The 'Masse Kernels' were weaponized algorithms (an algorithm is a finite sequence of instructions, an explicit, step-by-step procedure for solving a problem, often used for calculating and data processing) developed by Phillip Masse. The Kernels attacked the United States (U.S. or US) electronically, making the nation vunerable to attacks. The main reason for the kernels being built was to send chaos of both the U.S. military and U.S. government from quickly responding to a inpending attacks. Such electronic warfare would render the military useless if a nuclear attack would have happened.
Sam Fisher was able to prevent further damage by the Masse Kernels by removing Georgian President Kombayn Nikoladze from office. Though since Kombayn and Phillip still had the ability to do another attack, Sam assassinated both Nikoladze and Masse. The Kernels on the other hand ended up in the hands of Displace International in which the intention was to stir a psuedo conflict in order to cause a rift between North Korea, Japan, and the United States.
Ultimately, Sam was able to prevent World War III and the kernels were finally destroyed in order to prevent it from falling into someone else's hands.
The Masse Kernels were used in Splinter Cell and Splinter Cell: Chaos Theory, and are key parts of the Information Warfare theme.