2006: The U.S. installs a temporary military base on East Timor to train the developing defense force of the “world’s youngest democracy.” Resistance to the U.S. military presence in Southeast Asia is widespread and passionate, but the threat Indonesian militias pose to Timorese democracy is deemed sufficient justification. Anti-U.S. resentment comes to a head under the leadership of guerrilla militia leader Suhadi Sadono, acting with the unofficial support of major corrupt factions of the Indonesian government. Suhadi’s men attack and occupy the U.S. Embassy in Jakarta, taking dozens of civilian and military personnel hostage.

Sam Fisher must defend and assist the U.S. military, both locally and from remote locations, until Suhadi's terror-driven policies can be subverted and the geurilla faction eradicated.