and Teresa shot as well. She warns them to be careful, and Trinidad appears again. Gabe pushes Lian aside and kills Trinidad, but is shot four times himself. He lies on the floor as Lian shouts and tries to revive him.