Jason Flemming (voiced by Nolan North) and his girlfriend Claire (voiced by Eliza Jane Schneider) are hiking in the Pacific Northwest when they find some strange caverns. Claire goes up to explore them, saying she used to come there as a kid, but when she doesn't respond to Jason, he follows her. He comes across a huge underground complex operated by many soldiers with high-tech equipment. He manages to follow men forcing Claire into the complex and is able to rescue her through complicated puzzles throughout the complex. However, the two have heard chatting among the soldiers about their group, The Progressive Restoration, which is going to launch attacks across America. Jason escorts Claire to the entrance to allow her to call for help, while Jason uses the high-tech devices he found and stolen to further infiltrate the complex and learn more about it. He comes to meet Lucius, the leader of the Restoration, who reveals a long-term goal of inciting a civil war in the United States, allowing their group to take control; Jason finds out that they have already killed the Vice President of the United States earlier that day and are now planning to launch an airship to attack San Francisco. He is able to destroy the airship with the complex's own missiles and corners Lucius before he can escape. Lucius attempts to offer while held at gunpoint by Jason, who can't shoot him. Suddenly Lucius is shot dead by Claire, who has arrived by helicopter. Claire reveals to Jason she is with the NSA that was investigating the Restoration and had gotten romantically close with Jason after finding him as a person capable of completing the infiltration of the base. Jason leaves the area with Claire. The story is continued in the novel Empire in which the President of the United States is dead hours after the vice president and the plans of civil war were about to start.
An alternate ending is available halfway through the game, where Jason can escape the complex and leave Claire to her fate. Jason is seen driving away in the Jeep and commenting "Eh, plenty of fish in the sea."