COBRA Unit: Led by The Boss, the COBRA unit was renowned for there victories at Normandy. Under The Boss' tutelage, the unit eventually separated from the U.S. and joined the ranks of the Soviets. Each member of the squad had unique abilities that made them formidable foes for Naked Snake during Operation Snake Eater. Naked Snake defeated each of the members of the COBRA Unit until finally facing The Boss - a final battle that would forever open the eyes of the man who would one day be known to the world as Big Boss (formerly known as Naked Snake).
FOX Unit: Major Zero was the man in charge for Operation Snake Eater, along with Paramedic and Naked Snake. After the successful mission and Naked Snake being awarded the title of Big Boss, the FOX Unit came under his command. Shortly after, the FOX Unit was disbanded by Major Zero. However, it appeared rogue factions of the FOX Unit were revolting, including Big Boss. Things were not as they appeared on the outside though. Gene, the new self-imposed leader of the FOX Unit, was at the command. Once more, it was up to Naked Snake, a.k.a. Big Boss, to disband a unit with which he was associated.
FOXHOUND: Formed out of the minds of Roy Campbell and Big Boss, FOXHOUND was to be the best operative organization imaginable. Initially led by Big Boss, the unit has changed leaders more than people change their underwear. After the betrayal of Big Boss, Colonel Roy Campbell became the figurehead of the organization. Shortly after the Zanzibar Land incident, both Solid Snake and Roy Campbell retired from FOXHOUND. Both men were called back into action when the unit went rogue under the leadership of Liquid Snake during the Shadow Moses incident. FOXHOUND is later reformed under its new leader Meryl Silverburgh.
Dead Cell: Once an anti-terrorist group, they become terrorists and call themselves "The Sons of Liberty," led by Solidus Snake during the Big Shell fiasco. Dead Cell was to serve as an analogue to the rogue FOXHOUND unit. Six months prior to the Big Shell incident, the group went rogue and only three members survived. Much like all the other organizations, the various members of Dead Cell carried unique abilities and skills to the team. In the end, one by one the unit is defeated by the combined efforts of Raiden and Solid Snake.
The Patriots: They originally called themselves the Philosophers. A pact between China, America, and Bolshevik Russia birthed the organization at the end of World War I for untold reasons. It was later revealed all of the members of the organization had been dead for nearly 100 years, with the last member passing away in the 1930s. The Patriots, also known as La-li-lu-le-lo, where formed in the 1970s when the original group broke apart after decades of turmoil and distrust. The Patriots believe in a new world order and will stop short of nothing to achieve their goal, including everything from blackmail, murder, and manipulation.