Part 3 – FOXDIE

Metal Gear Solid                                                                                                      

Special agents Raven, Decoy Octopus, Psycho-Mantis and Sniper-Wolf join Ocelot and Liquid’s FOXHOUND squad.

2002 - Naomi Hunter joins FOXHOUND's medical staff, and begins gene therapy research and experimentation on soldiers.

2003 - Dr. Clark/Para-Medic dies in a lab explosion caused by a revived Gray Fox, who manages to escape. This event was managed by EVA and Ocelot as part of their plan to secretly eliminate the three remaining members of the Patriots (the other two being Sigint and Zero).  Naomi Hunter buries the incident, faking Gray Fox's death, and takes over Dr. Clark's job (in the hopes of killing Solid Snake in the near future for revenge), but she is still mostly loyal to the Patriots.

Liquid decides to rebel against the Patriots for their world-domination plans (as well as for making him the ”recessive” gene recipient).  Ocelot contacts Sergei Gurlukovich, his childhood friend in Soviet Russia and promises that he will help return Russia to power with the support of Gurlukovich's support and armaments (such as an Hind-D).

2005 - January: A report is filed describing the Patriots’ Next-Generation Special Forces as acting strangely and consulting classified information about soldier genes, as well as conducting their own gene therapy experiments. 
Meryl Silverburgh, Former FOXHOUND commander Campbell’s daughter, is sent in to infiltrate the Genome Soldiers.  This is in part to guarantee Campbell’s cooperation later.

Shadow Moses Incident. FOXHOUND Rebellion under Liquid:
A test of the new DARPA/ArmsTech-developed Metal Gear REX is planned at a nuclear weapons testing facility on Shadow Moses Island.  This test is supposed to be secured by Liquid’s FOXHOUND squadron, but he and Ocelot choose this opportunity to openly rebel against the Patriots and demand a ransom from the US.  They wish to recover Big Boss’ body (Liquid to help the ailing Genome Soldiers and Ocelot to waken Big Boss from the nano-machine coma) and also to start a nuclear war using Metal Gear REX (recreating conditions for Big Boss’ dream, a new Outer Heaven).  Sigint, now DARPA Chief Donald Anderson, is kidnapped and executed by Ocelot in an “accident” (this was the 2nd of 3 necessary executions to eliminate Zero’s Patriots).
Kaz “Master” Miller is found assassinated in his home by an unknown assailant (actually Liquid). 
Roy Campbell is pulled out of retirement to recruit Solid Snake so that he can infiltrate Shadow Moses.  Solid is secretly injected with FOXDIE, a proximity virus which kills its victims based on DNA matching.  The Patriots have Naomi do this so FOXDIE can kill Liquid and the FOXHOUND unit when Solid Snake gets close enough to them.  Naomi also (on her own) alters the FOXDIE formula so that Solid Snake will die as well - this because Solid Snake maimed Gray Fox, her surrogate brother, in Zanzibar Land. 

Solid Snake enters the Shadow Moses base with support from Mei Ling, Natasha Romanenko, Roy Campbell and Master Miller (actually Liquid in disguise).  All the members of FOXHOUND (except Ocelot) are killed by Solid Snake, either by FOXDIE or Solid himself.  The president of ArmsTech, Kenneth Baker, is killed by FOXDIE as well, probably on the wishes of the Secretary of Defense Jim Houseman in order to cover up the development of a US nuclear Metal Gear project on the eve of disarmament talks.

Solid Snake rescues Hal Emmerich (Otacon) and Meryl Silverburgh. Gray Fox, with his new “ninja” exoskeleton (provided by the Patriots), infiltrates Shadow Moses (on his own suicide mission to die at Solid Snake’s hand) and slices off Ocelot’s arm.  He is eventually killed by Liquid Snake in REX. Solid Snake destroys Metal Gear REX. Liquid tells Snake the truth about their father and how they were created through Les Enfants Terribles.  After a long battle and car chase, Liquid Snake is killed by FOXDIE. Snake leaves with Meryl in an attempt to start a new life.  Ocelot escapes with the Metal Gear REX test data and plans, and reports to Solidus Snake (the POTUS at that time).  Their plan is to use the data on REX and the Genome army to expose the Patriots.

POST Shadow Moses
Naomi is placed into a high security prison. Three weeks later, she is broken out by Ocelot so that she can help him infiltrate the Patriots’ AI system, since the new system uses similar nano-machines to FOXDIE. Because both the US Government and Nastasha Romanenko (the latter after hearing from outside sources about the breakout) believed that Solid Snake was the one who broke Naomi out, the military also added Snake's supposed involvement in her escape to his rap sheet.

Nastasha Romanenko publishes her best-selling book In the Darkness of Shadow Moses: The Unofficial Truth, in order to expose the truth behind the incident, although it ended up being heavily abridged.

Ocelot sells the data for Metal Gear REX on the black market. Soon, every nation, military outfit and DotCom owns a pirated version of the weapon. Ocelot also gains in return enough money for him to buy a decent-sized nation, which he eventually uses to create his PMC mother corporation.

George Sears (Solidus Snake) is forced by Zero/the Patriots to resign as President for his attempt to expose the Patriots with the Metal Gear REX/Genome Army data . He avoids the Patriots' wrath by going underground.  James Johnson is appointed the new President.

Secdef Jim Houseman allegedly commits suicide due to a nervous breakdown relating to his job, although it is suspected that he was actually assassinated for failing to take the fall for the Patriots' plan.

Emma Emmerich joins the NSA in exchange for information regarding her brother Hal Emmerich, who had been involved in the Shadow Moses Incident.

Metal Gear Solid 2 - Sons of Liberty                                                                     

Late 2005/Early 2006 - In Lyon, France, Ocelot has Liquid Snake's arm grafted in place of the one Gray Fox cut off at Shadow Moses as part of a plot to rescue Big Boss's remains and free him.  He and EVA use hypnotherapy and nanomachines to make Ocelot think that Liquid Snake’s arm is starting to take control of him – however this was just a ploy to confuse the Patriots.  They at this point did not want the Patriots to know that Ocelot and EVA were openly rebelling yet.  They wanted Zero/the Patriots to think that it was only Liquid that was fighting against the Patriots.

2006 - Solid Snake and Otacon found the activist group Philanthropy, in order to put a stop to the construction of Metal Gear derivatives. Nastasha Romanenko donates half her profits from her book to their cause.

2006-2007 - Jack (Raiden) undergoes VR training as part of the U.S. Army's Force XXI trials.  Jack (Raiden) and Rosemary meet each other for the first time. 

Olga Gurlukovich becomes pregnant with Sunny.

2007 August 8th:  Solid Snake infiltrates the USS Discovery to investigate Metal Gear RAY. Otacon was anonymously leaked the info about MG RAY by the Patriots (Zero, Solidus and Ocelot).  A rogue Russian commando team led by Sergei Gurlukovich takes over the tanker with support from Ocelot.  Snake meets Olga Gurlukovich for the first time. Ocelot reveals that he’s actually working for the Patriots (not Mother Russia as Gurlukovich believed) and then kills Gurlukovich, hijacks RAY ("Liquid" takes over for short time when Solid is nearby, but re-submerges shortly after), sinks the tanker and brings RAY back to Zero and Solidus.
Philanthropy is blamed for the incident and goes underground, faking Snake's death. 

The real purpose of the tanker sabotage was so that the Patriots could create an excuse to build an R&D facility for Arsenal Gear and disguise it as an oil clean up facility.  Framing Solid Snake and obtaining RAY as an Arsenal protective force was a plus as well.

Dead Cell leader Colonel Jackson is arrested for allegedly misappropriating government funding and incarcerated in Leavenworth. He was actually framed by the Patriots.

Construction on the Big Shell offshore decontamination facility begins in Manhattan Bay.

Emma Emmerich leaves the NSA. She is recruited by the Patriots to begin work on GW.

2008 - February: Olga Gurlukovich gives birth to Sunny, who is promptly taken by the Patriots.

November:  Dead Cell is caught in a surprise attack, losing two of its key members (Chinaman and Old Boy). Only Fatman, Fortune and Vamp survive.

James Johnson was re-elected as President, officially due to the policies he made, although it was largely due to the Patriots' manipulations.

2009 - April 29th: Big Shell Incident
Solidus Snake and Dead Cell are manipulated by the Patriots (and Ocelot) into hijacking the Big Shell in order to create conditions for the “S3 Plan” simulation.  They hope to create their own “Solid Snake” by duplicating the events of Shadow Moses.  Solidus realizes this and decides to detonate a nuke to free himself and Manhattan island from the Patriots and GW (the EMP would disable the Patriots’ AI).  He calls his anti-Patriot faction the “Sons of Liberty”.  Ocelot pretends to be allied with Solidus against the Patriots.

Raiden and Solid Snake infiltrate the Big Shell separately. Raiden is unknowingly used as a guinea pig in the Patriots' S3 Plan in order to provide complex simulation data for GW. Raiden is variously assisted and opposed by both Snake and the new Cyborg Ninja (Olga Gurlukovich) (actually an involuntary agent of the Patriots). The incident results in the deaths of Fatman, Emma Emmerich, Olga, Richard Ames, Peter Stillman, every member of SEAL Team 10, and the 44th President of the USA, James Johnson.

April 30th: Arsenal Gear emerges. Ocelot appears and claims that he is actually working for the Patriots.  Fortune is shot by Revolver Ocelot. Then Ocelot's implanted “Liquid” persona emerges and says he’s against the Patriots again (which is part of Ocelot & EVA’s plan to divert attention from themselves and pretend it’s “Liquid’s arm” who is the danger).

Ocelot then proceeds to escape in Metal Gear RAY.  “Liquid” sets Arsenal Gear to crash into Manhattan, so he can later extract GW from its wreckage (for use as a way to access the JD AI). Solidus dies after being defeated by Raiden (but his body is saved for later use by EVA). Otacon discovers that the original Wisemen's Committee has been dead for almost 100 years, and that one member (likely Zero) was also one of the top financial backers of Philanthropy.

Metal Gear Solid 4 - Guns of the Patriots                                                            

Revolver Ocelot has Liquid Snake's arm removed from his body so that the Patriots will think that “Liquid” can no longer take control of Ocelot. It is replaced with a cybernetic prosthetic.  However the “Liquid” persona has already established itself over Ocelot anyways and this persona continues to secretly plot against the Patriots.

Late 2009/Early 2010 - Rosemary has Raiden's baby, but tells Raiden she had a miscarriage so that the Patriots will not use the child to control Raiden. After Raiden leaves her, she pretends to be married to Roy Campbell to keep herself and her baby safe.

EVA contacts Raiden and gives him Sunny’s location in exchange for the location of Big Boss’ body (which he obtained from data retrieved from GW).

2011 - Raiden infiltrates Area 51 in order to rescue Sunny from Zero, who is then left to Solid Snake and Otacon. Sunny begins developing FOXALIVE, a virus to destroy the Patriots’ AI, based on Emma Emmerich’s original worm cluster.  EVA/Big Mama recovers Big Boss’ body from the Patriots with Raiden’s help and restores Big Boss’ body with pieces from Liquid and Solidus.  However he is still in a coma controlled by JD’s nanomachines.

2012 - Raiden is captured by Zero/the Patriots. They fit him with a cybernetic suit as part of their Exoskeletal Enhancement project.  Raiden is rescued by Big Mama and the Paradise Lost Army and Dr. Madnar (seemingly no relationship to the Dr. Madnar who created Metal Gear TX-55) manages to save Raiden's life.

Worldwide demands for PMCs increase, with disputes intensifying. The five largest PMCs are now run by a single mother company known as Outer Heaven, run by Liquid Ocelot under the Patriots’ authority.  ArmsTech Security (now known as AT Corp) implements the SOP system, which allows governments to keep check on all soldiers engaged in combat action. The SOP system is derived from Arsenal Gear’s AI.  America's nuclear arsenal has been replaced with reliable replacement warheads (RRWs) that are ID locked on JD's level.

2014 - An Eastern European country's government and the U.S. agree to build an oil pipeline and deploys some PMC teams as security. However, a riot (suspected of having been instigated by Liquid Ocelot) soon breaks out near the embassy since the populace is strongly opposed to the deal, resulting in the U.S. PMC Raven Sword quelling the disturbance. The country is later made into a checkpoint to suppress resistance movements, including the Paradise Lost Army (an anti-Patriots group led by EVA/Big Mama).

Five CID (internal investigations) units are killed by Liquid Ocelot while undercover. Meryl Silverburgh and her Rat Patrol 01 unit are dispatched.

Four days later, Solid Snake, now a recluse suffering from accelerated aging caused by FOXDIE, is unofficially requested by Roy Campbell to assassinate Liquid Ocelot. Liquid plans to destroy the Patriots’ SOP battlefield control system and create a rebellion against the Patriots, which unfortunately would also cause mass collapse of the world economic and information infrastructure.  The UN is afraid to fight Liquid since he’s part of the PMC war economy himself, therefore Solid’s mission is completely unofficial.

Solid Snake infiltrates the Middle East.  He meets Drebin, an anti-SOP arms dealer (who is actually working for the Patriots as a double agent).  Drebin injects Snake with nano-machines which allow Snake to use SOP weapons, but unbeknownst to Snake, it also contains a new form of FOXDIE which is designed to kill EVA, Ocelot and Big Boss – and destroy the original FOXDIE from Shadow Moses.  The Patriots plan to use Snake again as a carrier – like they did at Shadow Moses.  Snake meets Meryl Silverburgh’s Rat Patrol 01. Meryl believes that Liquid’s insurrection will fail because the SOP system will not allow Liquid’s troops to rebel, due to the nano-machines in all soldiers’ bodies. SOP should be able to lock out weapons access from these soldiers.  However, Liquid is able to access GW and JD/SOP using his own DNA as a genetic key.  Unfortunately, when Liquid takes SOP offline he not only frees the soldiers from SOP control, he also removes the emotional safeguards SOP provides and the soldiers have mental breakdowns.   Snake also begins to have seizures (from the scrambled SOP signals being sent to his own FOXDIE nano-machines) and fails in his mission to kill Liquid. 

Liquid decides that he must not destroy SOP, but instead take control of it (by destroying JD).  He calls this the "Guns of the Patriots" plan.

Solid Snake infiltrates South America to rescue Naomi Hunter and escapes with her and an injured Raiden.  Here, in a second attempt to control SOP, Liquid uses Solid Snake’s DNA from a blood sample obtained by Naomi, but it also fails to give Liquid control.  He decides he needs Big Boss’ DNA, since that is the original key to enter the AI’s command structure. Snake also learns that FOXDIE is mutating in his system and in 3 months will begin to kill indiscriminately, making him a doomsday bomb (however Naomi did not know that the new FOXDIE Drebin had given Snake was already working to remove this old mutated version of FOXDIE).  Naomi gives Snake a syringe whose shots can counteract the negative effects of the scrambled SOP system.  Naomi also helps create a GW virus with Sunny’s help, since she believes the SOP system will someday be used on all humans, not just soldiers

Solid Snake infiltrates Eastern Europe with the help of Meryl and Rat Patrol 01 (Liquid hunts Big Mama as well, since he knows she has Big Boss’ body) and meets up with EVA/Big Mama.  EVA pretends to be against Liquid, but in actuality wants Liquid to get Big Boss/Solidus’ body – she wants Liquid to access GW and destroy the Patriots, allowing Big Boss to awaken.  However she plays this charade for the Patriots’ benefit.

Liquid captures Big Boss’ body (actually Solidus, but close enough for his purposes) from EVA and uses his DNA to access the rebuilt GW AI (salvaged from Arsenal Gear) and is then able to infiltrate JD and control SOP without JD knowing it.  He locks down his attackers’ weapons and then blocks the SOP nano-machines, rendering the attacking American soldiers weaponless and mentally unhinged.  Liquid’s forces  massacre the US forces.  EVA, dies from exposure to the new FOXDIE virus, as per the Patriots’ plan.  Liquid renders weapons all over the world inoperable.

Liquid goes to Shadow Moses to acquire a non-JD controlled nuke and REX’s rail gun, which is also free from JD’s SOP control.  He plans to destroy JD (located on an orbiting satellite), after which GW will become the AI “head” (as well as Liquid himself).  Solid Snake fails to stop him.  Vamp and Naomi Hunter die.

Solid’s team joins with Mei Ling’s battleship to pursue Liquid’s “Outer Haven” (a modified version of Arsenal Gear stolen from the Patriots) to the location from where Liquid can launch his nuke at JD’s satellite location.

Solid Snake makes it onto Outer Haven.  He uploads the FOXALIVE virus (the GW virus created by Naomi & Sunny) to Liquid’s stolen GW, which infects JD, the Patriots' lead AI, destroying it. The SOP system collapses with it.  Liquid Ocelot tells Snake that that was what he wanted all along, he wanted the world to live free of the Patriots’ control and just be a chaotic “Wild West” mercenaries paradise. The “Liquid” persona "vanishes" (his brainwashing disappears) after a brutal fistfight with Snake, and Revolver Ocelot resurfaces just in time to be killed by the Patriots’ FOXDIE virus carried by Snake.  Otacon later tells Solid Snake that Sunny’s FOXALIVE virus did destroy the military elements of the AI but the social/infrastructure elements were spared – therefore the world’s information infrastructure was not destroyed.  In the end Solid Snake defeated Liquid’s world takeover as well as freeing the world from the Patriots’ control through AI – avoiding the meltdown of civilization. 

Meryl marries Johnny Sasaki and makes peace with her father. Rose makes her peace with Raiden.

Solid Snake visits the grave of his clone father, Big Boss. He attempts to commit suicide (thinking he’s still a doomsday weapon) but relents at the last moment, only to encounter the real Big Boss one final time.  When the the Patriots’ AI was destroyed, Big Boss was able to wake from his nano-machine-induced coma.  When GW was left open by FOXALIVE, Big Boss was also able to get the location of Zero.  Big Boss suffocates a now near-dead Zero by cutting off his life support system, and tells Solid that he’s not a doomsday device anymore from the original mutated FOXDIE virus.  He shortly dies from the Patriots’ new FOXDIE virus, accepting that the old generation of soldiers must die.
Solid Snake spends his final days living in solitude with Otacon and Sunny.

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