Big Shell Incident

Two years after the sinking of the tanker U.S.S. Discovery, with Solid Snake blamed and confirmed dead as a result, new FOXHOUND recruit Snake, (changed to Raiden) was sent to infiltrate the off-shore decontamination facility known as the Big Shell, which was constructed shortly after the sinking of the tanker, which, according the government, spilt thousands of gallons of crude oil into the New York Harbor.

The reason for the mission was this: on April 29th, 2009, terrorists known as the Sons of Liberty seized the Big Shell during a routine inspection tour, the Sons of Liberty consisting of special forces unit Dead Cell and led by Solidus Snake. They also took many hostages, one of whom was the 44th President James Johnson, who was on the inspection tour at the time. Their demands were $30 billion in cash, and they claimed that if their demands weren't met, they would destroy the Big Shell. This would cause the worst environmental disaster in history.

As Raiden began his mission, aided via codec by Colonel Campbell and girlfriend Rosemary, he discovered the many slaughtered bodies of SEAL Team 10 filling the hauls of Strut B. The one responsible was Vamp, a mysterious vampire-like member of Dead Cell who would have killed Raiden, had it not been for the rescue efforts of the single SEAL Team 10 survivor, Iroquois Pliskin. Pliskin provided Raiden with his first weapon, a SOCOM pistol, and Raiden headed forward.

Countdown to Disaster

As Raiden made it to the BC connecting bridge, he encountered Dead Cell member Fortune who, as if supernaturally, was able to make every bullet miss her. Rather than making his presence known, however, he chose to watch Fortune kill all the members of Alpha Zero and destroy half of the bridge. Suddenly, Vamp appeared once again, and called Fortune away. Raiden then received a call from Campbell, who informed him that they had received intelligence that a number of C4 explosives were planted across the Big Shell. By new mission objective, Raiden rendezvoused with bomb disposal expert Peter Stillman and, once again, Lieutenant JG Pliskin. Agreeing that Stillman would be safer hiding in Strut C, Raiden and Pliskin headed out to disarm the C4 planted around Shells 1 and 2 respectively by Dead Cell member Fatman. However, when the all the bombs were disarmed, Raiden received some shocking and disappointing news from a now mobile Stillman. It seemed that all of the "baby" C4s (which had not seemed right) were simply diversions for the real bombs, which were hidden in the basements of Strut A and H, and were large enough to disturb the structure's integrity and destroy the entire of the Big Shell if they both went off. It also turned out that the real bombs were programmed to activate after all of the baby C4s were frozen. Although Raiden was able to disarm the Strut A bomb, the Strut H bomb detonated and killed Stillman. Pliskin was able to survive unscathed.

As Raiden left Strut A, he was confronted by Fortune, who was apparently expecting someone other than Raiden. Nevertheless, remarking that he may still be able to "bring her death", she proceeded to trash the basement of Strut A and Raiden, unable to hit her, could only stand there and take it. As Vamp appeared again to take her away, Raiden took another shot, but the bullet once again swerved from Fortune, hitting Vamp in the front of the head. Amazingly, Vamp stood up unscathed, leaving with Fortune moments later.

Campbell told Raiden that Fatman was waiting for him on the roof on Strut E. Raiden headed there and confronted Fatman, managing to defeat him and neutralize one last bomb, which Fatman called the "biggest bomb in the place", and was hidden on his person. Raiden was then confronted by a Cyborg Ninja, who informed him that a man named Richard Ames, who knew the location of the President, was being held as hostage, and gave Raiden a uniform he could use to infiltrate Shell 1.

Metal Gear's Already Active

Once Raiden located Ames, Ames told him the President's location, and explained that he must be helping the terrorists under his own free will, as his vital signs acted as a biometric password needed to activate the nuke. Before Ames could give any more information, he suddenly suffered a heart attack. Raiden then headed to President Johnson's location, but on his way was confronted by Solidus Snake, the leader of Dead Cell. Pliskin revealed himself as Solid Snake and challenged Solidus from a Kasatka. Solidus boarded a Harrier along with Vamp, and Snake told Raiden to shoot it down. Successfully doing so, the Harrier plummeted, only to be caught by Metal Gear RAY. RAY proceeded to launch missiles into the air destroying sections of the Big Shell.

Snake and Otacon, who contacted Raiden by codec, explained that Otacon had recued Snake from the tanker two years earlier, and Snake faked his own death using the body of Liquid Snake in place of his own.

Shaken from RAY's sudden appearance, Raiden then headed to the Shell 2 core to rescue the President and found Olga Gurlukovich upon entering, who was talking to Solidus over a radio. He hid and listened in on their conversation, with Olga stating she had unfinished business with Snake, and that after this whole mess, she and her men were to leave for Russia and live for themselves. Raiden, not being able to get close to the President thanks to an electric walkway, went into the flooded lower floors of the Shell to locate a Nikita remote controlled missile launcher and successfully managed to destroy the control panel for the electricity.

The Revealed Truth

Raiden proceeded into the President's room, where, after Johnson mistook him for the female guard, he was told about The Patriots, a secret organization who secretly rule over America, even deciding who the next President will be, and that no one knew who The Patriots really were. He also explained how Solidus wanted to challenge them, unlike he himself who wanted to simply become one of them. He also uncovered that the Big Shell was merely a cover up for Arsenal Gear; a gigantic mobile fortress that used mass-produced pilot-less Metal Gear RAYs to defend itself. Arsenal Gear had the ability to fire nukes from anywhere on the planet, and was also being used to filter out information regarding the Patriots from the internet, and other such media, using an AI called GW.

Johnson’s last request was that he find Emma Emmerich, Otacon's stepsister, and get her to eradicate GW. Revolver Ocelot suddenly intervened, shooting Johnson before Raiden could act.

Raiden then headed to find Emma. On the way he fought and defeated Vamp, confused as to how he could still possibly be alive. Before his defeat Vamp revealed that even without the possibility of a Nuclear strike, they could still use Arsenal's purified hydrogen bomb to emit an EMP over Manhattan knocking it offline.

Raiden then rescued Emma. While taking a short break, Emma told Raiden what she knew about The Patriots. She explained that she had created GW, distributing a program to assist it in a program supposedly used to counter the Y2K virus. Luckily however, GW was not yet ready for activation and still lacked necessary factors for judging situations, Emma then mentioned that there was supposed to be a major test within the next few days which was to provide GW with complex data to study.

Twilight Sniping

The pair then proceeded to head to the Shell 1 Core. However, thanks to RAY's earlier missile attack, the bridge connecting the two Shells had been destroyed and they needed to take an Oil Fence from Shell 2 Strut L to Shell 1 Strut E. Emma slowly made her way across, with Raiden and Snake providing cover with sniper fire. Emma was almost all the way across, when Vamp appeared once again, holding Emma at knife point. Raiden quickly fired at Vamp, "killing" him once again, but before he fell into the ocean, he stabbed Emma. Snake then ran to Emma, picking her up and taking her to the Shell 1 Core. When Raiden got there they were inputting the virus that Emma created to destroy GW.

Emma and Otacon shared one final moment together, before she died as a result of her wound. At that moment, Snake discovered that the virus had not installed properly, and the trio came up with a plan to get inside Arsenal Gear, their only choice now being to take out Solidus and his men. Otacon, heartbroken, decided it would be best if he attempted to help out the hostages as he would only get in their way. Snake reassured him that he was the only one who could save those hostages, and Otacon set off.

Arsenal's Guts

After Otacon had left to rescue the hostages, Snake mentioned to Raiden that they may need a hand getting inside, as the Cyborg Ninja appeared once again and revealed himself to actually have been Olga in disguise. Raiden was then knocked unconscious by Olga, with Snake saying that he didn’t ever recall saying he was on Raiden’s side.

When Raiden came to, he was tied to a torture bed completely naked. Solidus and Ocelot talked to him, with Solidus remembering that he taught Raiden everything he knew during the Liberian Civil War, when Raiden’s real parents died. He was the star of Solidus’ Small Boy Unit, earning him nicknames like "Jack the Ripper" and "White Devil." Solidus now had an eye patch over his left eye (which was shot out when Raiden took down the Harrier) with Ocelot commenting that he’s the “spitting image of Big Boss. After Ocelot left, Olga walked in and told Raiden about her child, whom she had never met because she was stolen by The Patriots. Olga told Raiden that if he were to fail this mission, her child would be killed. Olga could not let this happen, and she had been sent in by The Patriots to assist Raiden. She told him that Snake was waiting up ahead, before leaving the room.

Raiden’s holds were then released followed by him receiving a call from Rose, and she asked him if what Solidus said was true, which he admitted. He was a child soldier, raised by Solidus to be a ruthless killing machine. After making his way through the hanger which housed many mass-produced Metal Gear RAY units, he was called by Rose again who nervously told Raiden that she had been a spy for the Patriots all along. She became his girlfriend, simply to keep keep an eye on him, but truly fell in love with him. She changed her appearance to suit his desires, but her transmission was eventually cut-off with her final words being "Jack… I’m… pregnant, Jack…"

Raiden, distressed, pressed on and met up with Snake. Snake apologized for his earlier "betrayal" saying he needed to use Raiden to sneak his way into Arsenal Gear. The two then battled their way through the Arsenal Tengu and, on the way, Otacon discovered that the Colonel Campbell who had been helping Raiden throughout the mission, wasn’t the real Colonel, but an AI created by GW, cobbled together from Raiden’s hopes and expectations. Just then, Snake was confronted by Fortune, who had been waiting for Snake as she believed that he killed her father, Scott Dolph. Snake and Fortune prepared to battle as Raiden headed up a nearby ladder, and Raiden appeared on a giant platform. Solidus began to speak to him, telling him about the S3 program, The Solid Snake Simulation. The perfect program devised to create the perfect warrior. Raiden then defeated a hoard of Metal Gear RAYs, before eventually giving in, falling to his knees. As Solidus emerged from his hiding place, he was ready to kill off Raiden before Olga then jumped out in front of them confronting Solidus. As she gave her life to save Raiden and, therefore, her child, Solidus ordered the remaining RAYs to kill Raiden, but Emma’s GW virus started to take effect. Angered by this new development, Solidus destroyed the remaining RAYs, damning the Patriots in the process. As Fortune walks on with a handcuffed Solid Snake, Raiden falls to his knees, passing out.

The World Needs Only One Big Boss!

When he awakened the next day, April 30th, he found himself, Solidus Snake, Revolver Ocelot, Fortune and a handcuffed Solid Snake atop of Arsenal Gear. Solidus then revealed his true intentions. Ocelot, seemingly amused by this then revealed that the entire incident was scripted by The Patriots and that similarities between the Shadow Moses Incident and the Big Shell crisis were much more than just coincidence. Dead Cell in the place of FOXHOUND, the relation between Raiden and Solidus, compared to the one between Snake and Big Boss, the Harrier that Raiden destroyed in a similar fashion to the Hind-D and the computer virus that mimicked FOXDIE were all elements scripted to turn Raiden into the perfect soldier. Solidus was also a pawn in The Patriots' plans, but the one thing that wasn't planned, however, was the appearance of the real Solid Snake which is why Campbell repeatedly tells Raiden that Snake isn't part of this simulation, and not to rely on Snake. Ocelot then proceeded to kill Fortune, revealing that her apparent supernatural abilities were simply the result of Patriot technology, and climbed aboard Metal Gear RAY. Suddenly his arm twitched and he was once again possessed by Liquid Snake.

Liquid said it was him that leaked information about Arsenal Gear to Solid Snake in order to get him out there. And now, armed with Ocelot’s knowledge of the Patriots, he intended to go and defeat them all. Liquid then climbed back inside RAY and took off, but Snake broke free of his handcuffs and dove into the ocean after Liquid.

Arsenal Is Going To Take Off!

Arsenal Gear proceeded on its course, crashing through the streets of lower Manhattan, stopping at Federal Hall. Solidus told Raiden that all he wanted was to be remembered, as he and his brothers were unable to pass on their genes. Solidus expressed frustration and being unable to pass on his own genetic legacy. He wanted to destroy the Patriots, not for his own greedy ends, but so he could take back things from them that they were about to take away such as freedom, civil rights and opportunities.

Raiden then received a call from JD, the core Patriot AI, in the form of Campbell. The AI explained to Raiden about The Patriots, hinting that they now existed in a digital plane of existence, and how now, thanks to the dawn of the digital age, trivial information would be kept intact forever, accessible by anyone, and exactly what information this would be would be decided purely by them. The Patriots then revealed yet another shocking truth. Ocelot did not know the whole truth about S3. Rather than standing for “Solid Snake Simulation”, it stood for “Selection for Societal Sanity”, and was created to test GW, echoing what Emma had said earlier.

The AI then ordered Raiden to kill Solidus, and he agreed when he realized that his victory depended on the lives of both Olga's child, and Rosemary. Solidus told Raiden that he needed to defeat him. In addition, it was Solidus who killed Raiden's parents and Raiden defeated Solidus.

Who Am I Really? As Raiden stood outside the front of Federal Hall, Snake appeared and informed him that he and Otacon were going to find the Patriots using the virus disc (as it was programmed to remove the names of the Patriots leaders, it should have some form of indicator to know what those names are). Raiden insisted on coming with them but Snake told him to stay. He still had things to do and to figure out. Although the mission was a simulation, everything he felt during the mission was his and his alone. It was up to him to decide what to pass onto the future, and to figure out his own purpose for himself. Suddenly, Rose appeared, and the two vowed to make a life together, both figuratively and literally.

Sometime later, Otacon and Snake successfully traced The Patriots, but discovered that all twelve of them were dead, and had been for the last hundred years. With this, Philanthropy had lost their only lead, the future of the Patriots uncertain.