*BIG SPOILERS! READ AT YOUR OWN RISK!*
In this article, we will also talk about real events that happened in real life and real organisation of real countries and will be shown in blue.
Two years after the events of San Hieronymo (Metal Gear Solid: Portable Ops) and eight after the Virtuous Mission and Operation Snake Eater (Metal Gear Solid 3: Snake Eater), Big Boss, who now prefers to be called Snake, had formed Militaires Sans Frontières (Soldiers Without Borders) with Kazuhira “Kaz” Miller, a soldier he met and saved on the battlefield. Militaires Sans Frontières is a private military company, set in San Hieronymo 2 years ago, specialising in a type of war business which offers a full range of military services and is composed of mercenaries without nation since they left their country. It is still the Cold War and there is still a lot at stake between the CIA (US) and the KGB (USSR).
Snake, leader of Militaires Sans Frontières
4th November 1974:
Ramón Gálvez Mena, posing as a professor who teaches peace, and his student, Paz Ortega Andrade, arrive from Costa Rica at Militaires Sans Frontières' base. As a matter of fact, Gálvez is from the KGB. He is here to ask Snake to get rid of a military army which has been recently formed in Costa Rica. In exchange for this, he will give Snake an offshore plant to use as an operating base off the coast of the Caribbean. Snake is intrigued by the idea that the CIA might be behind the unknown military army, and even more so when Gálvez tells him that Paz, who was looking for her friend, had been captured, imprisoned and tortured in their facility. She escaped from there with a cassette tape containing a recording made by her friend who is an ornithologist who records bird song. On the tape, Snake recognises a female voice that has to be The Boss, his deceased mentor that he had killed ten years before. Snake is reeling from the shock of learning that the CIA may still be scheming and that The Boss could be alive.
10th November 1974:
Snake arrives on Costa Rica's coast helped by Kaz via radio from their new base in the Caribbean: Mother Base. He reaches the facility where Paz was imprisoned and discovers that nukes are about to be brought into Irazu, Costa Rica. On his way to intercept the missiles transport, Snake meets the Sandinistas, a group of revolutionaries. Since taking over from her father who has been recently killed, Amanda Valenciano Libre is the new leader of the Sandinistas. She also has a little brother, Ricardo Valenciano Libre, also known as Chico. She explains to Snake the situation: the CIA is actually involved in all the recent events and the Sandinistas have been pushed out of Nicaragua and forced to flee. A few explanations later, they are interrupted by a big flying machine. Chico is snatched by the machine and the Sandinistas go after it. Snake sends an injured Amanda to Mother Base by Fulton and then heads to the mountains to rescue the little boy.
Amanda & Snake
After rescuing Chico, Snake reaches the facility and overhears a conversation between two men. One of them is Dr. Huey Emmerich, a mechanical engineer, and the other is Hot Coldman, the CIA's station chief for Central America. It seems like one of Huey's creations is involved ; a creation which came from blueprints that his father received from the scientist Aleksandr Leonovitch Granin, who was responsible for the first concept of a bipedal tank: Metal Gear. Coldman wants the final tests of the “Peace Walker” to be finished in order for it to be operational and show its capability of launching a strike. Once Coldman is gone, Snake comes to the rescue of Huey who has been pushed down the stairs by Coldman but he is interrupted by the big flying machine, the same machine that snatched Chico, which takes a bipedal machine away.
After Snake powerlessly witnesses this scene, another big machine intervenes: Pupa. After a long battle, Snake defeats Pupa and pulls out its Artificial Intelligence (AI) memory boards. These will later be used by Militaires Sans Frontières to build their own weapon, later known as Metal Gear ZEKE. Huey then joins Snake and explains that Metal Gear Peace Walker, the bipedal machine carried away, is loaded with nukes and that he is the designer of this unmanned weapon. He is also the designer of other unmanned weapons such as Pupa, the big flying machine called Chrysalis, and a treaded type called the Cocoon. Huey explains that Coldman thinks that an AI machine is more reliable than a human and so will prevent other countries from launching a nuke, as they would be scared of the inevitable retaliation. This would create his own version of deterrence and the current illusion of peace would end.
Huey then tells Snake that Metal Gear Peace Walker will be equipped with an AI which will provide a high-level decision-making ability to it. Huey asks Snake to destroy this AI, developed by Dr. Strangelove. Snake then asks Huey to join his “Outer Heaven”, Militaires Sans Frontières, and heads to the ruins where the laboratory is.
Huey Emmerich & Snake
19th November 1974:
On his way to the laboratory, Snake meets Cécile Cosima Caminades, an ornithologist. Snake assumes she is the friend of Paz and the one who had recorded the tape with the voice of The Boss. She reveals that she saw a pod in the laboratory from where the voice kept saying “Jack”, one of Snake's code names. He then extracts her by Fulton. Later, during a call, Kaz reveals to Snake that Cécile doesn't know Paz...
Snake finally reaches the ruins. There, he sees The Boss' horse and meets Dr. Strangelove who was waiting for him. She tells him that she loved The Boss, that she is "giving back her life" and introduces Snake to “her baby”: the same pod that Cécile described earlier is actually an AI, a complete individual with the “mind” of The Boss inside, and the dedicated “brain” for Metal Gear Peace Walker. Snake becomes confused by The Boss' voice and enters the AI pod. After being overcome by memories, he passes out.
Snake wakes up in a field of white flowers and sees the AI being carried away just before Chrysalis intervenes. Snake takes the machine out after a long battle and pulls out its AI memory. On The Boss' horse, Snake then heads to the facility, where Metal Gear Peace Walker is being assembled, with the aim of destroying its AI.
21st November 1974:
Snake arrives on the mine base where he is instantly stopped by the Cocoon. After a fierce and long battle, he pulls out its AI memory boards like he did with Pupa and Chrysalis in order to gather more elements for Metal Gear ZEKE.
Snake enters the facility
Inside the base, Snake finds Strangelove and Coldman preparing the final checks on Metal Gear Peace Walker. Snake reaches the hangar where the AI is and, overcome by memories again, tries to obtain answers from it in the hope to understand what really happened ten years before. The AI has no records of Grozny Grad's mission since the CIA did not give Strangelove access to the files in order to create the AI from The Boss. This convinces Snake to destroy the AI. However, just before firing on it, Snake is busted by Strangelove and Coldman, and he is surrounded by his men.
Coldman reveals that he has been part of Operation Snake Eater. He also explains his plan of “deterrence” by making use of AI, like Metal Gear Peace Walker, rather than humans who, for him, can be weak and capable of remorse and so “incapable of destroying themselves”.
Later, Snake is then interrogated by Strangelove. In order to finalise the AI, she asks what happened to The Boss ten years ago and if she really defected and betrayed her country. Snake is electro shocked several times for refusing to talk and sent back into jail.
Strangelove “interrogates” Snake
Snake manages to get out of his jail, heads back to the hangar and finds Coldman, Strangelove and Paz, who has been captured. The Boss is now “restored to life” thanks to the AI. Coldman tells Snake that he has already chosen the strike's target which is an offshore area in the Caribbean: Mother Base! Coldman and Strangelove leave with Paz. Snake tries to follow them but comes face to face with Metal Gear Peace Walker. After the fight, Coldman guides Metal Gear Peace Walker by asking it to follow his helicopter. Snake goes after it on The Boss' horse but fails to catch up and Coldman reaches Nicaragua with Metal Gear Peace Walker. With the horse badly wounded, Snake is faced with the task of putting an end to its misery, like he had to do with The Boss ten years before...
23rd November 1974:
Snake reaches the US missile base and gets into the control tower where Coldman and his men are waiting for him. Coldman, with an activation suitcase handcuffed to his hand, is on the verge of creating a simulation that will prove to the CIA that his project is finished and operational. All that in order to get back into their good graces. Indeed, he is going to launch a retaliation in response to false data, entered in Metal Gear Peace Walker, of a Soviet nuclear attack launched from the Mother Base coordinates on US soil. After doing all this, Coldman believes he will bring "true peace". Before entering the code, "professor" Gálvez appears!
His real name is revealed to be Vladimir Zadornov and him and his men now have the base under their control. He reveals that, until now, he has collaborated with Coldman. But his true objective is to launch a nuke on Cuba, an ally of the USSR, in order to make everyone believe it is a US attack. This would give the USSR a legitimate reason to retaliate. His wish is to make the entire world to hate the US. Zadornov neutralises Coldman and injures him, and makes Strangelove change the coordinates of the false data to point to Cuba.
Before Zadornov kills Snake, soldiers from Militaires Sans Frontières break into the room, save Snake and capture Zadornov and Coldman. Still, Snake has to destroy the AI...
Snake still has a mission
Unfortunately, while being taken to Mother Base, Coldman manages to enter the code for the fake Soviet nuclear strike data on Cuba but the data has been sent to NORAD (North American Air Defence). Because of this, the strike will be seen as a real one and retaliation will not only come from Metal Gear Peace Walker but, potentially, also from the US. But Coldman thinks that the US government will never retaliate since they are “only” human. Coldman, who is the only one who knows the abort code, dies: Metal Gear Peace Walker's retaliation is inevitable...
After a long and fierce battle, Snake neutralises Metal Gear Peace Walker which aborts the launch. However, he still has to destroy the AI in order to completely stop the transmission of false data to the NORAD. Despite the Metal Gear Peace Walker and its AI being almost completely destroyed, against all odds, the AI pod turns from red to yellow and Metal Gear Peace Walker makes a final journey to a lake near the base. As though inhabited by the ghost of The Boss, Metal Gear Peace Walker uses the water's pressure to stop the transmission, drowning itself.
The Metal Gear walks away, bringing Peace
After all these events, Snake considers another interpretation of The Boss' final mission. He feels betrayed and doesn't want to make the same choice as her. His future will be different. He can now bear his name: Big Boss!
Back to Mother Base, Huey informs Big Boss that Metal Gear ZEKE is now complete. Kaz has the idea of picking up the nuclear missile attached to Metal Gear Peace Walker from the bottom of the lake and load it up on Metal Gear ZEKE to create their own deterrent.
After several attempted escapes from Mother Base by Zadornov, obviously assisted from someone inside, Big Boss, to protect himself, has no other choice but to kill him. Straight after killing him, the alert of Mother Base rings. It becomes apparent that the escapes were in fact diversions which have made it possible for Paz to infiltrate Mother Base to gather information and, in the end, take control of Metal Gear ZEKE.
Big Boss heads to the upper deck of the platform where he notices Paz in the Metal Gear ZEKE. She seems in a daze and very different from the innocent Paz that he knows. She tells him that she works for “Cipher” and that her mission is to fulfil the real Peace Walker Project.
Paz explains her motives for working with Cipher: Big Boss and his old friend, Zero, with whom he worked for several years (in particular during the Virtuous Mission and Operation Snake Eater), wanted to carry on the wish of The Boss but because of disagreements they chose different paths. Paz implies that Big Boss has taken the wrong one and that she has teamed up with Zero, who controls the Patriots, currently both going by the name "Cipher".
Cipher's goal is to make a world without borders, like The Boss, but with everything controlled by a single will. Paz, on behalf of Cipher, asks Big Boss to be the protector of it, using Militaires Sans Frontières as a deterrent, until a “new world order” is in place. He refuses and now has no other choice but to fight against Metal Gear ZEKE (controlled by Paz) to prevent it being carried away and prevent Militaires Sans Frontières from being seen as extremists who had launched a nuke.
Big Boss vs Metal Gear ZEKE
Big Boss defeats Paz who is ejected from Metal Gear ZEKE into the ocean. It is over.
Kaz tells Big Boss that he knew all along who Zadornov and Paz really were. He used them to develop Militaires Sans Frontières and make it into a bigger entity. Paz was actually working as a triple agent for the CIA, Cipher and the KGB. Kaz knew that Big Boss would fight until the end no matter what. Thanks to this, a revolution is about to begin and will be known in the future as “Outer Heaven”. However, after these events, the entire world, including Cipher, will have an eye on them and they will catch the attention of both East and West. They now know they are at risk of being hunted and possibly taken down.
In a final conversation, Kaz is talking with a man, who is supposedly Zero, about how Big Boss does not know “the truth”. He tells him that he is not an enemy nor an ally but just a business partner. He also talks about the “sons” of Big Boss, Solid Snake and Liquid Snake, born from the “Les Enfants Terribles” Project, who seem to be in good health...
Another end with a new beginning