A raid, led by Ethan Carter is carried out by ATF agents against a militia group, the Brotherhood of Liberty.
Their leader, William Fain, is captured and his family is mistakenly killed in the raid. Seven years later, other persons from the same militia group break into a chemicals corporation called Cyberdyne Systems and steal anthrax.
Their plan is to use this anthrax to engineer a full-blown attack against the US government. Ethan must now use the imprisoned William to infiltrate the Brotherhood of Liberty and stop the attack against the government.