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.