S3 Plan

The S3 Plan (the Selection for Societal Sanity; initially believed to have stood for the Solid Snake Simulation due to misinformation) was a program run by the Patriots in order to manipulate world events and the decisions of individuals. The S3 Plan was tested during the Big Shell Incident, on Raiden, unknowingly an agent of the Patriots.

The Big Shell Incident was, in fact, a recreation of the Shadow Moses Incident four years prior, in which Solid Snake had become a legend, being the "Big Boss" of his age. The Patriots had designed the Big Shell Incident into a recreation of Shadow Moses as they considered it the ultimate exercise for the S3 Plan. Revolver Ocelot had been misled by the Patriots into believing S3 stood for "Solid Snake Simulation" and was a system capable of equipping every soldier with combat abilities equal to those of Solid Snake.

Similarities
There were many similarities between the two events, both planned and coincidental:


 * A "Snake" being in charge of the terrorists, and another Snake being sent in to stop them (though the second Snake was quickly renamed Raiden).
 * A "president" being held hostage.
 * The Sons of Liberty terrorists stood in for the Sons of Big Boss, with Dead Cell representing FOXHOUND, and the Gurlukovich Mercenaries representing the Genome Soldiers. In addition, Vamp and Fortune wore trench coats like the FOXHOUND members.
 * The seagulls that surrounded Fortune represented the ravens that surrounded FOXHOUND member Vulcan Raven.
 * The terrorist leader was a product of the Les Enfants Terribles project.
 * The appearance of a Cyborg Ninja.
 * The deaths of Richard Ames and James Johnson standing in for the deaths of Donald Anderson and Kenneth Baker, respectively. In both cases, one was a president and the other a member of the Patriots. Unlike in the Shadow Moses Incident, however, only Ames died from something comparable to a heart attack.
 * In both incidents, a second force was deployed as a diversion (the U.S. Air Force and SEAL Team 10) so that the operative could infiltrate the enemy facility more easily.
 * Solidus Snake shooting down the two SEAL Sikorsky Sea Hawks in a similar fashion to Liquid shooting down the F-16 Fighting Falcons.
 * In both incidents, the operative made his way into the facility by swimming (Solid Snake / Iroquois Pliskin even did it twice).
 * In both incidents there was a need to use a Nikita to destroy a high voltage circuit panel to reach a new location.
 * In both incidents, there was a third party who had an agent in the enemy base with Ocelot as the agent at Shadow Moses, and Fatman and Ocelot again during the Big Shell Incident.
 * The Harrier battle standing in for the Hind battle.
 * A mysterious Codec call from someone named "Deepthroat", though the contact would quickly changed their name to Mr. X. And like before, they warned about Claymore mines.
 * A new type of Metal Gear and a threat of a nuclear strike.
 * The (fake) ransom for $30 billion stands in for the ransom for $1 billion, Big Boss's body and the FOXDIE vaccine at Shadow Moses.
 * Emma's computer virus mimicking the effects of FOXDIE.
 * Richard Ames was involved in both incidents (though not seen at Shadow Moses).
 * Otacon wanting to rescue his stepsister Emma instead of Roy Campbell wanting to rescue his niece/daughter Meryl Silverburgh.
 * In both incidents, someone that Otacon loved was killed.
 * Revolver Ocelot was involved in both incidents.
 * Revolver Ocelot's right arm was severed by the Cyborg Ninja in Shadow Moses and an attempt to do the same was made by the Cyborg Ninja in the Big Shell.
 * Revolver Ocelot calls Snake/Raiden "carrier-boy," if only sarcastically in Raiden's case.
 * The bodies in the corridor before Raiden first saw Vamp were similar to the ones killed by the Cyborg Ninja just before Snake fought him.
 * Both incidents happened on areas in the middle of the ocean.
 * Snake/Raiden needing the help of a scientist that worked at the facility, with Emma filling in for Otacon, with both being related to Huey Emmerich (his son and stepdaughter, respectively)
 * Gurlukovich Mercenaries were involved in both incidents.
 * Solid Snake was involved in both incidents (although his involvement in the Big Shell Incident was not planned).
 * Johnny Sasaki was involved in both situations (although this might have been the one similarity that was purely coincidental).
 * In both incidents, a member of the support team who had been impersonated by the enemy, revealed their true identity near the end of the operations.
 * In both incidents, there was a threat of the bases being destroyed (Shadow Moses was not destroyed while the Big Shell was).
 * In both incidents, Raiden/Snake needed a card key to open higher level doors, in order to progress in their respective missions.
 * In both incidents, a member of the support team was blackmailed with the threat of someone close to them being killed. As a result, they were forced to betray their friends (Roy Campbell and Olga Gurlukovich, respectively).
 * In both incidents, there was more to the locations than met the eye as Shadow Moses was to test Metal Gear REX while the Big Shell was to cover up the construction for Arsenal Gear and for the S3 Plan itself.
 * Near the end of both incidents, the operative needed to fight Metal Gear(s) with a Stinger missile launcher.
 * Near the end of both incidents, the terrorist leader knocked out the operative and when they woke up the terrorist leader released them and fought them equally.
 * In both incidents, the Cyborg Ninja saved the operative from being killed by Metal Gears. This action ultimately led to the Cyborg Ninja being killed by the terrorist leader.
 * In both incidents, prior to being killed by the terrorist leader, the Cyborg Ninja personally addressed the operative with their final words.
 * Liquid Snake was involved in "both" incidents in some way.
 * Solidus Snake was involved in both incidents, the former from behind the scenes.
 * Roy Campbell was involved in "both" incidents, although the latter only as a facsimile.
 * The terrorist leaders of both incidents tried to revive Big Boss's dream of Outer Heaven.
 * In both incidents, a virus had two purposes: FOXDIE was to kill the Sons of Big Boss, those in the know about the REX project (i.e., Kenneth Baker), and (albeit unplanned) Solid Snake and at the same time ensure that REX and the Genome bodies could be recovered without risk of damage; while Emma's worm cluster was to stop Arsenal Gear and simulate FOXDIE's effects, as well as erase any leads to the Patriots.

In addition to the similarities between the Big Shell Incident and the Shadow Moses Incident, there was also at least one similarity between either the Outer Heaven Uprising or the Zanzibar Land Disturbance: the Patriots manipulated Solidus Snake and Raiden into encountering and fighting each other because of their relationship being similar to that of Big Boss and Solid Snake, respectively.

Final stages of the S3 Plan
However, after Arsenal Gear crashed into Manhattan, another AI contacted Raiden through his Codec and explained that Ocelot had been incorrect, and that S3 actually stood for Selection for Societal Sanity. By manipulating the information that surrounded the incident, the Patriots had proved that they could manipulate world events. Using the data they collected from this exercise, their AIs would be improved even more.

Though GW was presumed destroyed by Emma's worm cluster, the Patriots succeeded in obtaining the necessary data that it had accumulated. The worm, however, did delete any information about the Wisemen's Committee, the 12 people that supposedly headed the Patriots.

Aftermath
As a direct result of the S3 Plan, the Patriots' AIs began preparations to control people on the civilian level. They also created the Sons of the Patriots System through AT Corp and the war economy, thus perfecting what they saw as absolute control over warfare during their dominion, up until their demise via infection by FOXALIVE.

Raiden would briefly allude to the S3 Plan's connection to his mission to Courtney Collins, when he said, in reply to her commenting that his shooting down a Harrier with missiles must have been a "crazy op," that Courtney "didn't know the half of it."

Behind the scenes
If the player kills Solid Snake after reuniting with him in the Arsenal Gear portion of the Plant Chapter, sometimes the Colonel will be heard laughing during the Game Over sequence.

The true events of the Peace Walker Incident in Metal Gear Solid: Peace Walker, as told by Paz Ortega Andrade, bore several similarities to the head AI's exposition to the true nature of the S3 Plan.

A Codec conversation with Courtney Collins in Metal Gear Rising: Revengeance had Raiden mentioning that he and other recruits for FOXHOUND had trained in Fort Polk in a mockup of an Afghan village, hinting that there were other candidates besides Raiden to undergo the S3 Plan, although Raiden was ultimately chosen for the Big Shell Incident.

Appearances

 * Metal Gear Solid 2: Sons of Liberty (first appearance)


 * Metal Gear Solid 4: Guns of the Patriots (indirect mention)


 * Metal Gear Solid: Peace Walker (indirect mention)


 * Metal Gear Rising: Revengeance (indirect mention)