In 2001 Solid Snake is forced out of retirement UNDER GUN POINT! By his now retired former commander Roy Campbell, when 6 Members of Fox Hound and a Next Generation Special Forces, which have been genetically improved by gene therapy take over the small Alaskan island Shadow Moses
Snake’s mission was to rescue Donald Anderson, Kenneth Baker and to find out weather or not there are any active nuclear weapons.
Once their Snake finds out that he is not the only infiltrator, after further infiltration Snake Finds Donald Anderson and Meryl Silverburgh (Roy’s Niece) Snake finds out that a new Metal Gear had been constructed under the name “Rex”, rather suddenly Anderson suffers from some sort of heart attack and Meryl escapes under the cover of a guard.
Snake soon finds Kenneth Baker, after blowing up a few walls!
But is confronted by the infamous Revolver Ocelot, a gun battle ensues with no winner as the result, then a mysterious Ninja appears cutting ocelots hand off, freeing Baker from the explosive straps and then confronting Snake. Suffering from a major headache the mysterious Ninja runs off, Baker then explains about the reasons behind Rex and how it can be controlled, through a PAL Key. He then suffers a heart attack blaming the government for double crossing him. Reaching the snow plain between the 2 buildings Snake is confronted by Vulcan Raven in a Tank! Through using the different grenades Snake had at his disposal he managed to defeat the driver and co pilot. Reaching the nuclear storage building Snake goes in search of a scientist called Hal Emmerich, before reaching him; Snake is confronted with a hallway filled with the corpses, of what were the guards!
Once inside the lab, Snake finds the Ninja confronting Hal Emmerich, when the Ninja realises that Snake was there, he challenged Snake to a round of combat, giving reason for the slaughter outside.
The battle ensues, with Snake soon realising that any weapon was useless, moving to hand to hand combat, the Ninja still had the advantage with his great speed and skills.
But Snakes strong point was his smarts and managed to defeat the Ninja with emmence effort. Now defeated the Ninja reveals he was Grey Fox! Who had died in combat against Snake 3 years ago! Suffering another headache he runs away. Talking to Hal (Otacon) Snake finds out more information over the specifications of Rex and what happened in the uprising.
Meeting up with Meryl in the Girls Bathroom! Snake learns more over about her past and Snake receives the PAL card.
Making their way to the commander’s room Meryl comes under the control of a mysterious force.
After entering the room Meryl begins to point her gun and asking for love. At which point Psycho Mantis reveals himself and begins to show off his powers to Snake. As the battle ensued Mantis was now not able to read Snakes mind for some reason and was able to dodge Snakes gunfire, using a trick Campbell had surgested, Snake was able to fight back and as a result Mantis was eventually defeated
Mantis reveals the fact that Meryl had deep feelings for Snake and that he had a tortured past of nothing but evil deeds.
Carefully making his way through the caves filled with wolves, they both reach a narrow corridor, which lead to the communications tower, the only way to reach Rex, once past a small mine field, Meryl is gunned down by Sniper Wolf and Snake is forced to back track in search of a sniper rifle.
Once retrieved Snake confronts Wolf and under an immense disadvantage defeats wolf with a few shots, making his way to the towers base Snake thinks of Meryl who had been taken away and was nowhere to be seen. Once at the door Snake is caught out by a group of soldiers and Wolf, who knocks Snake unconscious.
Reawakening Snake is stretched on a metal bed, with Liquid and co in front of him, eventually Ocelot is the only one remaining, and challenges Snake to a series of torture sessions, eventually Snake manages to free himself through outside help (Otacon or Ninja depending on your skills) and retrieves his gear.
Making his way to back to the towers Snake could now climb them, unfortunately guards chase Snake all the way up! Once outside Snake is confronted by Liquid in the Hind-D and Snake is forced to descend the tower on some ropes. Dodging the gunfire and steam Snake reaches a gantry, which connected the 2 towers, once across Snake is chased inside by the Hind-D's gunfire. Descending the tower Snake finds the stairs are out and the lift was also not functioning, after talking to Otacon, Snake decides to take on the Hind-D with his newly acquired toy. In a display of reactions and skill Snake dodges the Hind D’s attacks and launch consecutive stinger missiles bringing down the powerful Hind-D. With the lift now fully operational Snake was now able to reach the bottom, but not before defeating 4 stealth guards! once outside, there was a vast blizzard as Snake moved forward through the snow, but Wolf was waiting and had made her warning shot, running for cover Snake had the choice of fighting with either the Nikita or Sniper Rifle, using his good aim Wolf was finally defeated, telling of her past and how big boss had raised her. Meeting up with Otacon, Snake asks him to find out as much about the Rex project and the PAL key as he could.
Making his way down into the depths of Shadow Moses, Snake enters a cold area filled with crows! Out of the mass of crows Vulcan Raven appeared, carrying a gatling gun normally found on a fighter aircraft!, snake is forced into a battle of cat and mouse!
Running around the containers, Snake uses some good timing and luck to shoot and dodge Raven’s heavy barrage. Defeated Raven reveals that Donald Anderson was actually Decoy Octopus, why this was important he didn’t say but as he died he said to Snake he would always haunt him for as long as Snake battled on.
Moving through a gun filled room Snake finally reaches Metal Gear Rex, making his way over Rex towards the control room, Otacon contacts Snake over what he had found so far and about why the Rex was created.
Reaching the control room Snake finds Liquid and Ocelot discussing their plans of where to launch the first nuke.
Otacon contacts Snake over the pal key, it turns out to be 3 cards in one due to the shape memory alloy it was created from being affected by the room temperature.
Discovered by Ocelot, he shoots the card out of Snake’s hand and down to the bottom of the area.
Forced back Snake eventually finds the card and makes his way back and forth inputting the different cards. Once the final card was input, the computer announced that the missiles where ready to launch, in disbelief at what he just did, Snake was contacted by Master. Thanking Snake for activating the launch codes, he reveals himself to be actually Liquid Snake and asks Snake to meet him.
Just outside Liquid is standing next to the head of Rex, he explains how Big Boss treated him, as Snake approached he jumped into Rex and the platform which Rex was standing on begins to rise.
Facing Rex as it stands up; Snake is bewildered at how he could stop this almost invincible machine, contacting Otacon Snake finds out that Rex’s weakness was a radome on Rex’s left shoulder. Using a combination of Chaff grenades and the Stinger launcher, Snake dodges the various attacks while disabling the radome, realising that the radome was still active, gun shoots appear out of nowhere and Snake was dragged behind a container.
Realising that it was Grey Fox, he explains how he killed Naomi’s parents and raised her as a member of his family, eventually realising that their cover was blown Grey Fox reveals himself and takes on Rex but he is eventually pinned on the wall by the head of Metal Gear Rex. With what little energy he had left he takes out the radome and the cockpit was finally opened, Grey Fox then ordered Snake to kill him, but Snake was unwilling to fire, eventually Liquid drops Grey Fox to the floor and crushes him under Rex’s foot.
With Grey Fox finally dead, Snake continues his battle with Rex now aiming for the cockpit. Eventually the systems that controlled Rex where destroyed and Rex fell to the ground, but in the proceeding explosion Snake is knocked unconscious.
Awakening, Snake finds himself on top of Rex without his gear, confronted by Liquid. He explains how he and Snake where created in a project called Les Enfant Terrible and how using selective breeding of over 20 embryos Snake and Liquid where created with Snake receiving the dominant genes and Liquid the recessive ones.
Liquid challenged Snake to hand to hand combat and the prizes were survival and Meryl! As Snake and Liquid fought, they where almost even, but through luck, good timing and Snake won the battle as Liquid fell from Rex’s head.
Now rescued by Snake, Meryl was thankful for her rescue and said that she never stopped fighting, as she believed Snake was doing the same. They make there way back out through a conveniently placed transport route, as they made their was up the route their were a number of check points that needed clearing, once past amazingly Liquid was chasing behind armed with a famas rifle.
As Liquid chased dodging most of Snakes fire, they took pot shots at each other, eventually they reached sunlight and both vehicles topple over just before the Cliffs edge!
Finding that they were both trapped under the vehicle, Liquid appears in a terrible state and begins to raise his rifle. Then all of a sudden he feels faint as the affects of the Fox Die virus took effect and Liquid died before their eyes, questioning when he may die Naomi informs him that he should chose to enjoy life and start living. Taking this advice Snake and Meryl set off into the vast lands of Alaska.
In 2002 Snake decides to join Philanthropy an organisation set up to eradicate and expose the existence of every Metal Gear Projects in the world
Felling remorse for Naomi being locked up because of her betrayal, Snake gets Otacon to find her location and under the cover of darkness Snake sneaks into the prison where Naomi was being held and manages to rescue her safely, but secretly.