Setting Guns of the Patriots is set within an
alternate history timeline in which the
Cold War continued into the 1990s, ending before the turn of the century. The events themselves take place in 2014, and form the final chapter in the storyline covering the character of Solid Snake, providing conclusions to the events that led up to
Guns of the Patriots. The world's economy relies on continuous civil wars fought by
private military companies (PMCs), which outnumber government military forces. Soldiers are equipped with
nanomachines that monitor and enhance their performance on the battlefield, controlled by a vast network known as the Sons of the Patriots (SOP) system.
Liquid Ocelot re-emerges from hiding to launch an
insurrection against
the Patriots, a secret
cabal that manipulates global affairs from the shadows. In the meantime, Solid Snake is experiencing accelerated aging and has little time left to live. He is living on board the airplane
Nomad with Dr. Hal Emmerich, nicknamed
Otacon, and
Olga Gurlukovich's daughter,
Sunny, a child prodigy in computer programming. Since the aftermath of the
Big Shell incident,
Raiden has drifted away from
Rose, who had apparently suffered a miscarriage with their child and gone to live with Snake's former commander, Colonel
Roy Campbell, and has become a cyborg ninja fighting against the Patriots.
Meryl Silverburgh commands a PMC inspection unit in the U.S. military, which includes
Johnny Sasaki.
Plot Five years after the Big Shell Incident, Snake is told by Otacon that he has only a year to live due to
Werner syndrome-like symptoms. Snake meets Campbell, now working with the
United Nations Security Council, who tells him that
Revolver Ocelot, missing since the Big Shell Incident, possessed by the will of
Liquid Snake, now under the guise of 'Liquid Ocelot', was located in the Middle East, and Snake is tasked to assassinate him. In a Middle-Eastern war zone occupied by one of Liquid's PMCs, Snake meets Drebin, an arms dealer who injects Snake with nanomachines to use the latest weaponry, and Meryl, now leader of Rat Patrol Team 01 and keeps a resentment against Campbell for being her biological father. Snake reaches Liquid, but the latter transmits a signal that incapacitates those nearby with nanomachines. Snake spots Dr.
Naomi Hunter, who assists him against the signal and then departs with Liquid. After waking up a day later in the Nomad, Snake and Otacon receive a video from Naomi, who reveals that she is in South America, kept as prisoner by Liquid to do research. In South America, Snake locates Naomi. She explains that Snake's accelerated aging is due to intentional
genetic mutations as a
human clone of
Big Boss, and that the
FOXDIE virus she infected him will also mutate within months, spreading to the general populace and causing a deadly
pandemic. She also explains that Liquid plans to use the
biometrics of Big Boss to access and take command of the Patriots' firearms control system. Liquid's PMC soldiers kidnap Naomi, but Snake rescues her, assisted by Drebin and Raiden, and they escape, though Raiden is injured by
Vamp. Snake finds an Eastern-European resistance group led by Big Mama (revealed as EVA, Snake and Liquid's surrogate mother). EVA reveals that after Operation Snake Eater, Major Zero used the Philosophers' Legacy to form the Patriots—composed of Zero, EVA, Ocelot, Sigint, Para-Medic, and Big Boss—to fulfill The Boss’s will. Zero used Big Boss as an icon but, as Big Boss resented this, Zero initiated the Les Enfant Terrible project with Para-Medic and EVA to clone replacements (Snake and Liquid). Big Boss left to oppose Zero, forming Outer Heaven, starting a secret war over The Boss's will. Big Boss failed to stage a coup with FOXHOUND, defeated by Snake in Outer Heaven and Zanzibar Land. Zero then put Big Boss in a coma and secured the Patriots' control via the AIs: GW, TJ, AL, TR, and JD. She reveals to Snake she is in possession of Big Boss' body. They move Big Boss' body by boat while Liquid's PMC soldiers attack decoys. Liquid captures the body and obtains the biometrics, intending to infiltrate the Patriots' system by using the repaired
artificial intelligence (AI) core, GW, as a
trojan. U.S. soldiers arrive to arrest Liquid, but he kills them after disabling their firearms. Big Boss' body is incinerated, and Snake saves EVA from the fire when she tries to save the body, but both are badly injured in the process. Naomi leaves with Liquid, but Otacon tracks them. EVA seemingly dies from her injuries. Snake and Otacon learn that Liquid aims to destroy the Patriots' master AI with a
nuclear strike, allowing GW to take control. A non-ID-tagged warhead is required from
Metal Gear REX at Shadow Moses in Alaska. There, Snake is ambushed by Vamp, accompanied by Naomi; but Vamp is killed when his self-healing nanomachines are disabled via injection. Naomi reveals she has terminal cancer; and, overcome with guilt for her mistakes, she disables the nanomachines keeping her alive and dies. Snake and Raiden use REX to escape and fend off Liquid piloting a
Metal Gear RAY. Liquid reveals
Outer Haven, a modified
Arsenal Gear. Raiden saves Snake from being crushed before the USS
Missouri, captained by
Mei Ling, arrives and forces Haven to retreat. Snake, Meryl, and Johnny board Haven when it surfaces in order to launch the nuke. At the core, Snake installs a
computer virus coded by Naomi and Sunny into Liquid's trojan, which destroys both the core AI as well as the entire Patriot network controlling global affairs, leaving the necessities for civilization to survive. Atop Haven, Liquid explains to Snake that he allowed the virus' installation in order to destroy the Patriots. The two fight, with Snake victorious and Liquid becoming Ocelot again before dying. Meryl reconciles with her father, Campbell, and marries Johnny. Raiden reunites with Rose after learning their child was not miscarried and that her marriage to Campbell was a ruse to protect them from the Patriots. Snake visits the grave of
The Boss at Arlington National Cemetery. Snake, feeling that he has no further purpose and must prevent an epidemic from his FOXDIE, attempts suicide, but hesitates at the last moment. Snake is then met by Big Boss with a vegetative Zero, with Big Boss explaining that the body burned in Europe was
Solidus Snake. He then reveals that the Patriots were founded to realize the will of the Boss, Big Boss' mentor. Differing interpretations split the group into two factions: Zero's, which stood for government control of society to prevent conflict, and Big Boss', where soldiers fought for personal beliefs, unrestrained by governments. Zero consigned control to AI networks, the Patriots. After Big Boss' downfall in Zanzibar Land, the Patriots placed him in an
induced coma, and later initiated the war economy, a vision far from the Boss' will. Ocelot and EVA planned to restore Big Boss by destroying the Patriots, with the possession of Ocelot through Liquid being a ruse to draw the Patriots' attention. Big Boss then kills Zero by cutting off his life support. He informs Snake that the nanomachines from Drebin contained FOXDIE, engineered by the Patriots to kill EVA, Ocelot, and Big Boss. With the new strain supplanting the mutated strain, Snake poses no risk of becoming a biological weapon unless he lives long enough for it to mutate. After understanding his mentor's will and telling Snake to find a new reason to keep living, Big Boss dies beside the Boss' grave. Snake decides to live the time he has left peacefully with Otacon and Sunny. ==Development==