Marv's OILIX formula, the new Metal Gear D, and a cache of atomic weapons makes Zanzibar Land the most dominant military force on a planet fast running out of oil.
Shortly after infiltrating the country Snake learns about the events which followed the destruction of Outer Heaven - the NATO airstrikes, the escape to the Middle East, and Big Boss' position as Zanzibar Land's leader.
Snake frees Dr. Marv but is attacked by Gray Fox in the cockpit of the Metal Gear D, and though Snake is able to escape he catches up with the doctor too late and finds him tortured to death.
Shortly after retrieving the OILIX formula from Marv's corpse, Snake fights the Metal Gear D once more, this time destroying the walking nuke launcher but losing the OILIX formula to Gray Fox. The two fight in a live minefield and Fox "dies" by Snake's hand just in time for Big Boss to arrive and ruminate on the nature of war, the way he usually does.
With all his equipment gone Snake improvises and torches the Boss with an aerosol can and a lighter, but not before learning that Big Boss is his father.
Snake would spend the next five years alone in the Alaskan wilderness; meanwhile, Big Boss' body is recovered and placed on ice by the Patriots.
2005: Metal Gear Solid 1
During a routine training mission at the nuclear weapons storage facility on Shadow Moses Island the new Liquid Snake-led FOXHOUND and a battalion of Genome Soldiers rebels against the United States government and threatens to launch a nuclear weapon against the White House.
They demand Big Boss' body and rename themselves the Sons of Big Boss - a literal truth in the case of Liquid and a semi-metaphorical truth in the case of the Big Boss gene-enhanced Genome Soldiers, who need Big Boss' genes to halt their own genetic degradation.
Dragged out of retirement, Snake infiltrates Shadow Moses under the orders of Roy Campbell to rescue the DARPA chief Donald Anderson, ArmsTech chief Kenneth Baker and confirm the Sons of Big Boss' ability to launch a nuke.
Both Anderson and Baker die from heart attacks shortly after meeting Snake - victims of the FOXDIE virus secretly implanted in Snake's body by FOXHOUND doctor Naomi Hunter.
Assisted by Campbell's daughter, Meryl Silverburgh, Snake sneaks through the base, fights Revolver Ocelot, and witnesses the return of Gray Fox as a cyborg ninja when Gray Fox slices off Ocelot's pistol hand.
Snake confirms the terrorists' ability to launch when he meets Metal Gear Rex designer Hal 'Otacon' Emmerich. Meryl is shot and Snake is captured but he escapes in time to rescue Meryl and battle REX, piloted by Liquid. Snake succeeds thanks to the intervention of Gray Fox but it costs Fox his life.
Solid and Liquid Snake fight atop Rex's hull and engage in a final chase as the Shadow Moses facility collapses around them. Liquid succumbs to the FOXDIE virus and Snake is left without knowing if FOXDIE will eventually kill him, too.
2007: Metal Gear Solid 2: Sons of Liberty
Otacon is contacted by his sister and creator of the GW AI, Emma Emmerich, about the development of the new anti-Metal Gear Metal Gear codenamed RAY.
Snake and Otacon plan to intercept and expose RAY on board the oil tanker being used to transport the machine before it leaves New York's harbour.
Shortly after Snake arrives on board the tanker is hijacked by mercenaries led by Sergei Gurlukovich under orders from Ocelot, now 'possessed' by Liquid's arm. Ocelot escapes in RAY and frames Snake for the destruction of the tanker which allegedly floods New York's harbour with oil.
Two years later the off-shore decontamination rig named Big Shell is seized by the Sons of Liberty, led by Solidus Snake, who kidnaps the current US president and threatens the destruction of the rig.