The Metal Gear Solid series is notorious for its dense storylines, filled with plot twists and schemes-within-schemes. Even if you've played all the games, it can be hard to keep the plot straight in your head.
Before you play Metal Gear Solid 5: The Phantom Pain, refresh your memory of the story to date with a brief run-down of the events from the games that lead up to it.
Big Boss
Big Boss (aka Naked Snake, Venom Snake, Punished Snake) was once a decorated covert operative for the United States during the Cold War. However, his commitment to his country is shaken by the events of Metal Gear Solid 3 in 1964. He was sent to stop a Soviet splinter group from attacking the United States with an experimental superweapon. To complete his mission he was forced to kill his mentor Boss, who had apparently joined the terrorists.
As it turns out, though, the mission had a secret objective: the United States wanted to secure the Philosopher's Legacy, a vast fortune acquired by the rogue Soviet group. Boss had willingly acted as a traitor to help the U.S. secure the fortune and then let her protege kill her to keep this secret.
Big Boss' disillusionment over being used as a pawn by his government eventually leads him to go rogue. In 1970, he's invited to join a new organization called The Patriots by his former CIA commander Zero and covert agent Ocelot. This group's goal was to fulfill Boss' goal of a unified world. However, Big Boss leaves after a dispute with Zero over the group's direction.
By the events of Metal Gear Solid: Peace Walker in 1974, Big Boss is now leading his own mercenary army called Militaires Sans Frontieres (MSF). He has a very idealistic objective for the group: providing aid to countries or individuals in need of help regardless of politics. He essentially wants soldiers to be able to make their own decisions instead of being driven by politicians. While MSF grows into a powerful force, its success doesn't last (more on that later).
Philosopher's Legacy
The secret wars and conspiracies of the Metal Gear Solid universe can be tied back to a cache of money called the Philosopher's Legacy. A hundred billion dollars was pooled together by the elite of China, the Soviet Union, and the United States during World War 2 to help them win the conflict. These elite called themselves the Philosophers. The Legacy was supposed to be divided up equally at the end of the war but was stolen and hidden in banks throughout the world.
In response, the three nations each tried to recover the fortune for themselves. This conflict between the three branches of the Philosophers led to the Cold War. During the events of Metal Gear Solid 3, the CIA recovers half of the fortune.
By the end of Metal Gear Solid: Portable Ops (1970), though, the CIA's half has been stolen by an unexpected fourth party: covert agent Ocelot. He also locates the other half and uses these funds to form the Patriots along with Zero and Big Boss.
The Patriots
Soon after the Patriots were formed, it was clear that Big Boss and Zero had very different opinions on how to unite the world. Zero felt that the only way to bring the world together was by controlling it. Big Boss, who had seen his mentor and other soldiers sent to their deaths to serve others' agendas, had no desire to become one of Zero's puppets.
Zero realized that a soldier with Big Boss' skills and fame had value, though. To guard against the possibility that Big Boss would leave, Zero secretly created two clones of him. The discover of these clones, who would grow to become Solid Snake and Liquid Snake, led Boss to quit the Patriots in disgust.
After Big Boss left, the Patriots began using the alias Cipher. Zero, meanwhile, went into hiding and began delivering his orders through third parties. In Peace Walker, Cipher tried to recruit Big Boss' Militaires Sans Frontieres to help them gain global power. When Big Boss refused, the organization unsuccessfully tried to frame them as terrorists.
Cipher still viewed MSF as a threat, though, and launched a more successful attack in Metal Gear Solid 5: Ground Zeroes.
Paz
One of the enemies Big Boss defeated in Peace Walker was the Cipher agent Paz. A year after their fight, he finds out that she's still alive and being held in a secret U.S. military prison. Ground Zeroes follows Boss as he infiltrates the base and tries to rescue her. His belief is that she'll be able to give him vital information on Cipher's operations.
Although Big Boss is able to successfully extract her by helicopter, he soon learns she's been rigged with an explosive. She leaps out of the chopper just before she explodes.
As it turns out, someone had reached Paz first: a badly burned commander known as Skull Face. Skull Face, the commander of a commando group known as XOF, brutally tortured Paz to find out the location of Zero (again, who had gone into hiding) as well as the location of MSF's base.
XOF
XOF and Skull Face are affiliated with Cipher in some way. It's interesting, though, that Skull Face was trying to track down Zero. Is he planning a coup? Or is he working on behalf of someone else trying to take over Cipher?
Regardless, XOF manages to accomplish a major goal of Cipher: the destruction of MSF. While Big Boss is trying to rescue Paz in Cuba, the commandos strike MSF's oil rig base and eradicate most of the soldiers there. Big Boss arrives at the base just in time to help some of his troops evacuate but is severely wounded. He falls into a coma shortly afterward.
Metal Gear Solid 5: The Phantom Pain begins as Big Boss wakes from his coma nine years later.
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