Before the events of Splinter Cell: Essentials, Sam Fisher must deal with the recent loss of his daughter to a drunk driving accident. But he has little time to mourn, as he soon has to go on an undercover assignment which requires him to pose as a criminal in order to infiltrate a terrorist group based in the United States. This new mission forces Fisher into a new and very dangerous gray area, where the line between right and wrong is blurred even beyond what Fisher is used to, and thousands of innocent lives are in the balance.
On September 2007, Sam Fisher and rookie field agent John Hodge are being flown to Iceland to investigate suspicious activities at a geothermal plant, which is also John's training mission. After he averts a missile strike by terrorists during which Hodge is killed, he is met by Colonel Irving Lambert aboard the V-22 Osprey, who bears bad news: Sarah Fisher, Sam's only child, has died after being hit by a drunk driver. Overcome with grief, he is pulled out of active service.
Lambert offers him a job as a nonofficial cover operative, hoping that it will help him refocus. The NSA stages multiple bank robberies and killings to set up Fisher to infiltrate a domestic terror organization known as John Brown's Army (JBA). He is planned by the CIA to be sent to Ellsworth Prison in Kansas where he is placed in the same cell block as Jamie Washington, a JBA member, and begins digging a tunnel for escape. By February 2008, Fisher helps Washington escape, and is welcomed into the JBA.
At their compound, Emile Dufraisne, the leader of the JBA, gives Sam the order to shoot Cole Yeager, the pilot of the helicopter used to escape the prison, affecting Fisher's standing between the JBA and NSA. He is then sent on a mission to take over a Russian oil tanker in the Sea of Okhotsk, while receiving radio contact from Enrica Villablanca, the JBA's weapons expert. Sam needs to take over the tanker so that JBA ally Massoud Ibn-Yussif can use it to deliver one of Emile's bombs.
As soon as Fisher is finished, he is quickly flown to the Jin Mao Hotel in Shanghai. CIA operative Hisham Hamza, who has infiltrated Yussif's organization, orders him to record a meeting between Emile and a Pakistani nuclear scientist, Dr. Aswat. During the meeting, Aswat sells Emile several kilograms of red mercury, an explosive material that can detonate with the force of a thermonuclear bomb. With Third Echelon on high alert, Fisher is told to collect a sample from the safe in the meeting room. While he does this, Carson Moss, the JBA's head of security, radios in and orders him to steal notes from Aswat's hotel room. The NSA then orders Aswat's assassination.
With both the red mercury and Dr. Aswat's notes, the JBA constructs a bomb which they wish to test. Emile sends Fisher to Cozumel to blow up a cruise ship. The success of the bomb is determined by the player and is therefore the first of the three major events. Fisher can choose to either let the bomb detonate, maintaining his cover with the JBA, prevent the explosion by jamming the signal, or framing Enrica by using her disarm code, if the player acquires it from her office during the third JBA HQ mission. Jamming the signal makes player lose JBA trust, while framing Enrica maintains both NSA and JBA trust. In both of these cases, non-detonation causes Dufraisne to kill Enrica in a fit of anger.
Emile then goes to a meeting in Kinshasa with Yussif and Alejandro Takfir, another ally of the JBA. Fisher bugs the meeting and finds out that the three terrorist leaders each have Red Mercury bombs. They plan to destroy Mexico City, Los Angeles and New York City. During the meeting, Hisham's cover is blown.
Emile orders Fisher to kill Hisham, who has fled to the Congolese presidential palace in a war-torn Kinshasa. Fisher takes up a position from the top of a radio tower with a sniper rifle. Fisher may shoot Hisham, or spare and extract him.
When Fisher returns to the headquarters, he is ordered to shoot Lambert, who was captured sneaking around the complex. The player can decide to either shoot Lambert or Washington. Shooting Lambert will maintain the JBA's trust, while shooting Washington will send the JBA into high alert and reveal Fisher as a traitor. Enrica, if she is still alive, discovers Fisher's NOC status, but allows him to pass into the labs underneath the HQ, even giving him his equipment if he does not have it already. When Sam arrives at the labs, he manages to kill Emile (and Washington if he did not kill him earlier) and disarms the bomb. A SWAT team then storms the compound, crashing in through the ceiling. This version of Double Agent is the official version to the story-line.
