In March 2006, the United States has established a military presence in the newly-independent country of East Timor to train the East Timorese military in their fight against anti-separatist Indonesian guerrilla militias. Foremost among these militias is the Darah Dan Doa (English: Blood and Prayer), led by the charismatic Suhadi Sadono.
Sadono, once trained by the CIA to help fight communism in the region, has grown resentful of U.S. support of East Timor and its supposed interference with Indonesian sovereignty. Sadono orchestrates a suicide bombing and follow-up attack on the U.S. embassy in Dili, capturing a number of U.S. military and diplomatic personnel including Douglas Shetland, an old friend and comrade of Sam Fisher.
Meanwhile, Fisher is sent to infiltrate the embassy and gather intelligence on the Darah Dan Doa. Fisher succeeds in his mission, and the embassy is retaken by the U.S. Army's Delta Force. Sadono escapes, and the United States launches a military campaign in Indonesian territory in an attempt to hunt him down, much to the protests of the Indonesian government who is seeking to protect Sadono.
Fisher learns that Sadono has masterminded a scheme known as "Pandora Tomorrow", by placing a series of ND133 biological bombs, equipped with the smallpox virus, on U.S. soil. Every 24 hours, Sadono makes encrypted phone calls to each of the bomb carriers to delay the release of the virus. If he is killed or detained, the virus is released and millions of Americans will die. Because Sadono is fighting on the front lines in the conflict, the U.S. cannot risk killing him outright, and is forced to withdraw its forces.
