Hey Guys. This is my first fanfiction so please read, enjoy and review and I will update asap.

I do not own any of the characters I have written about, except those which are not featured in the metal gear series-these are my own ideas.

Chapter 1

A Message

Three months after the incidents at Big Shell, Solid Snake was finally returning to his 'normal' life. At this particular moment, he was strolling done a crowded Manhattan street, working against the steady flow of rush hour commuters. He slid his hand into the pocket of his thick coat and pulled out the packet of cigarettes he'd just brought. He drew one out with his lips and fumbled until he found his new Zippo lighter, quickly lighting the cigarette and slipping both items back into his coat. He sucked in a mouthful through his awaiting throat and heaved it out through his nose. A man in a suit coughed loudly and obnoxiously, passing on a huge anti-smoking message to Snake. He grimaced at the man's rudeness and ignorance, he'd saved his and his families life at least twice and he treats him like this? Ignorance. Snake frowned to himself as he continued to nudge his way through the crowded street. Another puff, another anti-smoker's glare. It almost made him laugh. He was shook out of his thoughts by a man ramming heavily into his right shoulder. Snake turned his head slightly, just enough to get a look at the man, who was obviously in a hurry.

"Oh, excuse me" the man blurted out, pulling his head down, embarrassed.

Snake just gave a half-shrug and turned, eager to get back to Philanthropy H.Q. It wasn't as though anything particularly important was happening there, it's just Snake still didn't like being out on the street in broad daylight. The fact that the Patriots, if they were alive, were yet to do anything obvious, except employ a new president, since the Big Shell incident worried Snake, and Otacon.

A few minutes later, Snake pulled himself off the cold street, down a small flight of stairs, and right to the door of the Philanthropy H.Q. There was an intercom system and a tiny peephole, like most rich houses would have. Except these one were both security methods designed by Otacon. The button on the intercom also worked as a thumb scan and there was a tiny camera hidden in the small glass coin of the peephole. Snake pressed his thumb against the button and grimaced, waiting for the inevitably and annoying response.

"Password" said Otacon's voice, crackling over the intercom speaker.

"Just let me in" Snake said, his breath fogging the glass of the peephole.

There was a slight pause and there was a click from the door. Snake shoved the handle down roughly and pushed the door open, stepping into the room and slamming the door closed with the back of his foot. He stepped a few steps down the narrow, dim foyer and into the glowing heart of Philanthropy.

"Hey" said Otacon, not looking up from the computer he was glaring at.

Snake mumbled a brief hello and took to the couch. The main room of Philanthropy was basically the computer counter at a department store. On each side, there were six computers built into a large flat panel, all hooked up to a single keyboard. Otacon was currently glued to one side of the room, as he almost always was, and Mei Ling was mimicking him on the opposite side of the room. Snake ground the cigarette into the hard wood floor and put his hands behind his head, lying along the couch.

"I did some research into the possibility of a Metal Gear in Texas" said Otacon, passing a brief glare at Snake "There isn't one"

Snake nodded. Ever since Big Shell either no new Metal Gears had been constructed or the Patriots were intent on making sure they didn't find out about them. Maybe they were trying to starve them out, Snake didn't know.

There was a sudden beep, which shattered the efficient hum of Philanthropy.

Otacon leaned over and a look of slight relief passed over his face. Jack, thought Snake, or Raiden as he preferred to be called inside Philanthropy. Otacon asked for a password and Snake could hear a quiet response through the speakers. There was a distant click and Snake heard the door slam. A few seconds later, in walked Raiden, his blonde hair looking wet and cold.

"It's raining out there now" he said, seeing Snake's look of contempt.

"Didn't wash it today, huh?" retorted Snake, partially smiling at the dripping Raiden.

Raiden ignored him, instead moving into the bunk room, past the pane of glass that separated the rooms and slid onto the top bunk, pulling out a loose paperback.

"Why do you even bother coming here everyday?" asked Mei Ling "By the looks of things, Metal Gear is dead"

"Until we're sure…" Raiden said, his voice wafting past the glass.

Mei Ling flicked her hair and rubbed her eyes, turning back to the computer

This is what Snake's day entailed. Alternating between V.R missions and smoking himself to death on the old, smoky couch. So far, he reckoned he'd cut about ten years off his life. Snake reached into the right pocket of his of jacket, digging around for a new cigarette.

That's how it began.

Snake found not two, but three things in this pocket. The familiar thin cardboard of the cigarette pack, the cool, sleek metal of his new lighter and something else. Something small and plastic. Snake quickly flashed back, quickly checking if he put anything that fitted that description in his pocket and drew a disheartening blank.

He clamped his hand around it, almost afraid to see what it was. Snake knew how silly it was, so slowly and cautiously drew the thing into the glow of the light.

It was a small plastic case, like a video game's, except smaller. It was blank, just a simple case with a slim plastic sheet over it. He stared at it for a moment, bemused, and then sat up.

"Otacon," he said, standing up and moving over to him "What the hell is this?"

Otacon looked up from the computers, irritated. He glanced at it quickly, and made an annoyed face.

"It's a U.M.D case" he said, turning back to the eerie glow of the computer "There everywhere, now days"

Snake nodded, thoughtfully and pressed the side of the case. He snapped it open, urgently and peered inside.

A blank disc. Simple in everyway, not even a manufacturer name.

"Otacon, I need to look at this" Snake said, layering his voice with quiet urgency.

"Why?" Otacon said, condescendingly "What is it?"

"I don't know" said Snake, making three pairs of ears in the room prick up.

Otacon swiveled on his computer chair "What?"

Snake did a recall of the day. Got up, breakfast at some dive by the Hudson, ciggs then back to here. Where did he get it?

Then it struck him, as violently as the man who'd slipped it into his pocket.

"A man, he bumped into me on the street. He must have slipped it into my pocket"

Raiden and Mei Ling came up behind the two, looking confused.

"Are you sure?" Otacon said, his face suddenly growing unnervingly serious.

Snake ran his hand over the back of his head "Must have been"

Otacon took the case from his hands and peered at it.

"Never seen one like this before" he said and popped the disk from its case.

"What do you mean?" Raiden asked.

"Almost every U.M.D I've ever seen has a serial number on it somewhere" Otacon said, sliding it into an awaiting disk drive.

"And a manufacturer" said Mei Ling.

There was a brief whir as the disk was read. Then Otacon's main computer screen came alive with a huge message.

Dear Solid Snake and Raiden

The room froze after reading only the first line.

"Damn it," cursed Snake "It's the oldest trick in the book"

The group read on.

I expect we are the last people on Earth you'd expect to be asking you for a favor. However, in our darkest hour, we have no choice. We, The Patriots, are in desperate need of your help.

"Holy Crap" said Snake, amazed beyond belief.

"What exactly is this?" Raiden said, looking at least ten times more puzzled than Snake.

Otacon, who was still reading frantically ssshed him.

We are about to tell you things that the citizens of America aren't meant to know. This is top secret information and we expect you to treat it as such.

Three days ago, a plane heading to Iceland was hijacked by a group of terrorists. This plane was then flown to Alaska, and landed just outside the remains of the facility formally known as Shadow Moses.

Snake saw Otacon shiver, then go blank. Memories of Sniper Wolf were being painfully dug up. He also flashed back to that cold, torture rack.

"This makes no sense"

Unfortunately, unbeknownst to the rest of the world, we had two superior Metal Gear designs in production during the Big Shell 'incident'. One was Arsenal, the destruction of which was luckily kept relatively hidden from the world. However, the second and more advanced Metal Gear was at risk from another such attack so we moved it to the last place we thought any one would ever think to find it. Deep under Shadow Moses, in a facility aptly named "Deep Moses". This is where the prototype of Metal Gear Hawk, the first airborne Metal Gear, is stored.

"Dear Lord" Mei Ling said, bringing her hands to her head.

Unfortunately, we were wrong and this information was somehow leaked. The group found it and is using the hostages and the possibility of a nuclear strike to hold us at ransom. Their demands are that we turn over all control of the United States America to them, within forty eight hours or they will begin wiping out a major city one by one until the country is gone.

"I still don't get what this has got to do with us" said Raiden; though Snake had a sick feeling he knew exactly where this was going.

Hawk uses the same electromagnetic technology that we used on the woman code-named "Fortune" except on a much grander scale, which makes it almost impossible to stop. If they launch a nuke we'll be powerless to stop them. It's also capable of flying at speeds greater than that of sound, giving it easy access to the world's cities. They've also said that any plane that leaves any Air Force base in the States will result in a preemptive strike, so that to, is out of the question. Our only option is a stealth mission, and that, Snake and Raiden, is where you come in.

We need you Snake, to infiltrate Deep Moses and kill the two terrorist leaders and disable the Metal Gear so that we can reclaim it while Raiden rescues the hostage who are being held somewhere in the original Shadow Moses.

"There crazy," said Snake "Why would we help them?"

You two are probably asking yourselves why you would ever help us. We have four good reasons.

The fact that we still have Olga's child in our care, who will suffer immensely if you do not do as we ask.

The fact we have snipers posted on three locations outside your headquarters.

We will be willing, if you perform this act for us, to turn a blind eye to future acts of Philanthropy

The fourth is the reason we know you will do it, far more compelling that any death threat of incentive could be. The two terrorist leaders are calling themselves Liquid and Solidus Snake. We have no proof confirming or denying this statement, but with today's medial procedures it may be possible.

"It can't be," said Snake, shaking his head wildly "I saw him die"

"I killed Solidus," said Raiden "He can't be alive"

"Read" said Otacon

Apparently, the two terrorist leaders have resurrected the Genome Project. Again, we have little proof except satellite photos. We suggest you do as we ask, if you wish to prevent the death of the ones you care about and the rest of the country. Usually, we'd get someone we trusted, but seeing how you disabled two of our other Metal Gears before, right under our noses, we though you and Raiden would be perfect for the job.

There will be a helicopter waiting for you at the Hudson Air Base tonight at six. Please be prompt. We will supply you with necessary weapons and equipment but you'll need to provide the pilot.

If you wish to be responsible for the death of the nation, don't turn up. However, if you couldn't handle that, be there at six.

From

The Patriots

The room was as silent as it had ever been. Snake was the first to speak up.

"What the hell?"

Otacon scrolled up and down the letter.

"They're all dead…" he managed to stutter.

Raiden didn't even bother responding, he just spun around slowly and moved quickly and quietly back to the bunk room. Snake didn't even look to see why.

"Could this be real?" Mei Ling asked.

Otacon shook his head, then after some thought nodded.

"In theory…"

Snake reached around and grabbed him by both shoulders, spinning him so his face was inches away.

"Is it?"

Otacon struggled his way out of the grab and pushed his glasses up onto the bridge of his nose.

"The lack of identification on the disk could be proof enough," he said, turning back to the screen "Also, they seem to know things that only they could-who else knows about all those incidents"

Snake reached into his pocket, finally getting the cigarette he'd been wanting and quickly lit it.

"Ocelot?" he said, with a half-shrug

"Possible, but why would he ask this?" Otacon replied, looking more puzzled than he Snake had hoped.

Raiden reentered the room, the high frequency blade clutched in his hand. Snake advanced on him.

"What the hell, kid?" he said, grabbing at the scabbard.

Raiden pulled back, clutching at it. "I'm going"

"We have no proof this…" Snake began but Raiden cut him off.

"If there's even the slightest chance he's alive, I'm going"

Snake frowned at him, taking another heavy drag on the cigarette.

"Tell him, Otacon" he said, looking pleadingly to Otacon.

Otacon shrugged "I think he may be right about this"

Snake whipped his head back suddenly "What?"

Otacon nodded solemnly, "Were dying of boredom here anyway, may as well use the time to help Philanthropy"

Mei Ling also spoke up "Besides, it's not looking like we have much of a choice. We better do something or we'll be responsible"

"But…Liquid is dead. I saw him die. The Foxdie got him" Snake said, trying to convince three people.

"Technically, he is still alive in Ocelot's arm. Maybe he's running it through him"

Raiden tucked the blade lightly under his jacket, "I'm going home to tell Rose and get my Skull Suit, and I'll see you there"

Snake put his arm out to stop him, but he knew it was useless.

"We…I…" he stuttered, but gave up when he saw no one in the room was on his side.

"Look what real choice do we have, it clearly states you both have to go to stop them. It's not pretty but they've got us" Otacon said, ejecting the disk and slipping it back into the case.

"This is insane. The Patriots are pure evil" Snake said, throwing his arms into the air.

"They've got Olga's child, we need to get it back" Raiden said, placing a single hand on Snake's shoulder "I need to do it"

Snake took a long drag of his cigarette and blew it out through pursed lips.

"What if it's a trick?" he said, thoughtfully.

"I'll be in the chopper to get you guys out" said Otacon "No problem"

Snake nodded "I don't like it"

The group went silent, none of the people knowing exactly what to say. Finally, Snake crumbled.

"Fine we'll do it. But if it goes wrong, I'm holding you responsible"

There was a quiet murmur of approval amongst the group as Snake went to his bunk and pulled out his old, dusty sneaking suit. If he was going back to Alaska, he'd need it.

A couple of hours later, Snake, Raiden and Otacon made there way to the chopper. It was still raining, but Snake barely noticed it. He was deep in thought.

Was it possible Liquid's death had been staged by The Patriots?

Had Solidus really died at all?

Why were The Patriots coming to them?

Too many questions that all had no obvious answer. Snake sighed.

They were at the chopper, a Kastka, like the one they'd used at Big Shell. It was in good enough condition, probably enough so to get them to Alaska.

Otacon, wearing a thick raincoat, looked the most miserable. He saw Snake, glaring at him, with an amused look.

"I like HQ better" he said with a whimper and Snake nodded, holding back a chuckle.

Raiden and Snake piled quickly into the back of the chopper as Otacon opened the unlocked pilot's door.

Raiden and Snake slipped on the earmuffs and looked around. The Kastka was almost exactly like the one he'd been using at Big Shell.

Raiden said something and tapped him on the shoulder. The communications weren't on, so Snake couldn't here what he said. He assumed it was something to do with the two large, hard plastic cases slid under the seats in front of them. He tucked his foot behind it and pulled one out.

SOCOM Mk23

Snake nodded, he suspected he's be given one of these.

He handed a case to Raiden and popped the top of his. In it sat a shiny new Socom, or Special Operations Command Pistol. There was a Government Issue silencer about 10cm long and about 10 extra full magazines lining the case. He pulled out the gun and peered down the barrel, pulling the trigger a couple of times. It clicked smoothly, it had been well oiled, and he slid a fully loaded magazine into it gently, pushing it with his palm until he heard a gentle click. He cocked it and slid the safety on the left side into the on position. He picked up the new suppressor and gently screwed it on, twisting it until it stuck tight. He checked the L.A.M and slid the gun, now about 30cm long into his holster. He noticed Raiden was doing the same. He gently took each magazine and slid it into a separate section of his gear bag, tightened around his waist. Then he heard a faint ringing in the back of his neck. He put his two fingers up to just beneath his ears and waited for the Codec to answer itself.

It was Otacon "You guys ready to go?"

Raiden answered before Snake could "Yeah, as we'll ever be"

Snake leaned forward and pulled the door of the helicopter closed. Then, a few seconds later they heard the whopping sound of it taking off.

Snake sat there for a minute or so, waiting for it to get off the ground, when he got another call.

"Good Evening, boys" the voice, which was metallic and hissy said.

"Who is this?" Snake said, already knowing who it would be.

"Well, for this situation I think Deepthroat would be appropriate"

"Are you one of them?" said Raiden, who'd also been included in the call.

"I work for The Patriots, yes. I'll be supervising this mission on their behalf"

"What do you want?" said Snake

"I just called to say it'd be best if you entered from the far side of Shadow Moses, they're heavily guarding the water ways this time"

Then the line went dead.

Snake felt sick. He was a puppet.

He flicked off his Codec and let himself slip into a light sleep.

He had a feeling he'd need it.