This is a work in progress; and (right-now) completely stolen from a person on reddit.
The Boss defects to the Soviet Union, taking two U.S. nuclear war heads with her.
When Volgin, a Soviet Russian Colonel with whom The Boss was closely associated with after her defection, uses one of the nuclear war heads in Soviet territory, the Soviets suspect that the U.S. is involved.
In order to convince the Soviets that they aren't involved, the U.S. sends in their greatest soldier, John, to kill The Boss and thus eliminate any suspicion that her defection was faux.
John reluctantly carries out his mission and kills The Boss, his former mentor. He is awarded the title of Big Boss upon completion of his mission.
He learns that The Boss's defection was a ruse setup so that she could get close enough to Volgin to gain possession of the Philosopher's Legacy.
After learning the truth, Big Boss comes to hate not only the U.S., but all world governments because they treat soldiers like pawns. He, Zero, Sigint, and Para Medic form The Patriots, an organization whose purpose is to fulfill the will of The Boss.
Overtime, conflicts begin to arise between Big Boss and Zero in regard to interpretation of The Boss's will: Zero wants to manipulate the entire world into unification. Big Boss wants to create a world where soldiers are always necessary and never treated like they are expendable (i.e. a world of constant warfare).
In 1972, Big Boss falls into a coma as a result of an injury he sustains while fighting a battle. While in his coma, Zero enacts a secret plan to take Big Boss's DNA and create clones of him (because at this point in time, Big Boss is considered to be the greatest soldier of the 20th Century). EVA serves as the surrogate mother to the clones.
When Big Boss awakens and learns that he has been cloned, he is pushed passed his breaking point and decides to leave The Patriots.
He eventually creates Outer Heaven, bringing to realization his interpretation of The Boss's will. Outer Heaven gradually grows in size, recruiting more soldiers and even becoming a nuclear super power.
In 1995, the U.S. receives intelligence that Outer Heaven harbors a Weapon of Mass Destruction. Solid Snake, a member of FOXHOUND and one of Big Boss's clones who was created in the secret plan known as Les Enfants Terribles, is then sent to infiltrate Outer Heaven, which is located in South Africa.
During the course of his mission, Solid Snake learns that the Weapon of Mass Destruction is Metal Gear, a bipedal nuclear tank. He also learns that his own commander, Big Boss, is the leader of Outer Heaven (Big Boss's involvement with Outer Heaven was unknown up until that point).
He destroys Metal Gear and defeats Big Boss.
He learns that the leader of Zanzibar Land is none other than Big Boss, who had survived their last battle.
Once again, Solid Snake destroys Metal Gear and defeats Big Boss, but this time by horribly burning him with a makeshift flamethrower made of a cigarette lighter and an aerosol can. However, shortly before Solid Snake defeats him, Big Boss reveals to Solid Snake that he is his father.
In 2005, years after Solid Snake has left FOXHOUND, it is being led by Liquid Snake, another clone of Big Boss.
Under Liquid's command, FOXHOUND raids and takes control of a nuclear weapons facility on Shadow Moses Island.
FOXHOUND demands that the U.S. Government hand over Big Boss's remains so that they can use it to derive a cure from his DNA for their mysterious genetic illness. They had been subjected to some sort of gene therapy using Big Boss's DNA so that their combat skills and senses could be improved, but then began suffering from side effects. They threaten a nuclear attack against the U.S. if their demands are not met.
Roy Campell, who served as FOXHOUD's commander after Big Boss's presumed death, is called in to respond to the situation. Campbell requests Solid Snake's assistance, asking him to infiltrate the nuclear facility and stop FOXHOUND.
Snake eventually defeats FOXHOUND, destroying Metal Gear REX and defeating his brother, Liquid Snake, in the process.
Ocelot survives the Shadow Moses incident and sells the design data of Metal Gear REX on the worldwide black market.
Dozens of organizations, including the U.S. Navy, use the data to develop their own Metal Gears. The Navy develops Metal Gear RAY.
Philanthropy receives classified intelligence of a new type of Metal Gear scheduled for transport on an oil tanker via a route through the Hudson River.
They devise a scheme to infiltrate the oil tanker and destroy the Metal Gear.
In the process, the oil tanker is raided by a mercenary group of Russian Soldiers, among whom is Revolver Ocelot. Ocelot hijacks the Metal Gear RAY and escapes with it, destroying the oil tanker in the process.
During his hijacking of Metal Gear RAY, he seems to be overcome by Liquid Snake's personality, possibly as a result of Liquid's arm which he has had transplanted onto his body.
He attacks Snake with Metal Gear RAY, seemingly killing him.
Two years later, an off shore cleanup facility has been constructed in the Hudson River where the oil tanker was destroyed. It is taken over by a terrorist group known as The Sons of Liberty). The group is led by someone calling themselves Solid Snake.
New FOXHOUND recruit, Raiden, is sent in to thwart the terrorist's plans.
In the midst of his infiltration, Raiden learns that he is a puppet and that the entire Big Shell incident is nothing more than a simulation of the Shadow Moses incident, crafted by the Patriots. Its purpose is to determine whether the Patriots can successfully orchestrate an event from the shadows and manipulate people into fulfilling their will, even if those people aren't aware of it.
Raiden also learns that the Big Shell is really just a cover up for Arsenal Gear, upon which it rests. In other words, Arsenal Gear rests on the floor of the Hudson River, beneath the Big Shell.
He discovers that the leader of The Sons of Liberty calling himself Solid Snake is really Solidus Snake, another clone of Big Boss.
Raiden, with the help of Otacon and the real Solid Snake, takes down Arsenal Gear and defeats all of the members of The Sons of Liberty, including Solidus Snake.
Five years later, in 2014, Snake has aged significantly as a result of an intentional side effect of the cloning process through which he was created.
Ocelot, who is now completely overtaken by Liquid's persona is known as Liquid Ocelot and is the head of the five largest Private Military Companies, which rival the entire United States' army in terms of size and capability.
For the last time, Roy Campbell requests Solid Snake's help. This time, he asks Snake to assassinate Liquid Ocelot, whose death would trigger the collapse of the War Economy since he is the head of the largest PMCs.
Enacting his scheme to rule the world, Liquid tracks down and takes possession of Big Boss's burned body, using his DNA to access the Patriot Computer System through which the entire world is manipulated.
Afterward, Liquid burns Big Boss's body and throws it overboard his ship and onto the nearby ship on which Solid Snake and EVA are located. EVA makes a futile attempt to put out the flames on Big Boss's body and Solid Snake tries to stop her, badly burning the side of his face in the process.
Eventually, Solid Snake defeats Liquid Ocelot and shuts down the Patriot Computer System, bringing an end to the War Economy and the Patriot's control over the world.
Days later, at the site of Big Boss's grave, Solid Snake lives out what he plans to be his final moments and then attempts to kill himself.
He is carrying a mutated strain of FOXDIE, a lethal virus that will mutate and kill everyone around him. It was secretly injected into him by Naomi Hunter shortly before he embarked on his mission to Shadow Moses, back in 2005. Its original purpose was to kill off the members of The Patriots, which it did each time Snake came into contact with any of them, such as Sigint during the Shadow Moses Incident.
After Snake fails to go through with his planned suicide, Big Boss shows up.
He reveals that it was actually Solidus's body that was burned and destroyed on the ship. While he was in a vegetable state after his last battle with Snake, his body was reassembled using parts from Solidus and Liquid. It was then switched with Solidus's. Since Solidus was a perfect clone of Big Boss, his DNA could access the Patriot Computer System, thus fooling everyone.
Big Boss also reveals that Ocelot transformed his mind into Liquid's through self-hypnosis. Ocelot's plan all along was to create the right circumstances which could lead to the end of the Patriots.
Shortly after informing Snake of everything, Big Boss reveals Zero, who he has brought along with him. Zero is in a wheelchair, in a vegetable likes sate, and being kept alive by machinery.
Big Boss terminates Zero by cutting off his oxygen supply, explaining that Zero had to be put down in order to assure that the Patriots never re-emerge.
Afterward, Big Boss dies from exposure to the mutated FOXDIE in Solid Snake.