Snake infiltrated the base alone, but quickly gained help in the form of Metal Gear REX developer Hal Emmerich and new FOXHOUND recruit Meryl Silverburgh, Campbell's niece, the latter of whom was actually Campbell's daughter, although Snake did not know this at the time. Metal Gear REX was a nuclear-armed bipedal walking tank developed in secret by the U.S. Army and ArmsTech. With the help of the two aforementioned, as well as his former comrade Gray Fox (now the Cyborg Ninja), Snake succeeded in destroying REX and defeating the members of FOXHOUND, including Liquid.
Added by BluerockHis mission, however, was a cleverly woven plot, prepared by the Pentagon. Through the secret, Pentagon-guided efforts of genetic engineer Naomi Hunter, Solid Snake's body became host to the artificial virus FOXDIE. Snake was outraged to hear that his mission was a government conspiracy, and that he was merely sent as a carrier of the virus, which was programmed to kill Baker (for knowing too much about the project), and the FOXHOUND operatives just to ensure that the bodies of the Genome Soldiers and Metal Gear REX could be recovered undamaged. He was also reminded of the possibility that he had willingly returned to the battlefield because he enjoyed war, as commented upon by Meryl Silverburgh, Psycho Mantis, and Liquid Snake, and echoing Big Boss's words in Zanzibar Land.
Throughout the incident, Snake suspected that Campbell was concealing important information regarding the mission's true nature, although he later forgave the Colonel, after learning that the Pentagon had used Meryl as leverage in order to force him to cooperate with them (they had deliberately sent Meryl to Shadow Moses the same day as the revolt). Snake also discovered that Naomi was the foster sister of Gray Fox, who desired revenge for what Snake had done to her bother and had modified the FOXDIE virus so that it would kill him in addition to FOXHOUND. However, she set the virus to a "wildcard" value, leaving him vulnerable at a later time.
Post-Shadow Moses Edit
Following the Shadow Moses Incident, Snake and Meryl disappeared after leaving the base, after Roy Campbell faked their deaths by claiming that they had died after their jeep crashed into the ocean. Sometime later, Snake lost contact with Meryl.