Intro/Epilogue:

"What the hell?!" "Its true, the data from GW says they have been dead for over 100 years! There is the possibility that the information was edited within Arsenal but..." "If so, then who are we after?!" "Well I can't be sure, is the tracking device I gave you working?" "Yeah Otacon, it seems active. Liquid is somewhere in the Atlantic, he is heading south..." Snake and Otacon left Federal Hall, which now lay, in ruins due to Arsenal Gear. Solidus Snake had drowned in a pool of his own blood under hoards of reporters, photographers, and New York Police. Raiden and Rose had disappeared among the many citizens headed to work that early mourning. "We need to lay low Snake, got any ideas?" asked Otacon "Yeah, I have a friend who should help us...."

"I never believed the media's accusations of you being a terrorist. So it was all planned to set up 'the hero of Shadow Moses' huh?" "That's right.... all a plan set up by the Patriots, have you heard of them? The Twelve Wiseman's Committee? The La-Lu-Le-Li-Lo?" Snake asked the master hacker "Of course, I have known about them for sometime now. I first hacked into their early files ten years ago, before they initiated their Y2K Bug plan." Snake was shocked that his new ally had known of something so secret long before anyone else. EinMk.11 was a legendary hacker and weapons collector that Snake had met sometime after the Shadow Moses incident. Ein used his codename in order to hide his identity from everyone, even those he could trust. He walked to the fridge and grabbed three beers. "I don't drink...." said Otacon "Great, more for me." replied Snake while lighting a cigarette. While Ein went to his computer to research, Snake sat at Ein's futon and turned on his 72-inch television.

He watched the breaking news about the recent "Big Shell" incident. A news reporter began: "The Big Shell, an oil clean-up facility has mysteriously been destroyed by a strange break in the foundation. In other news, President Johnson was found in his Long Island vacation home, dead from a heart attack-" "Damn cover-ups, the President's body is the harbor with the Big Shell!" said Snake furiously The news report continued: "George Sears, the ex-president who disappeared suddenly after resigning, has been found dead today outside of Federal Hall. His body was shredded by cuts from a high frequency blade. No info is known about his death or about the large military weapon that crashed into Federal Hall this mourning. It is believed that multiple Russian Terrorists wearing Tengu body armor piloted it. They were armed with katanas and many kinds of fire arms-" Snake turned off the television surprised. "I wonder why the Patriots revealed this much to the public?!" Before Snake could finish his sentence, the doors to Ein's apartment exploded and men in black suits began to shoot up the entire place. "Damn I just moved in, the owner is gonna be pissed. Watch the TV! Hey, my couch!!!" screamed Ein as a Richet bullet flew into his computer screen. "Arrrr...could it get any worse???" said the hacker as his CPU started to fall apart. "Everyone down!" Snake pulled out his FA-MAS, dove behind the futon, and quickly took out 5 intruders without missing once. About 5 more super soldiers headed up the staircase leading to Ein's apartment. "Take my stealth suit Ein, I owe you...." Snake had almost finished off the first unit. "No one fucks with me, I'm not leaving until I kill everyone of those last bastards!" A rare smile appeared on Snake's face as Ein entered his weapons room. He grabbed his sawed off shotgun from his illegally purchased weapons collection. Three blood-drenched bodies flew into a wall and then crashed through the floor into the old lady's apartment below. "Otacon what are you waiting for?! Go get the KA-60 Kasatka now!" "I'm on it Snake." Otacon ran toward the stairs as a bullet grazed his shoulder. Then Hal Emmerich activated Snake's stealth suit and quickly left the Manhattan apartment towards the close Heliport where he saved the hostages hours ago. After Ein took out an entire attack team not much was left of the unit. The men in black suits had proved to be nothin but a nuisance...Ein next returned to his weapons gallery to stock up. The master hacker had a love for guns almost as strong as his love for women and his computer. He packed his equipment case with his sawed off shotgun (which was now stained in blood), his Sniper Rifle (which he customized himself), an M16, and his favorite, the ancient Katana. Snake still had his M4, FA-MAS, RBG6, 9 millimeter Beretta, and a large amount of Stinger missiles. Solid Snake and EinMk.11 climbed the massive staircase leading to the roof. The Kasatka chopper lowered and the two jumped in. Ein looked out the window as he rocked back and forth due to Otacon's bad piloting skills. "Damn Snake, what the hell!? Why did the whole apartment building just collapse?!" "Well, I had to destroy any evidence of our presence which required me to.... destroy your apartment. Hey don't worry Ein, your neighbors surely evacuated upon the our attack and-" Snake's sarcasm was interrupted by loud angry screams. "AHHHH!!!!! Who cares about my neighbors, my beautiful home is destroyed! I just stocked my fridge with that lifetime supply of Shrimp I won!" As the three flew above the streets of New York, a mysterious man with a patch over his eye watched from an alleyway below. "And so it has begun...my equal...."

Chapter One: Dawn

(Note: Begins 6 months after The Big Shell)

"So is it complete?" "Yes, the exoskeleton is indestructible and the AI is fully operational." "Good, our work is finally done. Though, why were we moved from the new Metal Gear Project to this shity job, 'project eclipse'. It is a waste of my time with such little pay." "I agree, developers with our talent should work on more worthy studies. Why would he want us to rebuild a model of Gray Fox???" "When we returned Gray Fox from the grave before Shadow Moses, it was known no one could ever match his ability, even we cant create a Frank Jaeger from scratch...."

The two arms-tech developers continued to discuss their previous works. They recollected in their recent past when they brought back Frank Jaeger, the only member of FOX-HOUND to receive the Rank: Gray Fox, from the dead. Of course Gray Fox then escaped and greatly effected events during Shadow Moses. The Patriots had planned for Gray Fox to arrive at the Islands off the coast of Alaska in order to test Solid Snake those many years ago. Since then the Patriots realized the two scientists were worthless and made them work on unimportant research. Upon learning this, they wanted revenge on the Patriots and assisted the New FOX-HOUND.

"So how is your Hentai collection coming?" "I haven't added much to my original collection...but I did get one new addition." The two pervert scientists both stared at the art before them as a mysterious figure approached. "What the?! Its operational!" said one developer, while the other ignored everything he said, looking at the manga. "It wont respond! No stop!" The figure was invisible to the human eye all that could be seen was the Katana it grasped in its right hand. Swiftly with beautiful agility it appeared behind the developer and pierced through his chest with the blade. Blood sprayed on the wall as the body sank to the floor. By the time the other man realized what had just happened, his neck had been slit wide open... The technical masterminds had been killed by their own creation. It walked from the Assembly room of the complex to the computer room. There it killed a mass amount of soldiers as well as other computer analysts. The first level of Complex One of the Abandoned Military Facility was in ruins as the android wreaked havoc on everyone and everything. Large pools of blood filled vast areas as bodies sank beneath them.

The creation was an android assassin to be added as the last member of the New FOX-HOUND. It was modeled after the Cyborg Ninja, Gray Fox. It was a little above six feet tall. The outer frame of the android's exoskeleton was muscular but small. It carried a katana that was usually hidden inside its sheath. Like Gray Fox, it used a stealth camouflage suit. (Note: For further description look at a pic of Gray Fox, they are pretty similar) The Cyborg Shinobi was created to be a more skilled warrior then Gray Fox once was but it had its flaws... Soon, after scanning around the area, it sensed the presence of another and quickly disappeared into the shadows...

"So how have things been going at Philanthropy while I have been gone?" "Everything is getting better Snake, most people have forgotten about our 'acts of terrorism'. Mei Ling is here as an analyst for the mission, hey I finally got those proverbs right, wanna hear some?" "Ill pass...." said Snake through the codec as he and EinMk.11 had arrived at the military base in the Florida Keys. It seemed like an unusual place to house the latest type of Metal Gear, one of the last existing in the world... Snake and Ein decided to split up and both search through the facility alone. Snake would head through complex One. Ein would start at complex Five and make his way to the Core. There he would rendezvous with Snake after they had gotten the info they needed. Snake reached the entrance to Level 1 of the complex after easily breaking the neck of an enemy sentry. "Everything is fine here Otacon, besides the blood on the walls and the bodies on the floor...." Snake calmly walked down the hall to the Computer Room. "Snake.... I just learned something your not going to like..." "Yeah, what is it?" "Well I have been decoding a lot of hidden information from the GW disk and I just finished. There is more about the Patriots on the disk then I thought...It says their leader is...Big Boss!"

Chapter 1: Dawn Section 2

"That's not possible! I killed him during Outer Heaven all of those years ago!" "I know Snake but there is a-" "I killed him face to face, there is no way-" "Snake there is more... The disk also describes the elements of the S3 plan (Solid Snake Simulation), the new FOX-HOUND, and some strange organization called 'Knights of the council'." "Otacon, what the hell is going on?!" "Well, this knights thing is supposedly a group of the best soldiers and warriors in the world. They are mostly mercenaries who have been hired as lackeys for the Patriots. The data doesn't name them but it describes a gunslinger, a master with knives, a samurai, and an invincible soldier among a few others.... As for the new FOXHOUND, they are a group of rebels without a leader. Though Snake we don't know how much of this information is valid considering it took me 6 months to entirely decode the disk's hidden data." "What about the new Metal Gear that has been rumored to be being created here?!" Snake's voice showed his anger as he yelled through the codec "The prototype is rumored to be called Metal Gear Eagle, patriotic huh? We can't be sure how much the Patriots are involved but its surely being developed by the Air Force on this military base. Its design is like a mobile suit, it is equipped with ballistic missiles and nuclear warheads. Also it carries a large rail gun and a photon laser. This thing is gigantic, I'm not even sure a Stinger would affect it much... Not only that but it is designed to fly! I think it uses hydrogen propulsion but even I'm not sure how it can take flight. Hey Snake hold on- oh yeah Mei Ling said it should be deep underground in the core complex. She checked the online maps for the facility. Unfortunately there are no virtual maps to direct you...." "No problem, I never really needed them...." "Ok Snake, ill contact you later on the codec if I get any new info. Later..." With that Snake turned down the dark hallway into the blood stained computer room. Hazardous gas was shooting out of ruptured pipes and bodies layed over destroyed computers. "Damn there was some sort of conflict not too long ago." Snake pulled out his 9 millimeter berretta and cautiously walked toward the door leading to the assembly room but then froze as a m4 was pointed right to the back of his head. "What the, Air Force, I thought this was abandoned..." said Snake under his breath. "Freeze bastard, yyou'renot getting away with this! Drop your gun and don't move!"