The Beginning – The Philosophers
The Philosophers were a secret group of the wealthiest, most powerful minds from the United States, the Soviet Union, and the Republic of China, formed after World War I. They gathered about one hundred billion dollars. This money, known as the Philosophers' Legacy, was used to develop entirely new forms of warfare that would dominate global affairs for decades to come.
After World War II, with many tensions in the air, the Philosophers' Legacy was stolen by Boris Volgin, which divided the money and hide it in secret bank accounts. The records of the transactions were stored on a single microfilm; the only mean to access the vast fortune.
Volgin, a GRU colonel son of Boris, wanted to seize control of the Soviet Union and illegally acquired the Legacy and constructed Groznvj fortress in order to carry on new projects (such as the Shagohod).
He contacted The Boss, a CIA special agent, on July 24, 1964 using a Philosophers' spy network suggesting that she defect to the Soviet Union in order to overthrow Khrushchev, Soviet Union leader. The Boss accepted the offer, although he did not realize that this was actually intended by the U.S. Government in a plot to gain the Legacy, as well as inadvertently exposing the Shagohod's development to the government.
Note: The Boss did not defect, her mission was to recover the Legacy but the US government “betrayed” her.
MGS3 - Virtuous Mission
On August 1964, a spy within the Soviet Union reported that a new weapon built by scientist Sokolov was almost finished. The CIA then, convinced that this weapon would dramatically shift the balance of power, ordered Naked Snake (Big Boss), an operative of the newly formed FOX Unit, to recover Sokolov within three to four hours with support from Major Zero (FOX leader).
Snake met Sokolov, and the later explained him that the new weapon, called Shagohod, was a huge tank capable of firing a nuclear missile across large distances and that should it be completed, it would mean the end of the Cold War.
When trying to escape they were greeted by The Boss, only to find out that she had defected to the Soviet Union. Sokolov was captured by the Cobra Unit (The Boss’ unit), and The Boss explained that Sokolov, along with a couple of Davy Crocketts (miniature nuclear shells) were her gift to her new hosts. Colonel Volgin then joined and told The Boss to kill Snake. The Boss threw Snake off the bridge secretly knowing he would survive the fall.
Volgin then fired one of the Davy Crockett launchers to the URRS research facility assuming the intelligence would think that it was The Boss who pulled the trigger instead, creating an international incident.
MGS3 - Snake Eater Mission
Soviet Union blamed America for the attack as Volgin expected, and the U.S. President explained it was The Boss, who defected, alongside Volgin. The Soviet Union demanded America to prove its innocent by killing both The Boss and Volgin.
With the United States' reputation on the line and the two nations on the verge of World War III, Snake was sent back to the Soviet Union in order to eliminate The Boss and her Cobra Unit, and to rescue Sokolov once more. Additionally, he was tasked with eliminating Volgin and the threat posed by the nuclear-armed Shagohod.
Snake headed to find Sokolov. On his way, he encountered Dr. Granin, who told Snake of the Legacy. He found Sokolov. And when he was about to escort Sokolov out, they were confronted by Volgin, who took Snake to fortress’ prison to torture him. There Volgin killed Sokolov and tortured Snake asking him what the CIA knew and whether or not they were after the Legacy. He also revealed the location of the Legacy. During the torture, many things happened which provoked Snake getting injured in one of his eyes (hence his eyepatch). In the end, as Volgin left, a double agent called EVA/Tatyana helped Snake escape.
Snake managed to get to Shagohod hangar to destroy it but he was spotted by Volgin. Snake asked Volgin what exactly the Legacy was. Volgin explained that the Legacy was. Also, that he had a microfilm listing specifically where all the money was being kept. Volgin then challenged Snake, and Snake won. When Snake prepared to leave, the Shagohod being piloted by Volgin emerged and Snake destroyed it.
Snake reached the extraction point but stopped beside a field of white flowers nearby, where he knew The Boss would be waiting for him. The Boss told Snake that all she wanted was to make the world whole again and reunite the Philosophers using the Legacy. She also explained many things about her tough life and that wanted Snake to kill her. The two then had an immense and epic battle, with Snake eventually managing to defeat his old mentor. Just before dying, The Boss gave Snake a microfilm that contained the locations of the Philosophers' Legacy.
The Patriots (La-li-lu-le-lo)
Zero and Ocelot had the plan to make the world The Boss envisioned a reality. To make it happen, Zero decided to create a new organization called The Patriots as the reorganized version of the American Philosophers. Zero invited Ocelot to join and the later agreed under the condition that Big Boss joined as well. Zero then recruited: Ocelot, Big Boss, Sigint, Para-Medic and EVA. All six founding members where involved in Operation Snake Eater.
However, the views of Big Boss and Zero in regards to the interpretation of The Boss's world began to differ. Zero took the concept to mean control of the entire world by a group under a single will to ensure unification; Big Boss believed that The Boss wanted a world where soldiers would not be used as tools of the government.
Les Enfants Terribles Project
Tensions between Big Boss and Zero continued to grow. Afraid of losing the Patriots' idol, Zero carried out a secret project known as "Les Enfants Terribles", in which Para-Medic would use Big Boss's DNA to create a number of clones. With EVA serving as the surrogate mother, Solid Snake and Liquid Snake were born (a third son would be born at a later date). However, this proved to be the final straw between Big Boss and Zero, and the former left the organization with a determination to oppose them and later formed his own mercenary group (MSF) in an attempt to carry out his vision of The Boss's dying wish.
Big Boss’ MSF purpose was to be “just a gun” and offer military services to whoever needs it without control of any nation.
MGS Peace Walker
Two “Costa Ricans”, Ramon Galvez and Paz Ortega contact MSF asking for help in repelling the CIA force that invaded. In return, they offer a large base in the Atlantic where the MSF can call home (Mother Base). Kaz and Snake, after careful consideration, accepted.
Snake allies with a local rebel group, at which point he meets and aids Amanda and her brother, Chico. He invites them to take refuge at Mother Base.
While infiltrating Snake learns of the CIA intentions to launch a nuke and saves scientis Huey Emmerich. Huey then tells Snake about the development of Peace Walker, a walking nuclear deterrent device that is capable of retaliation without a second thought due to being an AI (eliminating emotion from the retaliation decision).
Huey joins MSF and begins development on MSF’s own mech while Snake sets out to locate another researcher, Dr. Strangelove. Snake meets Strangelove, who hated Snake for killing his mentor, The Boss. As it turns out, Strangelove had modeled Peace Walker’s AI after The Boss’s own intellect and emotional tendencies.
Snake makes his way to Peace Walker hangar where Paz has been taken hostage. Then Coldman (CIA leader there), with Paz in custody, escaped the facility with the active Peace Walker following him.
At the base, Coldman explained his plan but then Galvez interrupted them, revealing himself as Vladamir Zadornov, planning to steal Peace Walker for his own plans and shot Coldman. Before he could kill Snake however, MSF came to his rescue. MSF took all parties into their custody and Zadornov as a prisoner. Then Coldman, nearly dead, used his last strength to input the codes – finalizing his plan. With no other options, Snake rushed to find and destroy Peace Walker.
Snake was able to stop the launch, but not stop the data transmission sending false data. Suddenly, Peace Walker’s AI altered and the heart of The Boss seemed to surface from within. Peace Walker then walked into the lake, flooding its AI system and severing the transmission.
After the catastrophe was aborted. An even more motivated Big Boss continued to focus on the improvement of MSF by recruiting more soldiers and even overseeing the production of their own nuclear deterrent, a bipedal tank named Zeke.
With Zadornov as a prisoner, multiple escape attempts were made. In the final attempt, Snake was forced to kill him. Soon after, Zeke started moving and attacking the base, and once Snake arrived on the scene, Paz was revealed to be the pilot. She called herself Pacifica Ocean and claimed that her and Zadornov’s purpose in giving them the base and aiding in the build-up of MSF was really to initiate their building of Zeke so they could steal it and bring it back to the Patriots, to Zero (which she called “Cipher”). In light of the new information, Snake was forced to bring down the Paz-controlled Zeke. In the resulting explosion, Paz was thrown into the ocean.
Afterward, Kaz revealed he knew about the whole thing, but went along with it strictly to improve MSF’s status as a capable military body. Snake, disgusted at having to have “killed” Paz, announced to his soldiers that he and they are guns to be used by whoever needs them, and by selling ourselves, we will soon have a nation of our own, called, Outer Heaven.
MGS5 Ground Zeroes
Paz survived and was captured and held for interrogation at Camp Omega in Cuba by Zero after becoming suspicious of her loyalty. In actuality, however, XOF leader, Skull Face, planned to interrogate Paz to find the location of Zero and kill him. After several days, Paz gave up Zero's location.
Kaz informed Big Boss that Paz was alive. Big Boss wanted to kill her as she had important information regarding Mother Base. However, Kaz stated that MSF's "friends" at The Patriots, suspect Paz could be a double agent. At last, Big Boss and Miller both agreed that the wisest action is to save Paz who was their only link to Zero, along with Chico.
Meanwhile, there was an upcoming UN nuclear inspection of Mother Base, the "perfect" timing of which made Miller doubt Paz leaked information about the nature of MSF.
At midnight on March 16, 1975, Big Boss began his mission to rescue Paz and Chico. Minutes before Skull Face, the commander of XOF (the military group controlling the camp), and a group of soldiers went to the heliport for taking on a mission. Just before commencing the mission, Skull Face referred to the operation with "Trojan Horse" and "pirate crackdown" phrases. Before taking off, Skull Face and his troops removed XOF logo from their choppers and clothes.
Snake rescues both Chico and Paz, but upon arriving at Mother Base, they see that it is under attack by XOF forces. Big Boss finds Miller and they leave on helicopter. Paz exclaims she has a second bomb inside of her. She then jumps from the helicopter, only to have it explode feet away. The explosion hits Big Boss, and another helicopter is shown about to crash into the helicopter that he is in, causing Big Boss's coma.
At some point during the 1980s, Ocelot discovered the survivors of MSF, who had renamed themselves as the Diamond Dogs, and allied with them due to Big Boss's ties to the group. He was also leading the group in Big Boss's absence (who was in coma). Seems that somehow, Kaz ends up captured in Afghanistan.
- Nine years later, Snake awakes from his coma. Hospital escape.