Metal Gear Solid was originally released for the Sony Playstation. and was later re-released with updated graphics and features on the Nintendo Gamecube as "Metal Gear Solid: The Twin Snakes". It was also released on the Playstation Portable as somewhat of an interactive comic book called "Metal Gear Solid: Digital Graphic Novel"

With the Zanzibar Land mission a success, Snake returned to Alaska to forget his messy history. Despite going into retirement, the battle would not end for Snake. In 2005, he was approached by his former commander once again who informed him that terrorists had taken over a nuclear disposal facility. At first, Snake was somewhat reluctant, until he was told that he was essentially the world's only hope in preventing a nuclear disaster. Accepting the mission, Snake infilitrated the Shadow Moses facility where he found himself fighting the Next-Generation Special Forces and the reformed FOXHOUND. Snake's original mission was to rescue the DARPA chief, Donald Anderson, and the ArmsTech President, Kenneth Baker - both of which were being held as hostages. Later on, Snake encountered Meryl Silverburgh and Dr. Hal Emmerich ("Otacon") - both of which would assist him in his mission and inform him of the 'truth' about what was really going on. One by one, Snake eliminated all of the members of FOXHOUND and successfully destroyed Metal Gear REX - the latest Metal Gear incarnation. Unknown to Snake, one member of FOXHOUND had escaped from Shadow Moses - Revolver Ocelot, who would later be revealed as a double agent. Prior to his mission, Snake was injected with the FOXDIE virus by Dr. Naomi Hunter - who wanted Snake dead after what he did to Grey Fox at Zanzibar Land. This virus was also programmed to kill off the members of FOXHOUND, resulting in the 'death' of Liquid Snake.

In 2005, Campbell once again calls upon Solid Snake, bringing him out of retirement for a second time in order to quell the uprising at Shadow Moses, which was being orchestrated by members of FOXHOUND. Numerous important people were held hostage, including the DARPA Chief Donald Anderson and ArmsTech president Kenneth Baker. Campbell's daughter, Meryl Silverburgh, was also being held hostage - in addition she was used as a manipulation tool by Ames in order to use Campbell. Throughout Snake's mission, Campbell intentionally kept many secrets from Snake, such as the involvement of FOXDIE. Unable to cope with betraying his 'friend', Campbell tried to pay Snake back by cancelling the nuclear strike - which only resulted in his arrest at the hands of Jim Houseman, then-Secretary of Defense. Afterwards, thanks to Ames, Campbell was placed back in charge.

Naomi Hunter was born in Rhodesia in the early 1980s, though she was later orphaned as a result of the civil war that was taking place. She was eventually picked by a soldier, Frank Jaeger - who unbeknowst to Naomi had killed her real parents. In truth however, most of Naomi's history and background was fabricated and falsified, a fact which would be exposed in 2005 - the Shadow Moses incident. As a child, Naomi lived with Frank, who ridden with guilt over the death of Naomi's parents, adopted her as his own flesh and blood. They lived together until they were taken to the United States by Big Boss. In 1999, Naomi learned about the death of her 'brother', Frank, who had been almost killed in battle at Zanzibar Land at the hands of Solid Snake. Bitter at this fact and curious about the truth of her past, Naomi began studying genetics, later joining FOXHOUND - since it would offer her an opportunity to enact her revenge upon Solid Snake.
In 2003, Naomi covered up the death of her predecessor, Dr. Clark - who was killed by Frank Jaeger (Gray Fox) who had now been resurrected as a cybernetic 'ninja'. In addition, Dr. Naomi finished perfecting FOXDIE, under orders from Richard Ames. In 2005, Naomi serves on Snake's support team during his infilitration into Shadow Moses, on loan from ATGC, Inc. Before the mission however, Naomi injected Solid Snake with the FOXDIE virus, which was programmed to kill those with a specific genetic code. As Snake neared the end of his mission, Master Miller (Liquid in disguise) accused Dr. Naomi of being a spy when he revealed information which implicated her as an impostor. Naomi was immediately placed under arrest by Campbell and then charged with treason. However, three weeks after her arrest, Naomi escaped custody - an act which Snake may have had a hand in.

After the Uprising of Zanzibar Land and Colonel Campbell's retirement, Miller retired as well and moved to Alaska. He sometimes trained the Alaskan scouts during his free time. However, three or more days before the terrorist takeover of Shadow Moses, Miller was attacked and murdered in his home.

Mei Ling was born and raised in the United States, her parents immigrated from Guangdong, China. After qualifying at MIT, Mei Ling invented a new type of radar system known as the Soliton Radar - which surpassed the original radar used during the Zanzibar Riots. In 2005, she was assigned to Solid Snake's support team along with Col. Roy Campbell, Dr. Naomi Hunter, Nastasha Romanenko and Master Miller. Her duty in the mission was to process the data transmitted by Snake's nanomachines. Throughout Snake's mission, Mei Ling enlightens Snake with a variety of ancient proverbs. Mei Ling helped to unravel the true identity of Master Miller after discovering that his transmission signal came from somewhere within Shadow Moses. After the defeat of Liquid Snake, Mei Ling makes a hard copy of all the mission data in order to protect Snake and his support team.

Nastasha Romanenko is a Ukrainian weapons analyst. She helps Solid Snake via. Codec, giving him information on firearms and nuclear weapons.
She was born in Ukraine where her and her family where exposed to radiation due to the Chernobyl accident. This made her become very strongly opposed to nuclear weapons and nuclear power. She later got married to Richard Ames, but the marriage didn't last long. In 2005, Richard Ames made contact with her and pushed her into helping Solid Snake out in Shadow Moses via codec. She helped him by providing information on nuclear matters. After the Shadow Moses Incident was over, she wrote a book about it entitled In the Darkness of Shadow Moses: The Unofficial Truth.
After Shadow Moses, Nastasha set up the Anti-Metal Gear organisation Philanthropy, and recruited Otacon, Solid Snake and Mei Ling. As it stands, Nastasha is rumoured to be on the run from The Patriots, because of the book.

The man who introduced himself to Snake as "Deepthroat" via Codec had no video image of himself broadcast, and it was discovered that he was transmitting from somewhere on Shadow Moses Island. He would periodically call Snake with valuable information about traps, and ambushes, apparently following his progress throughout the entire mission. When asked who he was, his only response was, "One of your fans". Gray Fox would later reveal that he had been making the calls and was only helping Snake so that he would survive until their final battle could take place.

The man with the same codename as Snake. Liquid was one of three survivors of the Les Enfants Terribles project which commenced in 1972. Before his actual birth, Liquid was given to the British government by the American government as part of their 'special relationship'. Liquid was born and raised in the United Kingdom, serving in the British Special Air Service (SAS) during the Gulf War in 1991. His mission during that war was to locate and destroy Iraqi SCUD launchers. In reality, Liquid was operating as a sleeper agent for the British Secret Intelligence Service (SIS). However, Liquid was captured by Iraqi troops and was held as a POW until 1994. In 2000, Liquid joined the ranks of FOXHOUND and quickly rises up to become the leader of the unit. He is later incited by Ocelot into starting an uprising at the Shadow Moses nuclear disposal facility. During Shadow Moses, Liquid takes possession of Metal Gear REX - which Liquid uses in order to make demands with the U.S. government, which included the DNA of Big Boss - something which Liquid required in order to cure the Genome Army.
Later on, Liquid learns that his genetic clone brother - Solid Snake - had infilitrated Shadow Moses and as such he prepares for his arrival, later confronting him in a Hind-D gunship (provided by Col. Gurlukovich). After the destruction of the Hind, Liquid survives via a parachute and later confronts Snake again in the hangar where Metal Gear REX is stored, boarding and piloting REX. Thanks to Grey Fox, REX is eventually destroyed. Liquid drags Snake's unconscious body to the top of the fallen REX and once Snake regains consciousness, engages him in hand-to-hand battle. Liquid is defeated, falling from atop REX to his supposed 'death'. However, when Snake is making his escape from Shadow Moses, Liquid catches up with him in another jeep. In the end it was the genetic virus FOXDIE which killed Liquid. Unknown to Snake however, Liquid's arm is used in a transplant to replace the arm that Ocelot lost at Shadow Moses. It is through this arm that Liquid occasionally takes control over Ocelot, manipulating him into doing his bidding.
Ocelot took part in the takeover of Shadow Moses, along with his Foxhound colleagues. He was ordered by the President of the United States, to convince Liquid into taking over Shadow Moses with the GENOME Army and using Metal Gear REX's nuclear missile launching capabilities to threaten America into handing over the remains of Big Boss along with one billion dollars, in order to correct mutations in the GENOME Army, thus creating an army of super-soldiers. Liquid believed he was carrying on Big Boss’ legacy, even telling Ocelot to refer to Shadow Moses as “Outer Heaven.” Ocelot, being the master of torture that he was, was given the task of interrogating the DARPA Chief Donald Anderson, and the President of ArmsTech, Kenneth Baker in order to get the launch codes so that FOXHOUND could launch a nuke from REX.
Anderson knew of Ocelot's real identity and so he killed Anderson and made it look like an accidental death while interrogating him, which then gave Psycho Mantis the idea of tricking Solid Snake into using the PAL keys that Baker gave to Meryl to inadvertently activating REX. Shortly after Ocelot got Baker's launch code, he tied Baker to a pillar and connected the strings to C4. Then, when Solid Snake attempted to rescue Baker, Ocelot challenged Snake to a gun-duel. Snake eventually defeated him, and as Ocelot went to deliver a surprise shot, Ninja appeared and cut off Ocelot's right hand. Picking up his gun(and his hand), Ocelot then ran off, swearing revenge. Later, when Snake was captured by Sniper Wolf, she took Snake to the Prison Holds in the second basement of the main Tank Hangar. While he was there Ocelot tortured Snake in an attempt to find out what Kenneth Baker had told him about the PAL keys. After Snake's escape from the torture chamber, Ocelot was later seen talking to Liquid about their plans. After Snake defeated Liquid, and saved Meryl, Ocelot vanished. The last thing we hear from him is a conversation with the President of the United States, where he gives information about tracking Snake and Meryl, and it is revealed that the President is the third clone of Big Boss, Solidus Snake.

Psycho Mantis' mother died during child-birth. When he gained the ability to read people's minds he read his father's mind, only to discover that his father hated him, blaming him for the death of his mother. This caused him to go psychopathic and, using his telekinetic powers, he burned down the village that he lived in, killing everyone who lived there.
Later, he joined the KGB's ESP Intelligence unit, before eventually joining FOXHOUND in the early 2000's.
Psycho Mantis is one of the renegade members of FOXHOUND who took over Shadow Moses with the GENOME Army. He wears a gas-mask to help him, because when he's not wearing it people's thoughts "force their way into [his] mind." He took part in the Shadow Moses Incident, attempting to read Donald Anderson's and Kenneth Baker's minds. When Revolver Ocelot accidentally killed Anderson during a torture session, Mantis came up with the idea of tricking Solid Snake into getting the PAL Key from Baker and using the keys to activate Metal Gear REX while making Snake think he was de-activating REX. They made Decoy Octopus disguise himself as Anderson to talk Snake into the act.
Psycho Mantis was later killed by Solid Snake, after a heated battle. Before his death, Mantis read Snake's and Meryl's minds, telling them their futures were intertwined.

Born into a war torn country, Sniper Wolf was originally Kurdish and as such endured great hardships during her childhood. In 1988, Wolf witnessed the gassing of her friends and family at the hands of Iraqi soldiers during the Iran-Iraq War. Orphaned as a result, Wolf was taken in by the Iraqi Ministry of Internal Affairs, and was brainwashed into serving Iraq. It was during her military training that her exceptional abilities as a sniper were discovered. Wanting to tap into this ability, Wolf was trained by a Gurkha who taught her all he knew about sniping.
During the Gulf War in 1991, Wolf escaped and found herself at a refugee camp. It was here that she first met Big Boss, who saw great potential and talent within her. Big Boss brought the young Wolf to the United States, where she underwent mental deprogramming to remove the brainwashing she had received during her time in Iraq. Sniper Wolf looked up to Big Boss, seeing him as the legendary 'Saladin' - an honourable military leader who had defeated the Crusaders in the 12th century. After the death of Big Boss at the hands of Solid Snake, Sniper Wolf was later recruited by Liquid Snake - who had assumed command of FOXHOUND.
In 2005, Sniper Wolf took part in the Shadow Moses uprising led by Liquid Snake. Despite being a trained killer, Wolf held a strong bonding with the huskies at Shadow Moses, which Liquid would have ordered killed if it weren't for Wolf's intervention. It was during Shadow Moses that Wolf would meet Otacon, the man who later fall in love with her. Wolf battles Snake twice throughout Snake's mission, finally being defeated after the second duel. As she lay dying from her wounds, Wolf tells Snake that all along she was waiting for someone to kill her. At this point, Otacon announces his love for her though it is too late for her. As her final request, Wolf tells Snake to shoot her, to set her free from the world. A single shot rings out, marking the end of Sniper Wolf.

Vulcan Raven is one of the renegade members of FOXHOUND who take over Shadow Moses with the GENOME Army. He is a Shaman and was raised in the cold state of Alaska. He says that he excels in the Ear Pull contest at the World Eskimo-Indian Olympics. (It is an event where two people who are facing each other with a string loop connecting their ears try to pull back and keep the loop on their ear the longest.) His spirit animal and guide is the Raven, signifying that his life is nothing more than a path to death and destruction. He has many tattoos to celebrate this fate.
Vulcan Raven shares a history with Revolver Ocelot in the soviet union that has not been fully disclosed.
He, like the rest of the renegade FOXHOUND members, is killed by Solid Snake in battle. He is then eaten away by his own ravens as he tells Snake of the dark path he will continue to walk on.

Born in Mexico, Decoy Octopus grew up to become obsessed with Hollywood movies and special effects. Octopus possesses the remarkable ability to take on the appearance and personality of anyone. In order to fully mimic anyone, Octopus removed his own ears and shaved his cheek and jaw bones. He is even willing to inject himself with his target's blood, that is, if they're already dead. Originally working in the movie industry, Octopus was eventually approached by the CIA, who saw great potential and use in Octopus' abilities. It was the intention of the CIA to use Octopus as a decoy, where he would disguise himself perfectly as someone who was the target of assassination. Octopus was also fluent in over ten different languages, including Ebonics. In addition, he is able to dislocate his own joints in order to fully mimic the walking patterns of his copied target. Finally, he has also mastered an advanced form of biofeedback which permits him to vary his senses of touch.
Octopus sometimes believes that he actually is his target and as such he requests the military to give him a full mental deprogramming upon returning from his missions. Sometime later however, Octopus joined the ranks of FOXHOUND, and along with the rest of the unit took part in the armed uprising on Shadow Moses island. After the death of DARPA chief Donald Anderson, Octopus was ordered to masquerade as the chief. Unfortunately for Octopus, he wasn't able to deceive the Angel of Death, when he was killed by the FOXDIE virus which was being carried by Solid Snake.

Big Boss is the codename of the legendary soldier who founded the special forces unit FOXHOUND. He also served as the founder of the private military contractor Outer Heaven in South Africa and later founded the nation of Zanzibar Land in Central Asia. Big Boss was considered by some to be the "greatest soldier in the 20th century" and a brilliant military leader. He was hailed as a war hero by admirers and feared as a tyrant by his enemies. As a result of the Les Enfants Terribles project, he is the "father" of Solid Snake (his subordinate and then, nemesis) and his clone brothers, Liquid and Solidus.
Prior to earning the codename Big Boss, he served as a field operative for the FOX unit under the codename of Naked Snake during the Cold War. Big Boss' real name is classified. He has been known to introduced himself as John and has been called Jack by his close acquaintances.
Some people suspect that the reason the U.S. government wouldn't hand over the remains of Big Boss to the FOXHOUND defectors, was because there are no remains because Big Boss is still alive, and in hiding.

A man cursed, Frank Jaeger has endured countless manipulations by his superiors, both psychologically, and physically. In his early years as a child soldier he was already an accomplished killer, luring his enemies with a false sense of safety using the honest eyes, and frankness of a young boy. These acts would have him come to be called "The Frank Hunter" (Jaeger in German). Later he would be recruited into the F.O.X. unit by Gene (who took over the unit after Big Boss retired). During his time as a member of F.O.X., many tests and experiments were performed on him, his name was changed to a "product" number, and he was refered to as "the perfect soldier" with the codename "Null". Null was sent out on missions with orders of who he would kill, and upon his return his memory was wiped, and he was prepped for another killing mission. Emotionless, and highly skilled, he nearly bested Big Boss in combat, but was ultimately defeated. His defeat jarred him emotionally and his trance-like state gave way to more rational thought. Big Boss knew of Null from his days as a child soldier, and reminded him of his previous name. When Big Boss formed FOXHOUND, he took Frank along with him, and bestowed the name "Gray Fox" upon him, the highest hono
r given to any member of FOXHOUND.
During his mission to stop the Outer Heaven uprising, Gray Fox was captured, and a rookie who Fox had befriended, called Solid Snake was sent in to rescue him, and stop the uprising himself. Upon learning that it was Big Boss that had formed Outer Heaven, Fox joined the man who had "rescued" him years earlier, and became an enemy of FOXHOUND, although the friendship that had formed between himself and Solid Snake never faded, they were now two friends fighting for different sides.
Fox would later be defeated, and killed by Snake in a hand-to-hand battle in a minefield.
After the death of Big Boss and the downfall of Zanzibar Land, Fox's body was recovered on-site by a clean-up crew. He was taken by FOXHOUND's chief medic at the time, Dr. Clark, and became a guinea pig for Clark's gene-therapy project. In order to improve his mobility, an experimental exoskeleton resembling a ninja suit was grafted directly onto his body. Aside from improved agility and strength, the suit also allowed Fox to 'cloak' at will, using a new form of stealth technology which rendered the wearer near invisible to the naked eye (the stealth technology could not however, fool advanced sensory devices such as thermal goggles). In 2000, Fox's foster sister, now going under the alias of Naomi Hunter, joined FOXHOUND as Dr. Clark's assistant. She helped Fox escape his containment, and summarily covered up his actions when he killed Dr. Clark in 2003, reporting it as a laboratory accident.
In 2005, during the Shadow Moses Incident, Fox infiltrated the island in search of Solid Snake, who was on a mission to neutralize the now-corrupt FOXHOUND unit led by Liquid Snake. He first made contact with Snake after releasing Armstech President Kenneth Baker from captivity and attacking Revolver Ocelot, severing Ocelot's right forearm. Later, after taking out a large group of genome soldiers, Fox confronted Snake once again in the laboratory of Hal Emmerich, demanding that they fight to the death. At first, Snake did not recognize the man in the ninja suit, but after engaging him in hand-to-hand combat, Fox's identity was revealed. After a time, Snake began to prevail in the battle but before its ultimate conclusion was reached, Fox cried out in pain (presumably due to feedback from the experimental exoskeleton) and fled the laboratory. Fox later helped Snake in his mission by transmitting anonymous messages regarding dangers to Snake under the alias of Deepthroat.
When Snake is drawn into battle with Metal Gear REX, Gray Fox manages to damage it further by attacking REX's radome, interfering with the sealed cockpit's sensory input. As Liquid fought to locate Fox and Snake with REX's damaged sensors, Fox revealed to Snake that many years ago, he had been the one who had killed Naomi's parents in Rhodesia however he had been unable to bring himself to kill Naomi, who had been too young at the time to remember the incident. Fox begged Snake to tell her the truth. Following this exchange, Fox leapt from his hiding spot and again attacked Metal Gear REX, eventually destroying the Radome completely, and forcing Liquid to open the cockpit up. This made the tank vulnerable to well placed Stinger missiles.
During a second assault on REX, Fox was severely injured when one of his arms was sliced off by the tank's laser. He was then pinned against a wall by REX before being released to fall to the ground. As Fox lay on the hanger floor, Liquid tried to kill off Fox once and for all by crushing him under one of Metal Gear's massive legs, however Fox's grafted exoskeleton meant that this first attempt failed. With REX's second stomp however, the only man to ever achieve the "Fox" codename was no more. His last words were directed towards Snake,
After escaping the Shadow Moses compound, Snake contacted Naomi, informing her that Fox's last message had been that he would always love her. He did not inform her of Fox's final confession. 

According to official records, Meryl Silverburgh is the daughter of Roy Campbell's younger brother, Matt. However, circumstantial evidences suggest the possibility that Meryl was born from an affair between Roy Campbell himself and her mother, although they had yet to be verified. When Meryl was young, Matt Campbell was killed in action during the Gulf War and after that, she took on her mother's maiden name.
Raised in a house of military traditions, Meryl trained herself throughout her childhood in the 'arts' of soldiery. She admired the FOXHOUND unit (a high-tech special forces group), viewing the days when her uncle and Solid Snake were members as the unit’s heyday, and wears a paint tattoo of the unit's old logo on her left shoulder. She joined the armed forces after graduating high school and received extensive psychotherapy to prevent any attraction to the opposite sex. Her weapon of choice is a Desert Eagle she procured from the base's armoury.
She was recruited by the Next-Generation Special Forces U.S. military group and assigned to Shadow Moses island in 2005 as an emergency replacement when several soldiers were reported missing. Following her arrival on the island, the unit involved with the exercise revolted along with members of FOXHOUND and took over the nuclear disposal site on the island and the Metal Gear tank being developed there. Meryl refused to join in with the rebellion and was taken prisoner and placed on the same holding cell level with ArmsTech president Kenneth Baker. Baker gave Meryl the PAL card needed to activate REX before he underwent his torture session with Ocelot. Afterwards, she managed to escape confinement and met up with Solid Snake, who had been forced out of retirement by the U.S. government in order to neutralize the terrorists and the two eventually began working together. She managed to stay hidden by disguising herself as one of the Genome Soldiers using the clothes she stole from Johnny Sasaki, the guard that was watching her cell.
Later, the pair met up on the B1 Floor of the Nuclear Disposal Facility. She gave the PAL card to Snake and then the two headed to the Commander's Room where Psycho Mantis controlled Meryl's mind. Meryl held her gun against Snake, but Snake, realizing she was not herself, managed to knock her out. Snake then dispatched of Mantis and he and Meryl headed North in order to destroy Metal Gear. However, Meryl was shot and subsequently captured by FOXHOUND member Sniper Wolf. In an attempt to rescue Meryl and complete his mission, Snake engaged in a sniping duel with Wolf and was eventually lured into an ambush by her where he was also captured. Snake is then put through a series of torture trials by Revolver Ocelot.
However, Snake was strong enough to resist Ocelot's torture and manages to escape from his confinement. Meryl is later rescued by Snake after his battle with Liquid and the two manage to escape together after the destruction of Metal Gear REX.

Hal Emmerich was originally born to American parents, though after the death of his real mother, his father remarried. In his childhood, Emmerich had an affair with his own step-mother, who had seduced him. As a result, Hal's real father committed suicide via drowning, an incident which involved Emma Emmerich (Hal's step-sister). Afterwards, Emma fell out with Hal, blaming him for what happened. Ridden with guilt, Hal left his home and school behind, educating himself by using the Internet. Joining MIT, Hal studied for his Ph.D at Princeton University. Throughout his time at college, Hal was contacted by the FBI, who wished to recruit his ability for their Engineering Research Facility. However, Hal was fired when the FBI discovered that he had hacked into classified files.
Afterwards, Hal saw employment at ArmsTech Incorporated, and was asked to be the lead engineer of a new project involving the construction of a walking battle tank known as "Metal Gear". Being a fan of Japanese animes, Hal was eager to get involved, blissfully unaware that he was actually creating a nuclear equipped weapon that could mean the end of the entire world. It was his love of Japanese anime that urged him to create a nickname for himself, and thus Otacon was born as a result of combining the first three letters of the words Otaku Convention, an annual anime convention. In 2005, Otacon became caught up in the Shadow Moses incident, where he first met the legendary hero known as Solid Snake. Throughout Snake's mission, Otacon provided assistance via CODEC and in person, informing Snake about the specifications of Metal Gear REX - the doomsday weapon he had created. It was also during Shadow Moses that Otacon first fell in love, with none other than FOXHOUND's Sniper Wolf.
Thanks to Otacon, Solid Snake was successful in defeating and destroying Metal Gear REX, saving the world yet again from the brink of nuclear disaster. Otacon also helped Snake and Meryl escape from the facility, unlocking the security doors which they both would have needed to get through. However, the nuclear strike on Shadow Moses was aborted and Otacon was later rescued.

The Chief of The Defense Advanced Research Projects Agency (DARPA). Donald Anderson, along with certain other parties, participated in the design and creation of a new type of superweapon, a weapon that would change the world - Metal Gear REX. The money for which was used out of the 'black budget', a top secret sum of money that was set aside to be allocated for the most high level projects. Anderson was bribed by ArmsTech, who worked together with DARPA to create REX. In 2005, Anderson and Baker were inspecting the prototype of REX when they were taken captive during the FOXHOUND uprising. It was Anderson's intention to acquire the Metal Gear REX test data from Kenneth Baker, and then hand it over to his personal friend in the White House, Jim Houseman - the U.S. Secretary of Defense. However, Anderson is interrogated by Ocelot in order to find out his detonation code to disarm the safety device on REX. Ocelot, knowing that Anderson knew of his true identity as a spy, kills Anderson during the interrogation and makes it look like an accident.
With the Chief dead, Liquid orders Decoy Octopus to masquerade as the DARPA Chief.

Kenneth Baker served as the Chief Executive Officer of ArmsTech, Inc. Baker himself was a major proponent of the nuclear-deterrent theory. His company was once one of the world's most powerful military contractors, achieving rapid growth and expansion during the Cold War. Unfortunately, with the collapse of the Soviet Union and the ending of the Cold War, ArmsTech found itself becoming redundant. Coupled with the failure to secure the next line of fighter jet for the United States Air Force (USAF), ArmsTech was facing a severe crisis. In order to help his company recover, Baker arranged a series of bribes to the DARPA Chief, Donald Anderson. With the support of DARPA, Baker and ArmsTech could work on a new type of experimental weapon - their 'ace in the hole' that would revolutionise strategic warfare. In 2005, Baker was inspecting the development of REX at Shadow Moses along with Anderson.
However, he was taken prisoner during the uprising led by members of FOXHOUND. Whilst imprisoned, Baker entrusts the REX data disc and the PAL card to Meryl Silverburgh, a young woman also held captive. Tortured for information, Baker is successful in keeping his secrets from Psycho Mantis due to surgical implants in his brain which provide psychometric insulation. In order to lure out Snake, Ocelot rigs Baker up to a boobytrap consisting of C4 plastic explosives. After the defeat of Ocelot, Baker explains to Snake about REX as well as his company. However, his words are short lived when Baker falls victim to FOXDIE.

The Secretary of Defense, Jim Houseman oversaw the entire infilitration operation of Shadow Moses in 2005. Houseman had complete authority over the mission, though ultimately he had to answer to Richard Ames - who was a frontline operative of the Patriots. With the destruction of Metal Gear REX, Houseman immediately places Campbell under arrest and orders a nuclear strike on Shadow Moses in order to cover up the entire affair. In addition, Houseman was interested in the Metal Gear REX test data - which the DARPA Chief, Donald Anderson, should have brought back. With Anderson dead, however, Houseman decided to use the nuclear attack to cover everything up, eliminate the existence of the Genome Army, as well as wipe out everyone who knows anything. Unfortunately for Houseman, Ames disapproves of his method and cancels the bombing run. Instead, Ames plans on using Houseman as a fall guy. Angered, Houseman refused to take the blame - which eventually resulted in his death at the hands of the Patriots - which was covered up as a suicide.
Snake successfully infiltrated Shadow Moses. On the way he was contacted by his old master, Master Miller. Snake then achieved the first half of his first objective. He made his way into the Prison Cell’s where the DARPA Chief Donald Anderson was being held, and Anderson revealed to Snake about the existence of Metal Gear REX, which Snake didn’t know about at the time. Before Snake could escort the DARPA Chief to safety, the chief suffered from a heart attack and fell dead before Snake. As Snake made his way outside, he met Meryl Silverburgh. Snake then headed to the Basement to find the President of ARMSTech Kenneth Baker. When he got there he encountered Revolver Ocelot. The two had a gun showdown, before Ocelot decided to end the game. As he went to shoot Snake, Cyborg Ninja appeared and cut off Ocelot’s hand, as well as cutting the wires holding Baker (he was tied to a pillar rigged with C4). The Cyborg then vanished, and Ocelot ran off, with his severed hand. Afterwards, Baker tells Snake about the Metal Gear system over-ride keys and that there are three of them. He mentions that Meryl should have them and that her Codec number should be on the back of the CD Case. At that moment Baker dies of a heart attack, similar to the way Anderson died. Snake then contacted Meryl and she, disguised as a GENOME Soldier, opened the door to the other building for him.
On his way there, Snake got a call from an anonymous tipster naming himself “Deepthroat” saying he was “one of his fans” and he warned Snake of a tank up ahead. Sure enough, as he pressed on, he was confronted by a tank being driven by Vulcan Raven and two GENOME Soldiers. Snake destroyed the tank by throwing a grenade into the hatch. He then headed into the main building, in order to find Hal Emmerich (a.k.a. Otacon). When he got there, the Ninja appeared and confronted Snake. The Ninja eventually goes crazy and leaves telling Snake that he is Gray Fox. Otacon then told Snake that he developed Metal Gear REX, but not with the intention of it being nuclear-equipped. Otacon also tells Snake about the over-ride keys that Baker mentioned and again, that Meryl should have them. He then said that if the keys don’t work Snake will have no choice but to destroy Metal Gear. Snake then tracked down Meryl, but she only gave him one of the three detonation over-ride keys. Then on their way to the Communication Towers, Psycho Mantis appears and challenges Snake, while taking control of Meryl using his psychic powers. Snake had to knock Meryl out in order to save her. Snake then defeated Mantis and Mantis reads both their minds, saying a great turmoil awaits them.
On their way to the Towers, Meryl was shot by Sniper Wolf and she used her as bait to lure Snake out. Snake decides to head back and get a PSG-1 in order to battle Wolf. He eventually finds one and manages to out-snipe Wolf. Snake was then captured and tortured by Ocelot and he took the launch data that Baker gave to Snake. In the cell he saw the body of Donald Anderson, but mysteriously it seems like he had been dead for days. He then escapes from his cell thanks to Otacon and heads to the Communication Towers. Once atop the second tower he fought Liquid who was piloting a Hind-D. He destroys the Hind and heads out the tower. He reaches a snow field and once again battles Sniper Wolf. Once again he emerged victorious, and Wolf requested to Snake “finish me quick.” Just then, Otacon turned up. He admitted that he had fallen in love with Wolf. Snake then shoots Wolf at her request and Snake and Otacon parted ways.
Snake then headed to the control room where REX was being held. On the way there he fought and defeated Vulcan Raven. Raven then told him that the Donald Anderson he met in the cells who told him about Metal Gear was in fact, Decoy Octopus. Snake is then told by Master Miller that Naomi could be a spy. Based on information she gave earlier about her past, Miller made the deduction that she was lying and was most likely a spy. Snake then heard Liquid and Ocelot talking about their plans to turn Shadow Moses into the next Outer Heaven. Otacon then told Snake about the trick to the PAL key he has… it was made of a shape memory alloy that changes at different temperatures: Room Temperature, Ice Cold Temperature and Intense Heat Temperature. Naomi called Snake and told him that she was, in fact, a spy. She then mentioned that Frank Jaeger (a.k.a. Gray Fox) is her big brother, which comes as a shock to Snake.
Snake then input all three PAL Keys and the secret was revealed. It turned out that Snake was being used all along, and Metal Gear REX was now active! Ocelot never input the detonation codes from Baker and Anderson because Anderson never gave him his code. Master Miller then called Snake and reveals that it was actually Liquid Snake in disguise; the real Miller had been dead for at least three days. Liquid expressed his gratitude to Snake for activating the war-head. Then Snake went to confront Liquid, face-to-face, and Liquid explains everything. Liquid explains about the FOXDIE virus, and how it was programmed to kill off Donald Anderson (but killed Decoy Octopus instead because he was disguised as Anderson, even disguising his blood to be like Anderson’s) and Kenneth Baker. He then explained that Naomi made an unknown change to the program at the last second. No-one knew how or why.
Liquid then climbs aboard REX, and Snake had to destroy it. Snake fought valiantly against REX but, it seemed like he was getting nowhere. At that point, Gray Fox jumped out from the shadows, destroying REX’s radar, forcing Liquid to open up the cock-pit, and exposing himself. Fox and Snake then hid and Fox explained to Snake that he adopted Naomi, because he killed her parents, and felt guilty because of it. Fox then attempted to take out REX, but was eventually crushed under Rex. Snake then shot REX several times with the stinger and REX exploded, knocking Snake unconscious. Snake then awoke atop a destroyed REX. Liquid proceeded to explain his plans to Snake, about how he wanted to turn the world into a war zone where warriors such as him will always need a place. Then Liquid explains the Les Enfant Terribles project, and how they were both created by it. Twin clones of Big Boss, Liquid inferior and Solid superior. Snake then called Campbell and asked what the hell was going on. Campbell told Snake that a nuclear strike was on its way to Shadow Moses, but he said that he would try to buy him some time to escape. Suddenly, Campbell was arrested and Jim Houseman, Secretary of Defence, told Snake that a nuclear strike would destroy Shadow Moses. Snake and Liquid fought atop REX, and Snake eventually knocked Liquid over the side of REX’s cockpit.
Snake ran to check that Meryl was okay as Otacon called to tell Snake the way out and then said that he was about to leave. Snake and Meryl found a jeep nearby and drove out of the hangar. As they were making their escape Liquid chased them whilst shooting at them. Snake and Liquid shot at each other until they reached the end of the tunnel and they both crashed. Snake and Meryl were trapped under their jeep as Liquid slowly approaches… but just before he could shoot Snake he suffered from a heart attack just like Octopus and Baker… as it turned out the edit Naomi made to the FOXDIE virus was for the revenge of her older brother, it was designed to kill off Snake, but because Solid Snake and Liquid Snake had identical DNA coding it mistook him for Solid. Meryl and Snake then ride off into the Alaskan Wilderness alone together.