In 2008, the American domestic terrorist organization known as the JBA (John Brown's Army), led by the radical reformist Emile Dufraisne, sought to wreak havoc across the continental United States as a means of freeing the nation from the policies of the "corrupt" American government and to restore the country to its people. In order to accomplish this, Dufraisne sought out the mysterious substance known as "Red Mercury" on the black market, as its destructive yield purportedly mimicked the destructive power of a nuclear bomb, even if they possessed little more than a sample of it. Eventually, Dufraisne was successful in contacting rogue Pakistani nuclear scientist Abdul-Ahmad Aswat, who agreed to sell the Red Mercury in his possession to Emile in exchange for a sizable payment. The negotiations broke down when Emile deemed Aswat's price to be too high, and had Sam Fisher retrieve Aswat's files on the production of Red Mercury so that they may produce it themselves. Fisher was also successful in acquiring a small sample of the material for later analysis.
Eager to test the Red Mercury's effects, Dufraisne had a highly transportable bomb manufactured for later use on a cruise ship docked in Cozumel, Mexico. Sam Fisher was charged with planting the device after being inserted as an ordinary passenger on the vessel. During the mission, Fisher tampered with the ship's ventilation system as a means to force the local authorities to evacuate the ship's passengers and crew. After planting the bomb, Fisher returned to New York City to witness the bomb's detonation with the JBA leadership. The bomb was detonated remotely and the ship was completely destroyed in a massive explosion, which also triggered massive tidal waves that swept across Cozumel's coast. The success of the test prompted Emile to field Red Mercury for his larger goal: The destruction of the U.S.
Emile commissioned the manufacture of several more Red Mercury bombs, some of which he planned to sell to his allies Alejandro Takfir and Massoud Ibn-Yussiff, who also took an active role in the plot against the U.S. Meeting with his allies in Kinshasa in the Democratic Republic of the Congo, Emile declared that he would destroy New York City while the others destroyed Los Angeles and Mexico City. With the sale of the bombs complete, Emile returned to the U.S. to bring his plans to fruition.
On the night of the attack, Emile retreated to the underground levels of the JBA Headquarters to prepare the Red Mercury for its imminent detonation. To everybody's horror, Emile intended to take the lives of himself and his organization in order to see the bomb's successful detonation, refusing to evacuate his crew from the city. Fisher caught on to this and was eventually successful in killing Emile and disarming the bomb, only to learn that Carson Moss had a second bomb on hand for detonation in the Hudson River. Fisher evaded the NYPD, who stormed the facility, and pursued Moss into New York Harbor. Fisher too was successful in killing Moss and disabling the bomb, and then fled before the FBI destroyed the vessel on which the bomb had been planted. The loss of the Red Mercury bombs effectively saved New York City. Although the status of the defused Red Mercury is still not explained, presumably confiscated by the U.S. government.
Third Echelon warned the authorities of the impending destruction of both Los Angeles and Mexico City, ensuring the capture of Takfir and Ibn-Yussiff before the bombs were detonated. All Red Mercury samples were lost or seized with the failure of the JBA's plot.
- In Double Agent (Version 1), if the player fails to disarm the Red Mercury bomb in the JBA Headquarters - Part 4 level, there will be a special cutscene showing the bomb detonating in New York City, with emergency response helicopters hovering near the aftermath.
- Depending on player's choice in Version 1, it is possible to not have a single Red Mercury bomb detonated in the entire game.
- The Red Mercury Sam carried to the cruise ship could be a smaller prototype made by JBA, as other combat-ready bombs are significantly larger.
- Agent One and Agent Two in the last mission of co-op mode are tasked to disarm a series of Red Mercury bombs on the RSS Rublev. The Red Mercury on the supertanker are presumably meant to be delivered to L.A. and Mexico City. This is only seen in version 1 as version 2 has the Red Mercury already delivered.