Question regarding Raiden's cyborg body
Of particular note during this part is Ocelot's actions. When Snake is nearby, Ocelot's new arm twitches and Ocelot is overtaken by the persona of Liquid Snake. Ocelot's new arm is actually that of Liquid's, surgically grafted on, but Liquid is apparently able to control his host's mind and body. But more to come on that later...
The Big Shell Incident
Bear with me... it gets convoluted and intense here...
Two years after the Tanker Incident, in 2009, "Snake" infiltrates an off-shore oil cleanup facility known as the Big Shell. When the Tanker was sunk, thousands of gallons of crude oil seeped into the New York Harbor, but luckily crews set up a cleanup facility in no time at the site of the wreckage.
On this day, many public officials, including the President of the United States, were due to inspect and tour the facility. The Big Shell was attacked by a rogue Navy unit called Dead Cell. The unit consists of Vamp, a creepy, vampiritic man who is seemingly immortal, Fatman, an eccentric bomb expert, and Fortune, daughter of Scott Dolph, the Marine commander who was killed in the Tanker incident. Fortune is immune to all weaponry. Bullets curve to miss her, grenades fizzle out, and even close quarters encounters are useless.
Commanding this unit is someone claiming to be Solid Snake, despite reports that he died on the Tanker. Following that incident, the photos taken from the cypher were distributed, implying the Snake was the one that sunk the tanker. For this reason, the "Snake" infiltrating the Big Shell has his codename changed to Raiden.
Raiden finds that a hole in the fence has already been cut, and all of the soldiers (Gurlukovich's army now under the command of Olga) are unconscious in the area. Someone had beaten Raiden into the facility, but he doesn't know who.
Raiden progresses through, eventually confronting Vamp, who is driven off by a SEAL Team member named Iroquois Plisken. Plisken recognizes Raiden's FOXHOUND outfit, but is confused because FOXHOUND was supposedly disbanded following the Shadow Moses incident. Likewise, Raiden doesn't fully trust the Plisken is telling him the truth about why he and his team are there. Plisken was hurt in the confrontation with Vamp and stays behind while Raiden continues on.
Raiden eventually meets up with a bomb disposal expert called Peter Stillman, a man who trained Fatman years ago and was injured in one of Fatman's bomb plots. Together with Plisken, they sweep the entire facility diffusing bombs planted by Fatman. Fatman's goals apparently differ from the rest of Dead Cell; he just wants to blow things up. After Raiden diffuses the final bomb, it triggers a secondary explosive, catching Stillman in the blast and cause structural damage to the facility.
On his way to face off against Fatman, Raiden is confronted by Fortune. She seems disappointed that you are not the man she expected to encounter, but she tries to kill you anyway. After evading her attacks for a while, Vamp intervenes. Raiden shoots for Fortune, but the bullet curves around her and strikes Vamp in the skull, putting him down. Raiden escapes while Fortune grieves, but we learn that Vamp "cannot die" (his own words).
Raiden heads to face off against Fatman, and he meets Olga. She escapes, and Raiden confronts Fatman and defeats him. Fatman mocks Raiden and sets one more bomb, but Raiden locates it and diffuses it. On his was back, Raiden is confronted by a new cyborg ninja, who gives Raiden some items to help him succeed in his mission. When Raiden isn't looking, the ninja vanishes.
Having learned of a new type of Metal Gear being developed at the facility (from the ninja, IIRC), Raiden continues on. Raiden's next objective is to make it to the core of the facility where the hostages, including the President, are being held. On his way across an outdoor walkway, he meets the man calling himself Solid Snake. Plisken shows up in a helicopter, yelling at Raiden that that man isn't Snake. The man recognizes Plisken and outs him as Snake himself, revealing himself to be Solidus Snake, a third Big Boss clone.
In a short battle, Solidus is knocked from the platform but lands on a Harrier jet being piloted by Vamp. A battle ensues, with Raiden eventually shooting the jet out of the sky. Before it crashes into the ocean, Metal Gear Ray leaps from the water and catches the jet, saving the lives of Vamp and Solidus.
Snake reveals to Raiden that he and Otacon were both at the facility for their own reasons, not under orders from another. Raiden is awe-struck by the famous Solid Snake, and each go their separate ways for the time being.
Raiden meets up with the President, and he informs him that the terrorist have a nuclear weapon that they plan to launch. Rather than launch codes, the weapon needs biometric data from the President at multiple times of the day (heartbeat, breathing rates, etc.). If they do not consistently fall within certain parameters, the launch is deactivated. Because of this, the President asks Raiden to kill him, also killing any chance of a nuclear strike. Raiden doesn't want to, but Ocelot (also at the facility with Dead Cell) intervenes and shoots the President himself. Raiden is confused by this, since Ocelot basically destroyed his own chances of launching a nuke.
Eventually Raiden makes his way to the other hostages. Among them is Ames, a secret service agent. They are able to listen in on Ocelot and Solidus in a nearby room. Ocelot is Ocelot, but Liquid's persona continues to try and come out. Because of this, Ocelot knows Snake is nearby. Around this time, Raiden learns of a group called the Patriots, but no one seems to be able to talk about them.
Ocelot soon notices Raiden (who is in an enemy disguise) and moves to confront him. Ocelot realizes that Raiden is not one of their men. Before Raiden gets killed, Ames dies of an apparent heart attack.. very similar to FoxDie. As with Ocelot's battle with Solid Snake, the ninja intervenes. Ocelot nearly has his arm cut off again, and the ninja helps Raiden escape.
Raiden's next objective is to rescue Emma Emmerich, genius software designer who has created a virus that can shut the whole terrorist operation down. Emma is the step-sister of Otacon, though the two have not spoken in a number of years due to a falling out. On his way to her, Raiden faces Vamp again, apparently killing him (again.)
Emma is weak from paralytic drugs inject into her (so that she could not escape). Raiden must slowly escort her to safety. She regains a bit of strength and crosses a small bridge around the perimeter of the Big Shell while Raiden provides cover fire. Snake also shows up to give support. Before she makes it all the way, Vamp appears again and stabs Emma before Raiden and Snake can put him down.
They take Emma along with Otacon to the computer control room where they upload the virus. The virus installation appears to have failed, and Otacon is reunited with his sister only to say goodbye to her. By this point, we have slowly learned that the Big Shell was not designed to clean up oil, since none leaked out of the wrecked tanker. Instead, it is a cover for a larger operation. Arsenal Gear, and gigantic warship housing multiple Metal Gear Rays, is being developed by the Navy underneath the facility, and Raiden and Snake must find a way in.
(continued later.. I need a break and have some errands to run!)
Otacon goes off to take the hostages to shore via helicopter while Snake and Raiden try to find a way in. Arsenal Gear is about to launch, and when it does the entire Big Shell will come crumbling down. Snake says, "You can come out now," and the ninja appears, startling Raiden. The ninja is shown to be Olga Gurlukovich, and she knocks Raiden unconscious.
Raiden wakes back up in a torture room inside Aresenal. This part is very reminiscent of the Shadow Moses incident, because when Snake was captured, he was in an identical room in a very similar situation. Raiden wakes up to see Ocelot and Solidus, and this is where a lot of the important Raiden information comes in.
Solidus raised Raiden (real name: "Jack") as a child soldier during the Liberian civil war in the '80's and '90's. Solidus was a father figure to Raiden and taught him the art of war. Their relationship mirrors that of Big Boss and Solid Snake (an important point coming up). Solidus as a Big Boss figure is strengthened by his new eyepatch, covering an injury he sustained during the Harrier fight. Solidus is a "perfect" clone of Big Boss. Solid Snake received the dominant genes, Liquid received the recessive genes, but Solidus was created after those two. He was a direct copy, without any manipulation.
(One small but possibly important point is that while Solid Snake got "dominant" genes, they are actually worse than the ones that Liquid received. So while Snake's were dominant, such as his dark hair vs. Liquid's blonde hair, Liquid was still his genetic superior. The theme of the Shadow Moses Incident was that genes don't write your fate.)
Raiden gained notoriety for his combat efficiency at a young age, earning the names "Jack the Ripper" and "White Devil". He has tried hard to repress the memories, but they still bubble to the surface. He has severe PTSD, but he hides it, even from his girlfriend, Rose(mary), which is on his support unit along with Roy Campbell.
Raiden also learns more about the Patriots. The Patriots rule the country. Politics are simply a show they put on to keep the masses unaware. Their control goes so far that they can even circumvent communication about them via nanotechnology. Anyone who knows anything worthwhile about them can only respond with "La-Li-Lu-Le-Lo" when referring to the Patriots.
Their latest plan is one of global censorship. They want complete control of information, and they plan to do so with an artificial intelligence unit called GW that is housed somewhere in Arsenal Gear. The real objective of the Dead Cell team was to hijack Arsenal Gear and use it to wipe out the Patriots, giving people true free will without censorship and false information.
Solidus saw himself as some sort of patriot himself, bringing America back to its roots of freedom and self-governance, rather than constantly being controlled by forces behind the scenes.
Ocelot and Solidus leave to attend to matters, and Olga comes in. She agrees to free Raiden, because she needs Raiden to succeed in his mission. Olga was pregnant during the Tanker Incident, and her child was taken from her at birth. The Patriots had set up the Big Shell Incident as a test for their new program of information control. It is called the S3 Plan. Raiden was the subject, and Olga was forced by the Patriots to ensure that he survived. If she failed and he didn't live, the Patriots would kill her child.
She frees Raiden and he makes his way through Arsenal Gear. During this time, Campbell keeps calling Raiden, but the voice is distorted and full of static, and the things he says don't make any sense. This occurs for several minutes, until Rose finally calls. She is weeping, because she never knew of Raiden's horrible past. She regrets trying to force him to open up and forcing herself into his barren apartment. Soon, her voice becomes distorted, saying that she is pregnant.
After the call ends, Raiden runs into Snake. Snake gives him his equipment as well as Olga's sword. Raiden is shaken by the whole experience. The weird experience with Campbell has Otacon theorizing that the Campbell Raiden knows is an artificial intelligence working with Raiden's own nanomachines to create conversations and a persona. In other words, the Roy Campbell that Raiden has been speaking to is a technologically aided figment of imagination.
He doesn't know who to trust or what to believe in. The entire Big Shell has been a lie, an artificial recreation of Shadow Moses. He doesn't even trust that the Rose that he has been dating is a real person. Snake tries to shake him out of it as they fight through waves of soldiers. (The game really throws in mind games to the player here, popping up false "Mission Failed" (called "Fission Mailed") screens, and the in-game radar plays weird clips and videos.) As we are seeing the experience through Raiden, we are experiencing some of his angst and confusion.
Snake and Raiden finally come upon Fortune. Raiden leaves to confront Solidus while Snake stays back to fight Fortune. Raiden enters a room where Solidus reveals more about his plan, before Raiden is attacked by 25 massed produced Metal Gear Rays. Raiden destroys a number of them, but they are too overwhelming. Before the kill him, they start going haywire. The virus implanted by Snake and Otacon apparently started working. The artificial intelligence that controls them, and the one that controlled Campbell, was affected and started breaking down.
Solidus becomes frustrated and enters the battle, destroying the remaining Rays and attempting to kill Raiden. Ogla intervenes, sacrificing her life to save Raiden (and her child). Raiden is knocked unconscious once again.
Raiden wakes up on top of Arsenal Gear, which has surfaced in the middle of the ocean. Snake is in handcuffs, captured by Fortune. Solidus and Ocelot are present, along with the original, Marine model of Metal Gear Ray. (This Ray requires a pilot, so it is unaffected by the virus.)
Solidus reveals that the nanomachines inside Raiden's body contain tracking information that he can use to located the Patriots. With the mass-produced Ray units and without a way to launch a nuke (due to the President's death), Arsenal Gear is useless. Before Solidus can kill Raiden to extract the nanomachines, Ocelot reveals that he is a Patriot agent. He says the S3 Plan stands for "Solid Snake Simulation". The Big Shell was set up as a mirror of Shadow Moses, and the Patriots wanted to see if they could form a new Solid Snake by controlling the flow of information and events. Raiden was that new Snake.
He reveals the truth about the Tanker Incident, and he revealed to Fortune that he killed her father, not Snake as she had believed. Ocelot shoots her in the chest, and she is shocked that the bullet didn't curve out of her path. An electro-magnetic device had been planted on her that gave her her "powers". Without them, she is vulnerable and she dies. Soon, though, Liquid's persona rises in Ocelot once again. He takes Ray and leaps off of Arsenal into the ocean. Snake manages to break free from his handcuffs and chases after, leaping into the ocean alongside the gigantic machine.
Arsenal Gear is still on the move and headed towards Manhattan. It levels much of the island, coming to a halt at Federal Hall, knocking both Raiden and Solidus onto the roof of the building. About this time, Raiden receives a call from "Campbell".
"Campbell", along with "Rose" tell Raiden that they are not human. He is now talking directly to the Patriots, who are now artificial intelligences. Raiden is confused, because GW was destroyed by the virus. He hints that there are multiple AI units, and only one was destroyed.
The Patriots reveal that S3 was not "Solid Snake Simulation", but rather "Selection for Societal Sanity". The recreated setting was Shadow Moses, because if they could direct a rookie, Raiden, from Point A to Point Z under the extreme conditions of Shadow Moses, then they could direct the masses of people in their bland, daily lives.
They reveal the reason for selecting Raiden, namely his past and his connection to Solidus that mirrors the Snake/Big Boss relationship discussed earlier. They also reveal the reason for his codename. "Raiden" was a Japanese fighter jet in WWII that the Americans nicknamed "Jack". His naming literally recalled those of weapons.
Raiden understands he was manipulated, and he refuses to them to fight Solidus. That is, after all, what they want. But they have cornered him to where he has no other option. After all, Solidus is going to kill him anyway to get the nanomachine information. And if Raiden dies, so does Olga's child. Raiden has no choice but to fight, even if he doesn't want to. Even when he knows he is being manipulated, he gets manipulated into doing the Patriot's bidding.
Solidus and Raiden have a sword fight, and Raiden ends up victorious. Solidus dies at the base of a George Washington statue, a man that Solidus idolized. Raiden later meets up with Snake. Snake informs Raiden that he placed a tracker on Ocelot's (for all intents and purposes is now completely Liquid in mentality) Ray, and he says that Otacon will analyze the data from the computer virus to find out more about the Patriots. The virus was designed to wipe out data, and some of that data would be the names and locations of the Patriots. However, this information would turn out to be false. He also says that he will find Olga's child.
Raiden also meets up with the real Rosemary. He decides to throw away his old identity and start a new life with Rose and their child.
Post Big Shell
While his intentions are good, his PTSD is too severe. Between his childhood tragedy and recent mind**** at the Big Shell, Raiden falls into alcoholism and depression, eventually leaving after Rose tells him that she miscarried. (This, too, was a lie, possibly for her own protection or to get away from his drunken rages.)
Raiden disappears, eventually hooking up with the Paradise Lost Army, a group of anti-Patriot rebels. He agrees to steal the body of Big Boss, which is still biologically alive but little more than that, in exchange for the location of Olga's child. He succeeds in obtaining both, and he leaves Sunny, the child, with Snake and Otacon. Sometime after, Raiden is captured by forces of the Patriots and experimented on, turning him into a more enhanced cyborg ninja.
(At this point, it is unclear if his head is natural or artificial, but by the time Metal Gear Rising rolls around, he is simply a brain and spinal cord inside of a metal machine.)
The Guns of the Patriots Incident
Snake, who is now extremely aged due to genetic manipulation while being created, continues searching for Ocelot (now simply Liquid). He tracks him across the globe, eventually coming to South America. While fighting alongside rebels against a PMC (Private Military Company.. basically, mercenaries) controlled by Liquid, he receives calls from Raiden. Raiden states that, "Jack is dead" and that he is only Raiden now.
Snake meets back up with Naomi, who was broken out of custody by Ocelot after Shadow Moses (we assume, but Snake was wrongly blamed for it.) She states that she was wrong about FoxDie affecting him, because she assumed that Liquid and Snake were genetically identical. Fact is that they are slightly different, and that is why FoxDie didn't affect him. However, due to his rapid aging, FoxDie is mutating and becoming less discriminatory of who it will kill. Snake will soon become a walking bioweapon, killing anyone he meets.
Snake also learns of Liquid's plan, to hijack the Patriot's entire computer system by piecing together the broken GW. Since it was originally a Patriot asset, Liquid can use it as a trojan horse to get inside of the entire SOP (Sons of the Patriots, the name of the Patriot's control network) System. (This is often called simply "the System".) Ever since Arsenal Gear crashed into New York, people have been clamoring for more safety, and this came in the form of the System. Every weapon, from handguns to tanks, needed ID verification. If a soldier's ID did not match, the weapons would not work.
Snake and Naomi try to escape, but they run into Vamp, who still manages to live on. Raiden intervenes, a new cyborg ninja, and defeats Vamp. He is badly injured in the fight, but manages to escape with Snake. Raiden informs Snake of the Paradise Lost Army and that Big Mama can help him. Raiden is sent to a doctor (engineer? whatever) to heal up while Snake continues his search.
Naomi disappears around the time that Snake meets up with Big Mama. He is shocked to learn that Big Boss is still alive. He is a biomort: alive only on a biological level. Liquid wants Big Boss' body, because he needs his genetic sequence to unlock access to the System. Neither Liquid's nor Solid's are a perfect match, so he wanted the real thing. Liquid's army attacks the Paradise Lost Army and they flee. Eventually Liquid succeeds in catching up to them and taking the body. Big Mama is dies of the injuries she sustained, and Snake is badly burned.
While Liquid is fleeing, which Naomi now at his side, he is stopped by U.S. forces, among whom are Meryl Silverburgh and her team. Before they open fire upon Liquid, he seizes the system, jamming their weapons and causing their vehicles to shut down. Liquid is now in control of virtually every weapon on the globe, save for a few guns that Snake is able to purchase through black market acquisitions. Liquid's troops open fire, nearly killing Meryl and her team.
Snake learns that the Patriot's AI is divided up into four units, with one unit controlling those other four. JD, the main controller, is a satellite in orbit. Liquid still can't get his hands on a nuclear weapon, I believe due to increased restriction on those, so he decides to take the one from the Metal Gear Rex unit that was left at Shadow Moses. Following the Shadow Moses Incident, the facility was shut down and left to rot, left to be completely forgotten. Snake once again heads to Shadow Moses to stop Liquid.
Snake makes his way through the now barren facility and gets to Rex's hangar. The nuke and its launcher have already been taken by Liquid, but Vamp and Naomi appear together. Vamp is defeated by Snake, who uses a nanomachine suppressant to shut down his nanomachines. His advanced nanomachines regenerated tissue at an amazing rate, giving him apparent immortality. Now, however, he is mortal.
Raiden also reappears, and he battles Vamp on top of Metal Gear Rex. Raiden is again victorious, finally killing Vamp. Naomi reveals that she is dying of cancer and that only nanomachines have kept her alive. She injects herself with the suppressant, and she succumbs and dies. (Yes, it is as random and stupid as it sounds.)
Bombs start to go off, and Snake and Raiden must escape the facility by reactivating Rex. Raiden falls behind to fight off Gekko while Snake continues on. The path starts to crumble, and Raiden is partially trapped under debris. Snake, meanwhile, faces off against Liquid, who is piloting a newly upgraded Metal Gear Ray. Snake succeeds, but is badly injured.
Liquid runs off to a huge battle ship called Outer Haven. It had been previously hinted at that there was more than one Arsenal Gear, and this appears to be one.. complete with a fleet of mass-produced Metal Gear Rays.
Snake collapses from injury and exhaustion, and Liquid turnes Haven around to crush the entire dock. Raiden, who has only one arm free, uses his sword to cut off his pinned hand. He frees himself and collides with Haven as it reach the dock, somehow managing to stop its progress. Raiden appears to have been crushed underneath the ship, but Snake survived.
Raiden survives and is taken with Snake and Otacon onboard the U.S.S. Missouri, a retired warship that is now being used, because it was retired before the SOP System went into place. Therefore, it was not under Liquid's control. They follow Outer Haven and manage to get Snake on board with Meryl and Johnny, a member of Meryl's team.
Before she died, Naomi gave Snake and his team a virus that should be uploaded to the rebuilt GW, which is now housed in Arsenal Gear. It will cut off Liquid's access to the System and destroy the Patriot network. Snake makes his way to the server room, but his aging has been catching up with him. He nearly collapses before he can make it, making him easy prey for the soldier guarding the entrance.
Before he is killed, Raiden reappears, once again with a purpose in life. His interactions with Snake have helped clear his mind, and he is willing to sacrifice himself for the greater good. But Snake insists that the fight is his, and he makes way through a torturous room filled with microwaves to get to the server room. He uploads the virus before Liquid can fulfill his plans of destroying the Patriot satellite with a nuclear missile, and Liquid's forces fall.
An exhausted Snake is dragged away by Liquid, who explains that Snake's success was all part of his plan. The virus shut down everything that Patriots controlled, created a new "wild west". A new world where individuals had to fend for themselves, a very similar idea to that of Outer Heaven.
Snake and Liquid have one final fist-fight, more symbolic than anything, and Liquid is beaten to death. However, during the time that Naomi spent with Snake and Otacon, she met Sunny, Olga's daughter. Sunny has been raised by Otacon in relative isolation in order to keep her out of the hands of the Patriots. As a result, she is a technological genius, and she re-developed Naomi's incomplete virus so that it wouldn't destroy EVERY system. Important ones such as electricity and resources and such were still active. Thanks to her, the world was saved.
Post Guns of the Patriots
With Snake becoming a walking biological weapon, he had a duty to end his life so that we would not be a threat to others. However, before he can accomplish that, Big Boss appears. He reveals that the body used by Liquid to gain access to the System was Solidus, the direct clone of Big Boss. Big Boss, on the other hand, had been kept comatose by the Patriots elsewhere. Big Mama and Ocelot were secretly working together to free Big Boss, and to do so they had to destroy the Patriots.
Ocelot used nanomachines and hypnotherapy to implant Liquid's persona into himself. He did this, because the Patriots were, at their core, a pragmatic computer system. The Patriots had used Snake once to defeat Liquid, and Liquid was predictable. Ocelot, on the other hand, was constantly manipulative and a wildcard.. even being a Patriot agent for most of his career. Where Liquid was predictable, Ocelot could better predict how the Patriots would deal with him.
They knew Snake would be urged towards a certain path unknowingly by the Patriots, a path Ocelot had already planned. Ocelot's plan was to use the Patriots' own weapon, Snake, against them by having him implant the virus and destroy the System.
Big Boss already revealed that Snake had been secretly injected with a new FoxDie virus, one that had different genetic sequences programmed into it. It was designed to kill Big Mama (who did not actually die from her injuries), Ocelot/Liquid (who did not actually die from his), and Big Boss himself.
Big Boss also says that the new FoxDie is uprooting the old, dangerous, mutated FoxDie. By now, Snake should no longer be a biological threat. He notes, though, that it is only a matter of time before the new one mutates and the cycle begins anew. However, by that point, Snake will long be dead. His rapidly aging body will only hold up for about 6 more month, and Big Boss gives up his dream of a world wide warzone, Outer Heaven, and peacefully succumbs to death, once again, from Solid Snake.
Metal Gear Rising: Revengeance
I hope that isn't too jumpy for you. I tried to compress 25 years of lore into a handful of posts. I cut out a LOT of information (3 games' worth, actually, but they don't affect Raiden's story arc), but that is the basic gist of the story.