S3 Plan

According to Ocelot the reason for the sons of liberty incident was to create the S3 Program, Otherwise known as the Solid Snake Simulation. if The Patriots could recreate the Shadow Moses incident then it would be possible to turn an inexperienced rookie (such as Raiden) into an veteran soldier like Solid Snake.

There were many Simularities between the two events.
 * a Snake being in charge of the terrorists.
 * Dead Cell standing in for Fox-Hound.
 * The appearance of cyborg ninja.
 * a new type of metal gear.

After the completion of the exercise the data extracted from it would be used to create an army of Solid Snake clones using VR Training.

After Arsenal Crashed in Washington DC an AI revealing itself as JFK contacted Raiden through his Codec and explained that Ocelot was wrong. S3 actually stood for Selection for Societal Sanity. By manipulating the information that surrounded the Sons of Liberty incident. The Patriots had proven that they could manipulate world events. Using the data they collected from this exercise their AIs would be improved even more.