In 1995, Snake joined FOXHOUND after serving as a Green Beret. Surprising to many, Snake was hand chosen by Big Boss to infiltrate Outer Heaven, rescue fellow FOXHOUND member Gray Fox, Dr. Pettrovich Madnar, who was being forced to work on a new weapon called Metal Gear, he was also to destroy Metal Gear. Snake succeeded in rescuing Gray Fox, Dr. Pettrovich, as well as several other hostages; but as he continued the mission, he noticed that he was running into several traps, as if the enemy knew where he was. As he closed in on Metal Gear's location, Snake rescued a hostage who dropped a bomb shell on him. The hostage stated that it was Big Boss, the commander of FOXHOUND that was the leader of Outer Heaven. Snake continued on and managed to destroy Metal Gear. On his way to escape, Snake ran into Big Boss, who explained to Snake everything. Big Boss told Snake that he had sent Snake into Outer Heaven believing that he would fail his mission. Snake was able to defeat Big Boss, and he escaped Outer Heaven just before it's destruction. After the incident, Snake decided to leave FOXHOUND.

In 1999, Snake was called back into FOXHOUND by now commander Roy Campbell. Snake's new mission was to take down Zanzibar Land, an armed nation of mercenaries which had suddenly appeared in Central Asia. Snake's mission was to rescue Dr. Kio Marv, the scientist who's new invention OILIX would help the world's energy crisis, and take down Zanzibar Land. Snake successfully infiltrated Zanzibar Land, and once their, he discovered that Dr. Madnar was there. Madnar told Snake that he was once again being forced to work on Metal Gear and that the leader of Zanzibar Land was Big Boss, he had survived Outer Heaven. Snake now realized that he had to take down Metal Gear as well, and he came face to face with it sooner than he had hoped for. As Snake was traveling deep in Zanzibar Land, Gray Fox, whom Snake had saved in Outer Heaven, appeared before him behind Metal Gear's controls. Gray Fox ordered Snake to leave Zanzibar Land at once, or else he would face his death. Shocked by the betrayal of his friend, Snake managed to continue on his way to find Metal Gear. Snake eventually found Kio Marv in the same room as Dr. Madnar, but Marv had already been killed. As Snake looked at Marv's body, Madnar suddenly attacked him from behind and Snake realized that it was Madnar who had killed Marv. Snake succeeded in fighting off Madnar's attack, and with his dying breath Madnar told Snake how to destory Metal Gear. Snake confronted Metal Gear and was able to destroy it. Then Gray Fox challenged Snake to a hand to hand duel in the middle of a mindfield. The two fought in an odd moment of purity, but Snake managed to kill his friend. Snake then came face to face with the man he thought he had destroyed four years earlier, Big Boss. Before their epic duel, Big Boss told Snake that he was his father. Snake wasn't sure if he should believe him or not, but he continued to fight him. Unarmed, Snake managed to find a lighter as well as an aerosal can and used it as a flamethrower against Big Boss. Big Boss died, and Snake's ordeal was over.

Snake was traumatised from the whole incident, and to escape he retired once again from FOXHOUND and moved to Alaska. Alone, Snake took up dog sledding and his dogs became his only family. He stayed there for six years, before he was once again called upon.

In 2005, the next-generation special forces and members of FOXHOUND took over a nuclear weapons disposal facility on Shadow Moses island. Roy Campbell once again called on Snake to put down the threat. Snake's mission was to rescue two hostages; the Darpa Chief, Donald Anderson, and the President of Armstech, Kenneth Baker. Snake was also to investigate whether or not the terrorists actually had the ability to launch a nuclear weapon, and stop them if they did. During the mission, Snake would also combat Revolver Ocelot, Vulcan Raven, Psycho Mantis, Sniper Wolf, and Liquid Snake. 

Snake met up with both Donald Anderson and Kenneth Baker, but Snake was perplexed when both died of what appeared to be heart attacks shortly after he met them. Before Anderson's death, he told Snake that there was a new Metal Gear, codenamed Rex, being housed there. Snake now knew that there was more to this than meet's the eye, and he was determined to find out what. Snake continued on his mission and met up with the Colonel's niece, Meryl, and the two developed an affection for each other. Meryl would soon be captured by the terrorists though, and Snake found himself fighting with all his might to save her. Snake also met the engineer of Metal Gear, Hal Emmerich, aka "Otacon." Otacon didn't know that Metal Gear was actually being used as a nuclear weapon, and when Snake told him the truth, Otacon vowed to help Snake destroy it. Snake also met the Cyborg Ninja, who was later revealed to be Gray Fox, who had been revived and placed in an exoskeleton after the fall of Zanzibar Land. 

As Snake edged closer to Metal Gear Rex's lair, Naomi Hunter, the medical scientist who was a member of support team, was arrested. Snake was told that she had been sending coded messages to the base. But Naomi was able to get into contact with Snake herself. She told Snake that he had been injected with FOXDIE, the retro virus that killed Decoy Octopus disguised as Donald Anderson and Kenneth Baker, as a part of the exercise. She also stated that she had willingly injected Snake as revenge for killing her brother, Gray Fox. Snake then came face to face with Metal Gear Rex, and as Liquid controlled it, Snake attempted to fight it off. During the fight, Gray Fox intervened, but was killed after he saved Snake from Rex. Snake continued fighting Metal Gear, and was able to destroy it after several well placed Stinger missiles. But Liquid was not finished yet, he and Snake would fight once more atop Metal Gear Rex. Before the fight, Liquid revealed to Snake the truth of his past and that the two were a product of the Les Enfants Terribles project. Liquid was under the impression that he had the recessive genes of Big Boss and Solid had the dominant genes, and this is what gave Liquid his hatred for Snake and Big Boss. But Liquid was mistaken, the two twins actually had identical genes. Snake succeeded in defeating Liquid and saving Meryl. But as the two were escaping in a jeep, Liquid gave chase in a jeep of his own. The two jeeps collieded just after making it outside of the Shadow Moses complex, and Snake and Meryl were trapped under their jeep. But Liquid staggered out from his wrecked jeep and before he could shoot Snake, he was killed by FOXDIE.

Snake and Meryl continued their relationship after Shadow Moses, but the two would eventually part ways. Snake then joined Philanthropy along with Otacon, and he was determined to rid the world of Metal Gear.

In 2007, Otacon found out info about a new Metal Gear that was being created by the U.S. Marines. He discovered that it was being transported through the Hudson River in a disguised oil tanker. Snake, who's mission was to take photographs of the new Metal Gear so that Philanthropy could put them on the web, infiltrated the tanker. Shortly after Snake's arrival on the ship, the tanker was seized by Gurlukovich soldiers being led by Sergei Gurlukovich. Snake came into contact with Sergei's daughter, Olga, and was able to tranquilzer her. After the fight, Snake's picture was taken by a Cypher; but Snake didn't think much of it. He then made his way to the holds where Metal Gear Ray was being stored. After taking the photographs of Ray, Revolver Ocelot and Gurlukovich's men raided the holds and prepared to steal Ray. Ocelot revealed his true plans, then killed Gurlukovich and Marine Commandant Scott Dolph before sinking the tanker. Photographs taken by the Cypher were released to the media and Snake was accused of sinking the tanker. Otacon and Snake then stole Liquid Snake's body and planted it at the scene, making it appear that Snake had been killed during the incident.

On April 29th, 2009, Snake infiltrated the Big Shell disguised as Iroquis Plisken. Snake went to the Big Shell to uncover evidence about the new Metal Gear that was being housed there, codenamed Arsenal Gear. But it wasn't going to be easy as the Big Shell had been taken over by Solidus Snake, Dead Cell, and Gurlukovich soldiers; together they were calling themselves the "Sons of Liberty." Solidus hoped to find information on The Patriots whereabouts and kill them. Once in the Big Shell, Snake met Raiden, who stated that he was a FOXHOUND operative. Snake helped Raiden out in his mission, while also taking care of his own. Otacon also came along, but he was mainly there to rescue his sister, Emma, who created the AI that controlled Arsenal. But while being escorted to Otacon's location, Emma was killed by Vamp.

Snake later discovered that the whole incident, other than his presence, had been orchastrated by the Patriots. With the help of Olga Gurlukovich, Snake used Raiden as a decoy and infiltrated Arsenal Gear. Snake also replaced the disc that Raiden was holding that contained information on the Patriots with a fake disc. Snake fought alongside Raiden to take down dozens of Arsenal Tengu's, before being confronted by Fortune. As Raiden fought the Metal Gear Rays, Snake fought Fortune. Finally Snake realized that he couldn't beat her, so he surrendered to her. After the GW AI went haywire, Liquid took over Ocelot and prepared to go kill the Patriots in Metal Gear Ray. Snake broke free of his handcuffs and followed Liquid in Ray. Snake was unable to catch Liquid, but he placed a transmitter on his Ray to track him. After his mission, Snake and Otacon looked over the disc containing the information about the Patriots. Otacon discovered that the members of the Wiseman's Commettie had been dead for about 100 years, leaving them both wondering what was going on.