First Fic. yahoo!!

This will be a Sheppard centric story, multi chapter so give it a chance.

I odn't own any of the characters, don't resort to legal measures as it would yeild little fruit.

This was the story of how he died.

It was a day for cliché's. The sky was overcast and the waves were choppy. It could even be called a dark and stormy night, except that it was midday. The air was alive with the smell of ozone, lightning could be seen far away, jagged fissures in the slate colored sky. It had not started to rain over the city, but it would. It was going to rain cats and dogs. Weathermen would still have gotten that wrong, of that he was certain.

Col. John Sheppard stepped back from the edge of his balcony. It was his because he was one of the few who ever went there. It was the place he had first seen the city from, all those years ago when the city was still under water. By unspoken law it had become his. It was his own sanctuary, a place to be alone with his thoughts. More often than not his thoughts were dark. Today they were morose.

It was fitting for such a dark day.

He remembered the dead. There were so many. His hazel eyes stared down into the inky darkness of the turbulent water, trying to remember the first. The first casualty in a long line of casualties, in a never ending line of dead.

Who had it been? A woman. Yeah, a woman, in the military, if his memory was accurate, definitely military. Maybe he should have been glad it hadn't been one of the civilians. Somehow he couldn't muster the sarcasm that usually kept the horror at bay today. He could see her face, but the name escaped him. It had been 4 years ago. It was a long time to remember someone. An eternity in this place. He used tricks he had learned as a child. Focus on one or two details and let the rest flow.

She had had blonde hair. Pretty smile. Yeah her smile was nice, great teeth. He waited, not forcing it, knowing his memory would come to him at some point.

Lightning flashed and the thunder rode quickly in its wake. The storm was almost there. Weir hadn't raised the shield, and he knew she wouldn't. A bit of water they could handle, some rough seas were a bit inconvenient, but not life threatening. Running out of power, a constant fear with already taxed ZPM's, well that was something no one wanted to think about.

The lightening lit up the sky once again, blinding him for a moment. It was then he remembered.

Cadman. Laura Cadman.

Yeah that was her name. He couldn't remember how she had died exactly. Perhaps that was a small mercy, one for which he was grateful. Laura Cadman, a lieutenant, competent. The first to fall in this brutal war. Young, they were always too young, even when they were old. No one deserved to die like this, here, so far from home.

Was it even a war anymore?

He closed his eyes and tilted his head back, catching the first fat raindrops as they lost their battle with gravity and fell from the clouds. The deck shook with the force of thunder and the heavens opened, spilling rain in a drenching deluge. In seconds he was soaked, barely above freezing rain water running across his face. Oddly he didn't mind, it was refreshing, even if it was a bit painful, and he stood a moment in the cleansing rain. If only all of their problems could be as easily washed away.

His comm. Unit chirped in his ear and he sighed, the weight of the world reasserting itself in one single soft sound. Even the great storm couldn't drown out the call of his responsibilities, and they were many.

"Hell, been away long enough as it is." He said to the storm and turned and went inside, the door opening for him at his approach.

"Sheppard here."

"Come to the Gate room Col, we have a situation." Dr. Weir, head of what was left of the Atlantis expedition, ordered.

He sighed again, weary. "On my way."

There was always a situation. They were running out of power, food, clean water, medicine, just to name a few. They had been found. Again. His insides turned to ice.

Gods above and below, hell anyone who'll listen, not that, not so soon.

It was a silent prayer and one he did not expect answered. One thing had been made abundantly clear to him. Those with the power to did NOT intervene. However much they had been revered, the ancients were not gods, and if they were it was a cruel cosmic joke. If there were gods, real ones like they wrote about in Greek Mythology or used to worship in beautiful cathedrals on Earth, they were so far away they couldn't hear him. That was the cold hard truth.

But it didn't stop him from praying.

Or believing in miracles. He had seen a miracle. Just one. It hadn't been a cunning bit of technology or that last minute save that kept them alive for one more day. Those were plain dumb luck. His miracle was something more, and very simple. He hoped to see another in 8 months or so.

His thoughts did not linger there for long, the darkness clinging to the walls of the corridors seemed to seep into his head and prevent him from rising above the gloom. His thoughts remained dark.

His thoughts stayed with the dead, the old and the new. It still hurt. He took their deaths personally, a testament of his failure. His thoughts turned to his most recent failure. Major Evan Lorne, his second in command, a trusted friend.

He brushed the comm. in his hear. "Dr. Beckett."

"Aye, Col Sheppard." The Scotsman's brogue came through.

"How's Lorne doing?"

There was a loud sigh. "We're just getting ready to go into surgery. We'll know soon."

Sheppard tried to keep his voice even. "Keep me posted."

"Will do son, Carson out."

Lorne had been on a simple recon mission. They had received reliable, what they had believed to be reliable, Intel on a ZPM, and it was too good to pass up. They currently had 3, but 3 was the bare minimum they needed. Power was something they always required more of.

It had been his call. He had sent Lorne, the man was capable and could handle anything that came his way. It had been a set up. In hindsight he wished he had gone himself, not that things would have ended differently, but it was better him than anyone else. Their allies had sold them out. It had happened before. Honor was honor and it was in short supply these days.

It had been particularly bad this time. They had been ambushed and had to retreat through a mine field back to the gate. It had become one of the enemy's trademarks. Go through a gate and meet no resistance and everything looked just hunky dory. Then, while the teams were off exploring, negotiating, looking for whatever the reason for the mission dictated, they would set up these mobile mine fields. When they tried to go back the way they came, well there was a nice surprise waiting.

The entire team had been wounded, but Lorne had taken the worst. Lorne guarded their flank and had triggered the mine field as his team went threw the gate. The resulting concussive blast had discouraged pursuit, but had also thrown Lorne threw the gate at a tremendous velocity, not to mention the fire ball that travelled with him.

Long ago the Atlantis team had set up several beta sites, neutral unpopulated planets that were staging grounds. All outgoing teams went to Beta sites and then on to alternate destinations and same in reverse order. It kept the location of Atlantis itself safe.

Lorne had had to wait for the energy of the blast he caused to quit feeding the gate so it could close before his team could dial home. It had taken more than 20 minutes and that 20 minutes nearly cost the Major his life. He sustained severe burns to his hands and left arm, a major head injury and several broken bones, a punctured lung and he was bleeding internally. Sheppard was no doctor, but even he knew this was going to be close.

Lorne was a hero. He saved the lives of his team. Unfortunately, Lorne was one of a select few who they just simply could not afford to lose.

Lorne, of all the damned luck. Sheppard thought. There were only 4 left, only 4 who had the ancient gene, and the people within the city relied on these 4 for their lives. Without them, they were defenseless. And 2 of them weren't even military. Carson Beckett and his sister Ava. Both doctors, both working themselves into the ground. Both never complaining, just making due with limited medical supplies and limited staff and a never ending stream of injured making their way through their infirmary.

4 small lives away from being parked in this massive city, unable to move, unable to fight, the proverbial sitting duck.

His feet took him automatically to his destination, a path so familiar he didn't need to think about it anymore and his mind was free to wander and remember, remaining as dark as the sky outside.

Lists of the dead. There were so many. Faceless soldiers and scientist who had not expected the desperate fight for survival, and been crushed under the juggernaut of war. Teylas' s people had been hunted to near extinction. He remembered Halling. He remembered finding his broken body amongst the ruins of a tiny settlement.

So many others, just gone. Ford, lost early on. The pain was still fresh. Then there was Col Caldwell, bought his ship, Deadalus, time to get away with a suicide mission, ramming a nuclear bomb down their throat, and hoping they choked on it. Sheppard would never admit it, but he missed the older man. His experience would have been invaluable.

He should have felt anger at all the waste, but anger had died a long time ago. All that was left in its wake was defeat. There weren't enough of them left to mount that one final heroic battle. There was no going out in a blaze of glory for them. Theirs would be a slow agonizing death as supplies ran low and trust ran thin. Trade would stop, supplies would be scarce and then on one fateful day there would just not be enough, and it would end. That was how he saw it ending.

But not today.

And not tomorrow.

It was a date in the future, months maybe even years down the road. He momentarily wondered if he could start a pool, betting on the exact date of their demise. Nah, Elizabeth would probably shoot me herself for that one. He chuckled. She wouldn't be the only one. He could think of a few people who would join that firing squad.

He rounded the last corner and took the stairs two at a time. He stowed the darkness for later. Now he had to be what everyone needed him to be, the hope filled military commander of Atlantis. He found that persona and slapped it on, sure and confident.

"So what's the problem this time?" He said easily, hands hanging casually at his sides.

There was silence as Zalenka looked to Sheppard and Weir and she nodded. "An unknown signature has appeared at the far edge of the solar system."

"What do you mean unknown?" Sheppard's eyes narrowing.

"Meaning we have no idea what or who it is. We've never seen a hyper drive signature like it before."

Sheppard turned looking around the circle of the leaders of this "expedition". Weir looked worried, and haggard. Zalenka had bits of hair standing up in strange places and his glasses were a bit lopsided. He wondered when the last time the Czech scientist had slept.

Michael spoke up, his odd musical multi-toned voice cutting through the tense silence. "It is unfamiliar to us as well."

That did not bode well. There was silence for a moment as everyone looked at the small red dot at the edge of the solar system, willing it with their eyes alone to just keep on sailing right on by. Finally he broke the tense silence.

"Well, 2 possibilities. One: someone new and powerful, may be on our side." It was a possibility but the look that passed from Zalenka and Michael said it all. If it was an ally where the hell had they been all this time. "Or, two, they've come up with something knew." Everyone knew who they were.

"So either we sit here, wait and hope, or we pull up anchor and find somewhere else." Weir stated.

They had been down this road before. Too many times they had waited too long, hoping they wouldn't be seen, that the cloak would be enough. It had cost them in the past.

An annoying beeping started, coming from the computer monitor. Beeping in general was bad. It was like a bad episode of Star trek. Things only beeped when the ship was about to blown up, or the previously sexy peaceful aliens were insulted by some tradition no one knew about that had been disrespected, blah blah blah, ending in total destruction in 10 seconds.

. "No. no. no no no no." Zalenka said, Sheppard nearly smiled. Zalenka slipping into one of his McKayisms.

"What?" Weir asked, her shoulders tense and her face pale.

"They've picked up speed, and are heading straight for us."

Great. "Well that settles it. I'll head to the chair and get things going, time to leave." He had taken 5 steps towards the stairs when Zalenka spoke again.

"You don't understand."

"Zalenka!" he barked, he'd apologize later.

"Based on their current speed and the acceleration, and they are still accelerating"

"RADEK!"

"They will be here in less than 30 minutes."

Oh God. It took at least 30 minutes to ready the star drive for use. It had started taking longer as they had used it so often and, well 10 000 year old systems didn't last forever. The silence was absolute as everyone digested that information. They all knew how long it actually took to get airborne. They knew how long they really could last against them when it turned into a fire fight, once they were within weapons range.

"right". Sheppard said, digesting the new information and moving on. He brushed his ear piece. "Ava." He said.

"Go ahead." Her bright voice responded immediately.

"We have a situation, get to the chair and ready the star drive."

There was a pause, and finally an exhausted sigh. "On it."

"Ava."

"Yes."

"It needs to be done in record time."

There was another pause, he could imagine the look on her face, green eyes growing wide and a grim determination setting her mouth into a frown. He heard the baby coo in the background.

"Better get to it then." Was the reply and she was gone.

"I assume you have a plan." Weir said folding her arms and trying her best to look annoyed.

"I always have a plan." And he flashed his best cocky grin, selling it for all he was worth.

Sheppard was in the jumper bay. By his count he had 20 minutes until the unidentified vessel arrived.

"You don't have a plan." A musical voice intoned behind him.

"Of course I have a plan." He said not turning around and looking at the other occupant of the craft.

"In all of the years I have known you, John Sheppard, you have never had a plan."

Now he did turn and look, fixing Todd with his best bland I have no idea what you mean look. Todd just looked back, pale features gleaming in the half light waiting. The damn wraith had more patience than… Job.

"All right, I don't have a plan, but I will have one before that ship gets here." Todd, just grinned, a truly ferocious expression on a Wraith, and laughed his odd musical laugh. He moved forward and took the seat next to Sheppard.

"What the hell do you think you are doing?"

Golden eyes sparkled. "I am coming with you."

"No."

"Whatever last minute plan you concoct will be easier to accomplish with an extra set of hands." Todd stated.

There was a pause, a silence that was heavy with intention and words that would never be spoken.

"I'm most likely not coming back." Sheppard said simply. Todd smiled again, more a baring of teeth, than a real smile, but a smile none the less.

"Ah, so you do have a plan then. Excellent. This should be most entertaining." Todd still made no move to leave. Sheppard never would have admitted it, but he was suddenly very grateful to the man at his side. An unlikely ally, an unlikely friend.

"Well when you put it that way…" Sheppard responded with a wry grin.

The alien ship continued to accelerate. It was an insane speed for sub light engines. Zalenka shaved additional time off his original estimate of 30 minutes. If they were lucky, and they seldom were, the alien vessel would be within weapons range in 22 minutes, give or take a minute or two.

Weir stood on the balcony, overlooking the gate, arms crossed across her breast, an uneasy expression fixed to her face. Her eyes weren't focused on the organized chaos below her. The city was being evacuated to a Beta site, all nonessential personnel. The Deadalus and the Phoenix had already been sent ahead to the Beta site and they would guard the refuges until the all clear was given and Atlantis was safe in its new home.

The Persephone would remain with Atlantis, secure their escape. It was the ship they could afford to lose of the 3. Persephone had seen more than her fair share of battle and over the last year they had reduced her to more of a transport/ storage ship and were slowly cannibalizing the ship for spare parts to repair the other two.

"You are worried."

She inhaled sharply, "Michael, you startled me." She said. She couldn't' bring herself to smile. The years of running and hiding, the years of such terrible loss were taking their toll. "Just lost in my thoughts I guess. I'll feel better once we are in the air and far away from here."

He placed a hand on her shoulder, a hand that used to be a feeding hand, and now was just a hand like hers. He said no words just a reassuring pressure.

"Has Dr. Beckett been evacuated."

She frowned, "No, Major Lorne had just gone into surgery and there is no way to safely move him."

At that exact second the skeleton crew of the Persephone materialized on the gate platform.

"Major Harris, what are you doing here?" She asked from her bird's eye view of the room.

"Reporting as ordered ma'am."

She looked puzzled. " I didn't give that order Major."

Harris looked back at her. "But the Col." He started to say.

She held up a hand silencing him with a gesture. "Chuck get me on comm. with Persephone, now."

Sheppard looked at the device and then looked at Todd.

"Why couldn't he have just had a big red button that said 'push me'."

Todd shrugged and continued looking threw pages of code.

Only minutes left.

"Col Sheppard respond."

He wasn't surprised.

"Dr. Weir."

"What are you doing?"

"Well, Todd and I just felt like taking a pleasure cruise, see the sights." A proximity alarm sounded.

"What is that?" Weir shouted to be heard above the din.

"Alien ship closing fast, Sheppard. They have launched some kind of missile." Todd said ignoring Weir for now.

"Target?" Sheppard demanded and seized the controls of the ship.

Todd was silent for a moment. "Atlantis."

"Elizabeth…"

"Yes we copy."

"How long till the star drive is online?"

There was silence and then. "5 more minutes." He thought it might be Chuck.

He looked at Todd, who simply nodded.

"Right, my plan. We have the McKay."

"What, are you insane. No one knows if that thing will even work." Zalenka this time.

"It'll work." Sheppard said with confidence. The McKay was the last great invention of one Dr. Rodney McKay, self proclaimed smartest person to ever live. The device was essentially a bomb, but the rough gist of it was that it created an artificial black hole. If it was detonated near an enemy ship it would destroy the ship. The only side effect was that it would probably destroy the planet as well, and all too likely the solar system too. A singularity was a powerful thing, and there was no way to predict how big it would be.

"Yes but even if it works." Zalenka continued in panicked tones.

"I know. Look we are out of time."

There was a loud explosion and muffled shouting on the other end.

"What was that?" Sheppard demanded.

"Status!" Weir shouted.

"The gate is offline and that blast reduced the shields to" there was a pregnant pause. "… 45%" Zalenka answered quickly.

"45%?!" shock coloring weir's voice. The shields wouldn't survive another hit. If the shields went down, engaging the star drive would be pointless, the vacuum of space would kill everyone anyway.

"Elizabeth, you guys need to get out of there."

"I know!!! We need more time!"

Todd brought up the viewing screen. A blue and green orb materialized before them and it was such a beautiful scene, the clouds isolated to one part of the planet, the rest was under clear skies. The planet turned slowly, at peace, unaware of the fight for life taking place just outside of its atmosphere.

"Does this bucket of bolts still have functioning weapons?"

Todd quickly moved to another consol.

"According to this it does, but limited. Asgaurd weapons are only at 15% and there are 12 torpedoes and the rail guns, half are functioning." Sheppard thought for a moment.

"Shields?"

"No."

"Of course, that would make this easy." Todd laughed darkly. "Elizabeth how long do you need?"

There was muffled shouting and words exchanged, then "6 minutes." That was a long time.

"We're going to buy you some time." This was along the lines of the overall plan. Using the McKay was almost certain death anyway, what was a few extra minutes of fire fight.

"You don't have to do this, we'll find another way." She pled.

"Elizabeth, just be ready. We're setting the timer on the McKay for… 7 minutes. That should be enough time for you to get away."

"Col, you don't have to do this." Elizabeth begged. He didn't respond to that.

"Comm. is going dark, good Luck Atlantis."

"John!"

"Sheppard out." And he turned off communication with the city, went back to looking at the impressive vista of the planet.

There was a moment of silence. Digesting that this was indeed "it".

"Better set that timer, you know how to do that right?" Todd grunted and complied.

"7 minutes and counting."

"How long until we are in weapons range of the other vessel?"

Todd glanced at the consol. "1 minute and 12 seconds."

6 minutes flew by in the blink of an eye. The Persephone held up under the onslaught of the alien vessel. Predictably the Asgaurd weapons had no affect and they had tried to siphon the power there to the shields with limited success.

Sheppard flew and Todd controlled weapons, releasing everything they had to give Atlantis that few more minutes.

The ship shook with the force of another direct hit and sparks shot out of the ceiling, a fire spreading nearby. They were too busy to deal with the fire. Weapons were offline.

"Sheppard we are venting atmosphere."

"Can you seal off the area."

"Controls are not responding."

"How much longer?" He didn't really care if it was until the McKay blew or they lost all breathable air.

"1 minute for the McKay."

"Right." He angled the ship and plotted an intercept course. "can we see the city on that?" Todd said nothing, but brought up a static filled image of Atlantis, glowing with the orange light of the shield. He could almost feel it humming with power as the star drive came online.

"30 seconds."

There was a bright light and suddenly the city shuddered and began to rise. "Come on Ava fly that thing, move!" He yelled at the screen.

"15 seconds."

Sheppard had time for last thoughts.

Atlantis was now down to 3. Only 3 stood between life and death and he was sorry he left them shorthanded.

He wished he had had a chance to say goodbye.

The last thing he saw before the end was Atlantis in all her glory reaching for the stars, her golden spires gleaming in the light of the alien sun. She was beautiful.

At the exact instant Atlantis cleared the atmosphere and entered hyperspace, the proximity alarms sounded. The alien vessel was large in the screen.

"Well, I guess this is It buddy." Sheppard said.

"It has been an honor John Sheppard."

"Yeah."

There was only light. Endless light.

The McKay exploded in a brilliant flash of fire and splintering of metal. As the singularity grew, the explosion collapsed in on itself, dragging everything in with it, Persephone, the alien ship, and eventually the planet itself. Thousands of years in the future the sun would begin to fail and particles of hydrogen and helium would begin their long fall into the gapping maw of the vortex. For now it had accomplished its goal. The alien ship did not peruse, Atlantis had escaped.

The cost was terribly high.

John Sheppard, Colonel in the United States Air Force died, on Sept 23, at 13:15 hours, as Earth reckoned time. He was 41 years old. He didn't die alone and his death was heroic. He was survived by his wife, Ava Sheppard and their son, Ronon Rodney Sheppard aged 2 months.

There it is first Chapter, will get the next one up ASAP. review let me know what ya think.