PROLOGUE: Snake infiltrates Camp Omega, A U.S controlled black site prison facility in Cuba to rescue Chico and Cipher spy Paz. After rescuing them, Snake discovers a bomb in Paz which he and a surgeon takes out from her, saving a potential explosion. Meanwhile, A group of Cipher agents led by Skullface who have used the Alias XOF to trick U.S Forces into believing they are with the government. Skullface infiltrates Mother Base by pretending to be a U.N Inspection team. They have used one of their inside men, within Mother Base to launch a devastating attack on the base in an attempt of stealing Metal Gear Zeke. Snake returns to the base during the attack and saves his second in command, Kaz Miller and they depart as the base is destroyed. Paz, however wakes up and reveals she has another bomb and she exits the helicopter saving Snake in the process and after regaining control of the helicopter, they battle an XOF unit chasing them before going back to mother base to look for survivors, but find none. After making the landing, Chico is reunited with his sister, the leader of a resistance group, but they are attacked by a U.S mercenary unit, who mortally wounds Snake. Kaz and the other survivors are taken back to camp omega and tortured, but Kaz escapes and rescues Snake. Kaz uses his contacts to get them to a private hospital in Jamaica where Snake falls into a coma.
CHAPTER ONE: THE PHANTOM PAIN Snake has a flashback of Operation Snake Eater and re-lives fighting The Boss before waking in a hospital. His body is out of shape and he is weak. He is occasionally visited by a Nurse and his doctor who reveals that he has been in a coma for nine years. Snake has lost his left hand, wrist and has shrapnel lodged in his skull which will in the course of the next few months work its way out. Snake goes into a shock and reveals he has slight memory loss. Going back to sleep, he has flashbacks of how he learned of the innocence of The Boss, his decision to leave The American Philosophers. This is an organization created by his former Commander Zero due to their differences in interpreting the will of The Boss and how he came to be a mercenary in Central America. He also dreams about his occasional violent run-ins with a rival mercenary leader Kaz Miller. Finally the two men come to peace and create MSF together. Snake wakes up in shock when an explosion rips through the hospital and machine gun fire followed by people screaming. Snake is introduced to a man who calls himself Ishmael whom reveals he has been watching over Snake for the past nine years. He helps the weak Snake move through the hospital to safety. They are then attacked by several strange figures who at first seem hostile, but then are revealed to be trying to help Snake after they rescue him from a death squad of XOF soldiers.
Snake and Ishmael make it out of the hospital and try fleeing by car, but are attacked by helicopter(s). Snake is saved after the helicopter is taken out by a strange psychic figure. Snake also finds that Ishmael was just an illusion created by this Psychic in order to help Snake. Snake is then snatched by Revolver Ocelot who is shocked to learn that Snake does not remember him. Ocelot takes him away revealing that the people trying to kill him belong to Skullface, who has started a full-blown war against Cipher for unknown reasons. Skullface wants Snake dead because he wants Cipher’s icon and propaganda tool to be removed. Together, they fight off these strange figures who are working for Cipher before being rescued by Diamond Dog soldiers. Snake however, passes out after trying to fight them as he is still confused. In another flashback, Snake re-lives the moment he was introduced to Ocelot and remembers fighting him throughout operation Snake Eater. SNAKE is taken to an off shore plant similar to Mother Base. Ocelot reveals that when Snake was in a coma, Kaz went back to Camp Omega with the Sandinista and rescued the remaining MFS members. They began to rebuild their outfit, this time re-naming it Diamond Dogs. Ocelot lets Snake rest before his first mission. The next day, Snake is fitted with a robotic hand and wrist, which MSF took from a Russian KGB agent they killed a decade ago. Ocelot takes Snake to Afghanistan to rescue Kaz that has been captured, but kept alive over the week. Snake goes on his first ever mission since waking up and finds Kaz whom has both a leg and an arm missing. They fly back to their new home. Kaz explains what he went through in the last nine years. He reveals Ocelot came to him and helped financially as he owes Snake. Kaz also reveals that Skullface has a base in Afghanistan as he is trying to help the Soviets win the war and that is why he chose Afghanistan as a place of interest. Snake is also warmly greeted by the Diamond dog soldiers who see Snake as a living legend. Kaz gives Snake a series of mission objectives. The base at that moment is attacked by a rival mercenary outfit and later after the fight, Kaz reveals that the base needs improvements, better protection and more firepower and men. He encourages Snake to focus on both gaining them for their revenge and doing mercenary missions on the side to fund their quest.
CHAPTER TWO: DIAMOND DOGS Before going after Cipher and XOF for revenge, Snake goes back to Afghanistan to raise money for the new Mother Base by completing mercenary missions such as capturing Soviet and Mujaheddin bases, stealing Intel, equipment, personnel, doing assassination & sabotage missions, along with intelligence gathering missions for a corrupt CIA unit based there. They capture enemy armored vehicles and collect raw diamonds. Snake also does missions for both the Soviets and for the Mujaheddin in return for diamonds, money and resources. During one mission, Snake finds the person responsible for killing all of the men protecting Kaz and the same person who captured and delivered Kaz to the Russians. Her name is Quiet and she’s an expert sharpshooter. Snake rescues her from being raped and murdered after she kills a perverted Soviet commander. After Snake’s effort to help Mother Base expand into a now fully fledged mercenary outfit, Kaz and Ocelot approach him and reveal they have found the suspected Cipher spy, Huey Emmerich who resides under XOF’s close guard in a Bosnian mansion. Snake captures him and brings him back to Mother Base where he is then put through severe torture by Ocelot. Quiet was tortured also, escapes and Snake is given the mission of chasing after her since she has valuable information on Diamond Dogs. Snake tracks and locates Quiet, but she quickly turns the hunter into prey and has a sniper stand-off with Snake resulting in her being wounded. As Snake is about to mercy kill her, Kaz calls him with Intel on her background.
She’s from Ireland and her father, an IRA supporter was gunned down along with her brother in the Bloody Sunday incident by the British armed forces. She became a sniper for the IRA, but they betrayed her by attempting to hand her over to the UVF in return for some of their own men, but she killed them. She then moved to England, changed her name and joined the British Army. The trained sniper proceeds to work her way up so she could kill the men responsible for her father and brother’s death. She does so before being captured by the SAS and tortured to near death. They even go far enough to have her tongue cut off. She escaped and became a mercenary before finding herself working for the Soviets as an assassin. Snake feels sympathetic for her and offers her a place with Diamond dogs which she accepts. Back at Mother base, Diamond Dogs is given a new series of mercenary missions, similar to the ones before. During one mission in which Snake is to assassinate the leader of a rebel group known only as The Orphans, Snake discovers they are a small rag-tag group of kids who had lost family due to the ongoing war. Snake finds their leader Eli and instead of killing him, Snake recruits him and his companions. Mother Base has now expanded even further and has more men, equipment and contracts. After returning to Mother base, it is attacked by a Soviet assault team in revenge for Snake not completing his mission of killing Eli. He then learns from torturing the last remaining Soviet that they aren’t in fact soviet, but Americans working for Skullface. They kidnapped Eli from Cipher and were using him as a bargaining chip, but after the boy escaped for the tenth time in six days, Skullface ordered the boy to be executed. Eli however, kills the man before he can say why. Snake decides to let the boy stay on Mother Base in a hope to find out why Cipher value the boy so much.
CHAPTER THREE: A GHOST IN THE MACHINE Huey finally breaks and reveals he was helping cipher. He reveals that Cipher threatened to kill his fiance if he did not help. He also goes on to say that he was aware that Paz might not go through with her plans so he contacted Cipher. He then leaked information to Cipher. He created the entire fake inspection plot. He then explains that the team were to come in and simply take Metal Gear Zeke and then leave, but they instead planting explosives, killed half of MSF and kidnapped Huey before destroying MSF’s mother base altogether. Huey cries that his actions in betraying Snake has caused him PTSD and he is now a heavy drinker. The direct result of his actions has led his marriage to ruins. Snake himself then tortured Huey out of anger, but forgives him later on. Huey tells Snake that Skullface knows both Zero and Snake personally from the 1960′s and gives Snake the location of one of Skullface’s bases in Afghanistan. Snake finds the outpost and infiltrates it in an attempt to capture or kill Skullface, but is detected by the base. As Snake’s extraction fails, he is stranded and has to fight a group of other Cipher assassins, deformed Super Soldiers. Snake barely survives, he beats them, but is surrounded by XOF soldiers, he is rescued by The Mujaheddin who takes him to their camp. Snake, without communication helps the Mujaheddin fight off a large number of Soviet forces before Diamond Dog soldiers arrive. A battle occurs in which many Diamond dog soldiers are killed in the process. Quiet also dies during the battle after sacrificing herself to save Snake. After returning to the base, Snake and his men mourn their fallen comrades and this fuels his desire for revenge even deeper. The base is then visited by Skullface and his men unexpectedly and instead of fighting, Skullface comes to make peace. He reveals himself to be Aleksandar Antov who was once an agent with Fox alongside Snake back in the early 60s. In the mid 60s his wife and children were killed by Major Zero who was in charge of the American Philosophers in retaliation for refusing to kill Eva, a woman from Snake’s past. Skullface explains that he has been keeping his friends close, but his enemies even closer. He wishes to kill Zero who is now in charge of Cipher, but needs help doing so. Despite the protests from Kaz, Snake agrees. Skullface hands Snake a dossier before leaving. The dossier reveals that Cipher has a base in South Africa where they are developing weapons to surpass Metal Gear and that Zero will be there. Skullface continues to reveal that Eli was part of a secret project conducted by Cipher in which Zero used Snake’s genetics to create three cloned baby boys, one of them being Eli. A shocked Snake then later sends Eli off to London with fake papers and enough money to survive to lead a normal life away from both he and Zero, but Eli sees this as abandonment. Snake then tells his men that their time in Afghanistan is over.
CHAPTER FOUR: A COUNTRY WITHOUT BORDERS The war tore the South African country of Zawbowii apart. They have no government and aren’t even recognized within the UN. It is made up of desert, a mountainous region, dense jungle and swampland with hundreds of small villages scattered all over it. Snake is told by Kaz that the country is gripped in a civil war between the Christian south and the Muslim north. Snake arrives and is given the mission of infiltrating a rebel there. After doing so, he finds that the rebels are being equipped and paid by Cipher. Snake finds civilian prisoners whom he releases, one of them begging Snake to save their children who are kept prisoners and forced to become boy soldiers. Snake agrees and goes there to find small boys being trained how to fight. Snake rescues them and takes them back to mother base. Kaz disagrees with using boy soldiers, but Snake persuades him. Snake also becomes a friend for one of the small boys named Vosoloo. Snake is given a series of mercenary missions to complete. After completing a mission, snake is suddenly attacked by a demon like fiery figure that was seen at the hospital. Snake kills the figure before heading back to mother base, which he expands even further.
CHAPTER FIVE: BLOOD DIAMOND Snake gets Intel that Cipher has a large facility with compounds and decides to head toward it, in order to kill Zero once and for all. Snake comes across a village on his way to the facility and finds all the rebels dead. He finds two lone survivors, a teenage boy named Frank Jaeger and his sister Naomi. Snake saves their lives. Frank puts up a fight, but Snake wins and subdues him. He tells Frank that he can give him a real cause to fight for and sends them both back to mother base. Snake reaches and infiltrates the cipher facility where he fights the strange psychic and beats him. The Psychic reads Snake’s future before departing from the facility, but tells Snake they will meet again in another life. Snake finds Zero and is about to kill him however, he gets captured resulting in torture. Zero reveals to Snake that they have developed Nano technology and what he has in store for the world, is a future the boss would be proud of. Snake frees himself and causes a self-destruct on the facility. Snakes escapes before it explodes. It is unknown if Zero survives or not.
Snake makes it to a village and discovers that Cipher is sending the entire force to get him. Snake calls in for all of his men to arrive, which they do and they all prepare for battle. This includes the child soldiers. The battle rages after Cipher and the Rebels attack. Snake and his men are heavily outnumbered and surrounded. Snake calls for air support. Napalm and cluster bombs are dropped on their location killing almost everyone. Snake then begins to execute the wounded cipher and rebel soldiers one by one before mercy killing a wounded vosoloo. Kaz and the others arrive to witness the aftermath and the bodies that Snake mutilated. Back at mother base, Snake and his men cremate and hold a ceremony for the dead. Snake then goes to extreme measures and orders his men to take the whole country by force, keeping its people on a tight leash. Snake even has some of his own men punished by death for refusing to kill civilians. Many abandon Diamond Dogs and even Kaz starts to question the cause and even the war that they are fighting. Snake goes on a series of missions in, which he and his forces go from village to jungles to even bases, wiping out everyone on sight, including civilians.
Ocelot leaves Diamond Dogs, stating that his mother would hate what Snake has become. The next morning, Snake wakes up to discover that half of the men at Diamond Dogs have gone up and left without warning. Snake orders Kaz to gather up as many men as possible for an assault on the country’s capital city where the ruling royal family live. Snake and his men, including Kaz, attack the city. Snake orders the deaths of the royal family and the civilian population who are rioting at them. Snake kills several of his own men who refuse to fire at the civilians, much to the shock and horror of Kaz. Back at mother base, Kaz questions Snake and Snake reveals that Cipher is planning on taking over the world, not by force, but within, via the brain through technology and he wishes to put an end to it. When asked how Snake will accomplish this, Snake suggests that they acquire nuclear weapons and simply reduce the Earth’s population.This will result in the destruction of every capital city in the most powerful countries. Kaz, now sickened by what Snake has become secretly plans a takeover with the diamond dog soldiers who all agree. Snake is attacked by his own men who try to subdue him, but Snake kills them and launches a one man assault on his own base, killing his own men. Kaz and the others try to fight back, but Skullface and his unit arrive. Skullface launches the same type of devastation on Mother Base as they did a decade earlier, but only this time is helped by Snake himself. Kaz escapes along with a traumatized Huey. Skullface accept Snake for who he is and even agrees with Snake’s plan on saving the world from Cipher.