

Sam then learns after interrogating a guard that Lacerda has left the area aboard a ship called the Maria Narcissa, which has suspected involvement in illegal arms trade. While on site Fisher locates the information that was extracted from Morgenholt concerning the Masse Kernels and the team promptly has it deleted. Fisher is also sent to assassinate Lacerda as a target of opportunity. When Fisher locates Morgenholt it is too late, as he discovers he has been tortured to death by Lacerda's thugs.

Sam discovers that Lacerda was hired by a third party for the kidnapping and his group have been paid in advanced weaponry and equipment, beyond that of usual terrorists. It is revealed that Morgenholt was kidnapped by Lacerda so his knowledge of Philip Masse's information warfare algorithms could be obtained. He infiltrates via zodiac to find and rescue a computer programmer - Bruce Morgenholt - who has been captured by a Peruvian revolutionary group known as 'The People's Voice', led by Hugo Lacerda. Sam Fisher is dispatched to a lighthouse off the coast of Peru.

Meanwhile across the world, Sam Fisher is sent by Third Echelon into Peru to rescue a programmer who worked on reverse engineering the Masse Kernels. Walsh, into the Yellow Sea hoping China and North Korea will back down. They send their most advanced ship, the USS Clarence E. China and North Korea set up a blockade in the Yellow Sea and the United States is forced to respond, as per their agreement with Japan following World War II. In 2007 China and North Korea are unhappy with Japan's new Information Self-Defense Force as they believe it violates Article 9 of the post World War II constitution (there is a news report about the I-SDF in a cutscene in Pandora Tomorrow), which restricts Japan from possessing any armed military force capable of striking outside its own borders. Chaos Theory was later remade for the Nintendo 3DS as called Tom Clancy's Splinter Cell 3D and it is also part of the Tom Clancy's Splinter Cell Trilogy for PlayStation 3. A demo was released for OXM in which the lighthouse mission can be played. It is unknown why Ubisoft Montreal decided to go with this rating but speculation suggests they wanted a more realistic Splinter Cell game than in the past. This is also the first game in the franchise in which it is rated M for mature. Michael Ironside returns as Sam Fisher while Don Jordan returns as Lambert who was previously voiced by Dennis Haysbert in the last game.

They also added Co-Op storyline that works side by side with the main campaign. From the point where when it rains, Sam becomes wet. In doing so, they used a modified Unreal Engine 2.5 to create a more detailed game. Ubisoft Montreal returned to develop the third title in the franchise.
