In 2016, a nuclear attack occurs in Saudi Arabia, killing six million people and crippling the supply of oil from the Middle East, plunging the world into an unprecedented energy crisis. The following year, the United States of America and the European Union sign the historic SLAMS (Space-Land-Air Missile Shield) Treaty, agreeing to co-develop technologies for a comprehensive, interlocking anti-ballistic missile system.

Shortly after the events of Chaos Theory, Sam Fisher must deal with the recent loss of his daughter to a drunk driving accident. But he has little time to mourn, he soon has to go on an undercover assignment which requires him to pose as a criminal in order to infiltrate a terrorist group based in the United States. This new mission forces Fisher into a new and very dangerous gray area, where the line between right and wrong is blurred even beyond what Fisher is used to, and thousands of innocent lives are in the balance.