When the events of Shadow Moses drew to a close, the acts of President George Sears (Solidus) allowed everything to be exposed to the public. The
disposal facility, the Genome army, and most of all Metal Gear Rex were all revealed to the public. The greatest revelation of all was the man responsible for
averting the catastrophic results of those events.
The Patriots had not intended Shadow Moses be revealed. Solid Snake was a national hero who had narrowly averted armageddon. The Patriots never desired a
hero that was not of their own creation. A hero they made and controlled, however, could be yet another powerful influence over the nation. The S3 plan was born.
S3, the 'Solid Snake Simulation,' (or 'Selection for Societal Sanity,' see 'THE PATRIOTS' section) was to take a single impressionable soldier, use VR training to
mold together his potential, and then create a scenario that ultimately mirrors the threats and situations of Shadow Moses to put him through. With the Patriots
pulling all the strings on both sides, that soldier would be guaranteed success, but only by the narrowest margins possible. The level of challenge is just enough
to drive him to his utmost potential. In the end, he would emerge victorious amidst a frenzied and worshipping public... and he would still be under the control of
The entirety of S3 was to replicate a Solid Snake, a national hero, with variables the Patriots could monitor and control. The entire concept was in place, so
the Patriots were ready to put into action as soon as they could remove one thorn from their side; the real Solid Snake.
Solid Snake and Hal 'Otacon' Emmerich went underground almost immediately after Shadow Moses. Snake and Otacon had both found what they wanted
to fight for with their lives; the eradication of Metal Gear technology for the sake of mankind. Metal Gear proliferation threatened every nation in the world.
Snake and Otacon began a series of independent operations to disable Metal Gear variations in numerous nations. Rex's technology and schematics
survived Shadow Moses, no doubt thanks to Revolver Ocelot. Dozens of Rex derivatives were operational around the globe within two years of the
Snake and Otacon's destructive actions earned them the labels of international terrorists. The label was further encouraged by the Patriots so as
to drive away Snake's status as a 'hero' icon.
Ray was being transported down the Hudson River in the holds of a false oil tanker. Snake got himself aboard and secured the evidence needed, but
before he could pull out, the unthinkable happened. A mercenary force, led by Revolver Ocelot, seized control of the tanker. Ocelot boarded Ray and
blasted his way out of the tanker, sinking it with his own allies and the marines onboard. Ocelot escaped into the ocean with Ray, leaving the wreckage
in Hudson Bay.
Snake escaped alive, however the Patriots' plan was already in motion. Footage of Snake onboard the tanker leaked out to the public. The press and
media was universally informed that, in an act of outright terrorism, Solid Snake sank a loaded oil tanker in the Hudson river bay. Snake and Otacon's
attempts to bring Metal Gear Ray to light were useless, as they were deluged by the allegations. They remained in hiding, now wanted international
To ensure their safety, Snake and Otacon procured Liquid Snake's corpse from shadow moses and arranged for it to be 'recovered' at the tanker
site soonafter. nearly identical on a genetic level, Liquid's corpse was confirmed to be Snake, and he was officially declared dead. The record would state
that he went down with the tanker.
Alive or dead, Snake was defamed and politically neutralized, as was the Patriots' intent. He was no longer a public threat to them, so they were
free to move forward with the S3 plan; Arsenal Gear began construction under the bay, with the Big Shell built above to manage the 'cleanup' of the
tanker oil spill. Of course, there never was an actual oil spill; the Patriots replicated the effect of a small-scale crude spill and immediately put the Big
Shell into place. The Big Shell quickly became a symbol of government benevolence; it was an icon of environmental responsibility and served as
the legacy of Solid Snake's dishonor. In the following years, Snake and Otacon became fully aware of the Patriots, their intents, and the purpose
of the Big Shell.
The Big Shell and the S3 plan came to a head in approximately 2009. Raiden, under the guise of a FOXHOUND agent, inflitrated the
Big Shell to rescue the President and neutralize the 'Sons of Liberty.' At the same time, Snake and Otacon were tipped off to the situation by
an informant. Simultaneously with Raiden's infiltration, Snake surfaced from hiding and made his way through the Big Shell disguised as a Navy
SEAL. It was there that he met Raiden, an together they began to assemble the details of Solidus' plans and furthermore, the extent of the
Patriots' grip over the entire situation.
Snake's presence in the story of Sons of Liberty is that of a mythological hero; a presence which he denounces, but has rightfully earned after
Shadow Moses. He is not the player character because he is no longer the everyman. Snake is now the elite, the master, and simultaneously
a relic of a story past. He guides Raiden through his ordeals as a sort of uncompassionate mentor. Snake knows more about the situation
than he ever lets on, has a greater wealth of experience than we can comprehend at this point, and is instrumental in the revelations that follow.
With the assistance of a mysterious cyborg ninja calling itself Mr. X, Raiden locates the President, and discovers that the Big Shell is the development
facility for a new Metal Gear. Known as Arsenal Gear, it houses a powerful AI supercomputer, "GW", capable of controlling information transmitted over
the Internet. The President also claims the democratic process is a sham, and the true rulers of the United States are an organization known as
the Patriots. Revolver Ocelot kills him soon after, and Raiden proceeds to his final objective: disabling Arsenal Gear and thus halting a nuclear strike.
Pliskin, having revealed himself as the true Solid Snake, and Emma Emmerich, an Arsenal Gear engineer, assist Raiden in attempting to destroy the
"GW" AI by uploading a virus. However, the transfer is aborted partway through, and Emma dies in the ensuing attack. Snake and Raiden are left
with no choice but to disable Arsenal physically. As Snake's partner Otacon escapes with the surviving hostages by helicopter, Mr. X returns,
revealing itself to be Olga Gurlukovich, and knocks Raiden unconscious by hitting him in the back with her sword.
Awakening naked in an Arsenal torture chamber, Raiden is probed by Solidus Snake, the true terrorist leader. Solidus reveals that he once
adopted Raiden, a former child soldier, as his son during an unspecified African civil war and that Raiden is now a Patriot agent. Olga,
working as a Patriot double-agent within the Sons of Liberty, helps Raiden escape, and he locates Snake within Arsenal Gear. As they
fight through the mammoth vessel, Raiden's commanding officer begins to act extremely erratically. It becomes apparent that the "Colonel"
that Raiden has been taking orders from is actually a creation of the GW super-computer, pieced together from information about
Colonel Roy Campbell coupled with Raiden's own expectations in order to manipulate him. The erratic behavior of the simulation is
the result of the virus uploaded earlier beginning to damage GW's systems.
With Snake holding off a vengeful Fortune, Raiden is forced into battle with the battalion of 25 Metal Gear RAY units guarding the Big
Shell. Olga intervenes to protect him, but is restrained by one of Solidus' robotic tentacles. Olga explains that 2 years ago, right after giving birth
to her child, the Patriots took her away and have been holding her child hostage ever since. Olga continues to explain that the Patriots blackmailed
her, ordering her to become a double-agent and make the S3 plan a success or her child would be killed. After explaining, Solidus shoots Olga
in the head and throws her corpse out of the way. Her last words are: "Live, you have to!" The RAY units begin to malfunction, attacking each
other and Solidus as the virus tears through the GW AI's program. Arsenal begins an emergency ascent, and Snake- now restrained by Fortune,
Solidus, and Raiden are carried to the roof of the fortress as it surfaces. To Solidus' increasing rage, Ocelot reveals that he too is a Patriot
agent, the entire episode of the day was a carefully coordinated attempt to reenact the events of the Shadow Moses Incident; what Ocelot describes
as the 'S3 Plan', or Solid Snake Simulation, designed to turn Raiden into the perfect soldier. He kills Fortune and boards the prototype Metal Gear
RAY stolen from the Tanker two years previous, and attempts to finish off the survivors of the exercise. However, Liquid possesses him, and announces
his plan to hunt down the Patriots based on his host's knowledge. Setting Arsenal on a collision-course with New York, Liquid-Ocelot launches RAY
into the ocean, followed by Snake.
Arsenal comes to a halt in downtown New York, launching Raiden and Solidus onto the roof of Federal Hall. Solidus reveals to Raiden his reasons
for trying to steal Arsenal: a nuclear electro-magnetic pulse would take down Manhattan's digital infrastructure and allow Solidus to lead it as a
republic against the Patriots, a nation of "Sons of Liberty". Likewise the Patriots, via another AI contact Raiden to reveal the truth of their actions,
the AIs being programmed to becoming "digital censors", removing trite and needless information from the electronic world in what they call
"Selection for Societal Sanity", or "S3 Plan". The information fed to Ocelot was another part of this plan. However, with such a control over the
flow of digital information, they could as easily be manipulating perceived history for the Patriot's needs. Believing the only option available is
to track down the Patriots using the information in Raiden's neural implants, Solidus offers his son one final duel.
Raiden defeats Solidus, and as crowds descend upon the wreckage of Arsenal Gear, Snake and Raiden meet one last time, where his mentor
informs him that only he can choose what to believe in, and that he must pass on what he believes to be true. Having planted a tracking device
on Liquid-Ocelot's Metal Gear, he and Otacon plan to follow him, and to hunt down the Patriots, whose details were hidden in the GW computer
virus disc. As Snake disappears into the crowd, Raiden is finally reunited with Rose, on April 30, 2009 - the 220th anniversary of George
Washington's inauguration as President of the United States, and the anniversary of Rose and Raiden's first meeting.
In a brief epilogue, Otacon and Snake discuss the decoding of the virus disc, which reveals that all 12 members of the Wisemen's Committee
(the Patriots' high council) have been dead for approximately 100 years, and that one of them is a major sponsor of Philanthropy.