Lost, a stargate: atlantis fanfic

John Sheppard pulled his holdall onto his shoulder and took a last glance around his room – well for a while anyway – he was going to miss his room, his team, the Atlantis sights at night and he had to admit even Rodney McKay even though Sheppard knew no one as arrogant as McKay or had a bigger ego than him for that matter "I'll be back soon enough" he said silently to himself. Sheppard let out a sigh before leaving the room waving his hand in front of the scanner and the doors shutting behind him.
"Sheppard, wait up!" McKay shouted as he started to run to catch up.
Sheppard stopped and turned towards him before starting to walk again as McKay slowed to a walk beside him.
"You're going to miss me that much Rodney" Sheppard smirked and raised an eyebrow at him, Sheppard always managed to plant a joke on McKay no matter how arrogant and Sheppard loved it because no could ever break through his ego.
McKay flashed a sign of uncertainty towards Sheppard "Er…no…well maybe a little…"
"I'm touched" Sheppard held the smirk he had on his lips
"…but not in the way you think" McKay shot back "I have found…maybe with a little help from Zelenka…a possible, now uninhabited planet with a ZPM, and by the looks of the sub-space scanners no one has found it yet or even been there in hundreds maybe even thousands of years" McKay flashed his signature smile, the smile McKay always showed when he was onto something that could help the city and get him appraised for his work.
"Well…that's pretty good McKay but how does this have anything to do with you missing me, even if it is just a little bit?" Sheppard raised an eyebrow at him

McKay's smiled faded slightly "The ZPM is off-world and well we can't go off-world until you get back from whatever…err…you're doing back on Ea…" McKay was cut off by the sound of Elizabeth Weirs' voice over the city intercom "Colonel Sheppard, we are ready for you in the gate room"
Sheppard looked up as if he were slightly confused by her voice, then turned to McKay "Well looks like you're going to have wait a couple of weeks then Rodney" Sheppard tapped him on the shoulder and headed off down the corridor

Ronon Dex, Teyla Emmagen and Elizabeth Weir stood waiting in the centre of the embarkation room, the gate was not yet in use and the massive ring sat at the back of the room its nine blue chevrons glowed softly on the circumference of the ring. Elizabeth was the first to turn towards John and Rodney as they left the corridor and entered the gate room "By the time it took you to get here John, makes me think you don't want to get back to Earth" Elizabeth said while raising an eyebrow at him"
"Sorry about that I got a little held up by something or someone should I say" Rodney glanced at Sheppard disapprovingly before stopping beside him "I wouldn't want to miss a rare opportunity to sit and talk with the IOA now would I" Sheppard added with a loud sigh "What if you guys and Atlantis need my help while I am gone?"
"We'll be fine Sheppard, that's why you invited me onto your team right?" Ronon grinned at Sheppard and slapped him on the back
"I invited you on the team because you would be a valuable asset, and maybe partly because of your reason" Sheppard shrugged
Teyla turned her gaze from Ronon to Sheppard "Ronon is right Colonel Sheppard we will be fine while you're gone, and you will only be gone a week or so" Teyla smiled
"Yeah true" I still prefer to stay on Atlantis just in case. Sheppard nodded and looked up towards the control room and raised his voice slightly "Dial the gate Chuck"
"Sir" Chuck returned to the dialling station and began dialling Earth, a whizzing sound filled the room as the gate came into life and each chevron on the gate lit up brighter along with a small symbol underneath. Once each of the eight chevrons were brightly illuminated a blue wave burst towards the team with a loud kawoosh before receding back to the gate leaving a blue 'puddle' like wormhole filling the open section of the ring.
Sheppard moved his eyes across the faces of his team each of them giving him a nod before he walked towards the wormhole and disappeared through the 'puddle'. After Sheppard had left through the gate the team moved from the gateroom and up into the control room, overlooking the gate on a balcony Elizabeth tapped her earpiece which gave back a buzz to indicate it was engaged "Stargate Command this is Weir, Sheppard has just left through the gate, do you read?"
After a few seconds her earpiece engaged again but this time with a man's voice "Atlantis this is Stargate Command, we read you but Colonel Sheppard has not come through on our end, are you sure he went through?"

When Sheppard entered the gateroom of Stargate Command he was expecting, a warm welcome from General Landry and the rest of the crew from SGC, instead he was met by nothing but a darkened empty room which was illuminated only by the open wormhole. What the hell is going on? Sheppard thought to himself and walked a little down the catwalk pulling his holdall tighter on to his shoulder. Sheppard looked around the room which was covered by debris from the walls and ceiling.
"You can stop the surprise now, it's not my birthday" Sheppard shouted into the darkness, hoping for a reply or at least the lights turning back on, but he was only welcomed by more darkness to the gate shutting off.
"Ahh great" Sheppard turned towards the gate before scanning the room for an exit as the only door leaving the gateroom was tightly shut.

Elizabeth frowned a little "I'm perfectly sure, we just watched him walk through, wait a few more seconds maybe he'll come through, there is a big distance between the Milky Way and Pegasus" Replying quickly
"No, we still have nothing but an empty wormhole"
Elizabeth turned to Chuck "Are there any travellers inside the wormhole?"
Chuck looked down at his laptop screen and shook his head "No wormhole is clear, according to this Sheppard made it through"
By this time the rest of the team began to give Elizabeth curious looks "Doctor Weir is everything alright?" Teyla said with slight worry in her voice
Teyla's voice was interrupted by Stargate Command "Atlantis, the gate has been open for its intended time, to conserve power to the ZPM we're going to have to shut off the gate"
Elizabeth thought for a second resting her chin on her hand, then nodded slightly "Ok shut off the gate"
"Elizabeth what happened to Sheppard?" McKay raised his voice a little towards her working out what had probably happened, McKay reverted his eyes to the sound of the gate shutting off
"Sheppard didn't make it through" Elizabeth turned to Ronon, Teyla and McKay "They don't know what happened"
"What do you mean he didn't make it through?" Teyla replied, raising her eyebrow a little curiously
"This is impossible, he should have re-materialized back on…No, wait a minute" McKay turned and sat down infront of his laptop
"What is it Rodney?" Elizabeth raised an eyebrow at him crossing her arms over her chest
"I knew it…just before Sheppard walked through the gate, a solar storm from the nearest star hit the planet causing a malfunction in the DHD" McKay scratched his head and sighed
"What does this mean Rodney?" Teyla asked
McKay looked up at her from his laptop "It means that we dialled Earth but Sheppard wouldn't appear at that gate…"
"So he just disappeared?" Ronon interrupted with a shrug
"...that's not what I said, he could have popped up anywhere in the space continuum. This is very bad; we may not ever get Sheppard back"

Sheppard banged his fist against the huge steel door hoping for a reply from the control room or at least a bang back on the other side of the door although Sheppard knew he probably wasn't going to get anything back at all
"Where the hell is everybody?" Sheppard muttered to himself getting slightly annoyed he gripped a ridge on the door and dug his boots into the concrete floor and pushed with all his body weight to try and pry it open, but with no luck "Damn" Sheppard kicked a brick across the floor then turned to look back round the room again and ran a hand through his dark black hair, he stopped as a though came into his head, giving himself a slap over the head "Duh" He moved across the room to the brick he had just kicked and picked it up, aiming for the control room window he launched it across the room shattering the glass into tiny crystal looking pieces of glass "There we go" Sheppard smiled to himself happily and threw his holdall through the now clear window and into the control room knocking over a pencil pot and a chair, he then jumped up into the window pane and holstered himself into the even darker control room "Jesus, someone not pay the electric bill?" Sheppard looked around the room which by the looks of everything strewn all over the floor that SGC was abandoned –and pretty quickly – he turned towards the row of computer terminals and tapped a few keys to try and turn one on but the terminal still remained lifeless. Sheppard was awoken from his thinking state with a slight jump as a computer terminal to his right came to life breaking the silence with a bleep "At least we have some power" The screen shows two words which read 'Power On?' Sheppard stared at the screen for a few seconds before sliding his fingers over the keyboard keys and tapping the enter button, all of a sudden every computer one by one came to life followed by the lights then the lock on the gateroom door disengaging and opening up. Now that wasn't too hard was it John? He chuckled to himself, unaware of his current situation.

"Ok, so what are our options Rodney?" Elizabeth said to McKay after a few seconds of silence and crossed her arms over her chest
"We have a few options" McKay replied not looking up from his tablet has he pressed a few buttons
This gained the attention of Ronon and Teyla this time too "Would you like to share Rodney?" Elizabeth asked
"Well…I don't know what those options are just yet" Rodney looked up at them all with a shrug
Elizabeth shot him a disapproving look "I am still failing to see how 'We have a few options' works with that"
McKay sighed and moved between various laptops and studied the screens "It works with that because I don't have those options appearing just yet, but when we locate where Sheppard is, then and only then will the options present themselves" McKay turned to them all again one hand in his pocket "Until then we can't do anything"
Teyla frowned a little "You said Sheppard could have appeared anywhere, where exactly is anywhere?"
McKay looked up at her quickly before typing on a computer "Anywhere being literally anywhere, a different planet in the Pegasus Galaxy or another planet in a galaxy we don't even know exists or he may have made it to Earth"
"But we know he didn't make it to Earth?" Teyla shrugged a little confused
"Well Earth but just years into the past or future" McKay looked at her showing a little worry in his face "Which means I have to be working to solve the problem" McKay started to walk towards the control room exit "I will be in my lab, I'll radio in when I have something" With that McKay disappeared down the stairs and down a corridor.
Elizabeth nodded and looked down towards the floor, where are you John? The same question ran through her mind

Sheppard stepped back from the computer terminal he was at and moved across to the security feeds the other side of the room to see if the cameras had picked anyone up, this was unlikely because he was certain that the complex had been abandoned, he knew this for a start because the control room wasn't being manned. Sheppard eyed the four screens flicking between images of different corridors and rooms but they all showed almost the same image, debris strewn and lifeless. Sheppard was about to look away when something caught his eye, he creased his brow and moved his head closer to the screen to make sure he was seeing it correctly. Has to be something to do with the system shutdown? He thought as he looked at the date in the upper left hand corner of the monitor which read 'Monday – February 3 – 2113.' Sheppard pushed in the reset button and the screens went black before lighting back up again a few seconds later, but not with good results. The date was exactly the same. "Now this could be a problem" Sheppard said to himself and he quickly ran out of the room and into one of the documentation rooms and ripped open one of the filing cabinets draws, he pulled out one of the many of files and took a deep breath before opening it up and reading the date. Sheppard froze as he read the year '2113' stamped at the top, in a sudden rage he threw the file across the room causing the papers inside to fly lose around the floor and slammed his fist into the side of the metal cabinet. Sheppard sat in thought for a few minutes when he was disturbed by the sound of slow footsteps in the corridor, he moved quickly towards the door then stopped, as happy as he was for life inside the building, he had no idea who – or what – it was. He pressed himself up against the wall by the door and waited for the stranger to walk by.

Sheppard moved himself tighter against the wall as he heard the footsteps closer but then suddenly stop as if the stranger in the corridor could sense his presence. Come on, he said to himself as if trying to urge the stranger forward. While he had the chance Sheppard looked around the storage room for something he could use as a weapon but there was nothing around he could use without straining himself, he quickly pushed himself up against the wall again as the footsteps started drawing closer. Sheppard softened breathing as what looked like a soldier wearing urban khaki combats stopped and aimed his P90 sub-machine gun into the room "I know you are in there, show yourself!" The soldier commanded.
Sheppard sighed annoyingly and raised his hands above his head before stepping away from the wall and stopping in the opening of the doorway, Sheppard could now make out the features of Sergeant Tyler – so his name tag said – dressed in the SGC military uniform. Still with his hands raised, Sheppard eyed the Sergeant up and down before saying "Hi, I got a little lost on the way to the restroom, don't suppose you…" Sheppard stopped talking as he was interrupted by the Sergeant "How did you get in here?" He commanded again not altering his aim or his line of sight. Sheppard looked at the Sergeant with a slight confusion, he obviously had no idea who he was "I came through the Stargate, you know the big circular ring, covered in symbols, you can't miss it" He nodded towards the corridor in which he came from "Colonel Sheppard by the way in case you hadn't noticed Sergeant" Sheppard added with a little more emphasis.
The Sergeant returned his gaze and suddenly looked uncomfortable, he looked as if he had seen a ghost; he lowered his weapon and swallowed, "Colonel Sheppard?" he said as if to ask for confirmation. "Yeah" Sheppard now ever more confused "There a problem?"
The Sergeant swallowed again, looking as if he was finding it hard to say his words "You're supposed to be dead"

McKay scratched the back of his head and sat back in his chair staring at the laptop screen infront of him with a disapproving look "There is nothing I can do" He muttered to himself and sighed loudly partly because of the fact Doctor Rodney McKay was completely stumped and partly the fact that Sheppard may never return. McKay's silence was interrupted by the static of his radio followed by the voice of Doctor Weir "McKay, have you worked anything out?" Then the radio went dead, McKay picked up his radio and pressed the button on the side activation the microphone "Nothing yet and frankly I…" He paused not wanting to say the words "Frankly I don't think there is anything I can do"
There was a brief moment of silence then McKay's radio buzzed again "Ok…well come to my office and we can discuss the options we have" McKay could sense the sorrow in Elizabeth's voice, McKay clipped his radio to his belt and left his lab locking the door behind him. Elizabeth read through the files she had on her desk and sighed to herself, she couldn't help but think about where Sheppard was or if he was even still alive, her train of thought was interrupted as Teyla and McKay entered her office before she could say anything McKay burst out "I have something" Elizabeth and Teyla both looked over at him with a little more hope "I thought you said you have nothing?" Elizabeth raised an eyebrow at him, McKay looked at her and nodded "Yes, yes about five minutes ago I didn't, but on the way over here I thought up an idea to where he might have gone" he began pressing buttons on his pad furiously. Teyla averted her eyes from McKay towards Elizabeth "Well we can use the Stargate to go and find him"
"Well originally that is what I thought, meaning that the solar flare hitting the planet at the same time the gate was dialled would have opened a wormhole somewhere else in the system…" McKay said with a finger raised
Teyla looked back at McKay and Elizabeth cocked her head slightly trying to keep up with the information "Ok so then what?" Replied Elizabeth
"…then I realised that this can't have happened due to the fact that the gate was open on Earth so he is on Earth" McKay waves his free hand around as he explains
"But we know he didn't get to Earth" Teyla replied quickly, a little confused
McKay locked his eyes on Teyla and grinned "Exactly, he didn't get to Earth, but he did in the future."

The guard lowered his weapon and stepped closer towards Sheppard as he lowered his hands
"Well that's not the welcome I was expecting at all" Sheppard shot a look towards the Sergeant and frowned "How can I be dead?"
"Well you were about to come back to Earth from Atlantis, and you disappeared after you stepped through the gate and." Sheppard cut him short
"Whoa wait what do you mean I just disappeared, I am standing here right in front of you" He looked around again as if just remembering his surroundings "And what the hell happened here?" Looking back at the Sergeant
"Follow me, I'll take you to the General" The Sergeant flicked his head up the corridor from which he came "He will explain it all"
After this he started to walk up the corridor Sheppard just behind him, each corridor they had walked down was just like every other room, silent, eerie and littered with debris, expended rounds and paper. After what seemed like a long five minute walk they entered the a room which Sheppard had never seen before again there was signs of life "I still don't see any stars on uniforms" Sheppard said with slight sarcasm
"Through the door, I need to get back with my patrol" The Sergeant buzzed his radio and spoke into it "I have a guest to see the General"
After a short silence the radio buzzed back with a voice on the other side "Understood, the General is on his way out"
The door which stated Z-21 in big black writing slid back and three more soldiers stood behind it, two in khaki fatigues like Sergeant Stone and another in plain green, he was a tall broad man and he definitely fit the description of General perfectly. The General had his eyes locked on to Sheppard and he showed no facial expression
"New General I presume?" Sheppard said, still not receiving a word or any facial movement from him "Colonel Sheppard sir"
"I know who you are Colonel" He looked at his men "Dismissed" They all nodded and they got back to their previous work "Major General John McKay, commander of the SGC and the remaining military forces left on Earth"

"Is that possible? I thought the gate only transported matter from one side to the other and not through time?" Teyla asked a little confused with McKay's announcement.
Without looking up from his tablet he replied quickly "Well yes that is what it is supposed to do, but sometimes something, in this case a solar flare, can cause the gate to malfunction" Now looking up at Elizabeth and Teyla "It happened a few years ago to SG-1…"
"SG-1?" Teyla asked curiously
"A military team back on Earth" McKay dismissed it with a wave of his hand "Anyway, SG-1 were sent back almost 30 years after they stepped through the gate due to a recent solar flare, and to get back they used the same principle by using the next solar flare to go forward in time back to their original time"
"So what are you saying?" Elizabeth asked not seeing where he was going with this
"Well, we could do the same and bring him back" McKay smiled "Only one problem is, we are going to have to wait a long time for this to work" McKay's smile faded slightly
"How long?" Elizabeth raised an eyebrow toward him
"Could be from one hundred to a thousand years, we need to come up with some way Sheppard can predict an upcoming solar flare and use that to return home, that should be easy enough with the Ancient Equipment we have here" McKay sighed and though for a second "We just need to work out a way we can get it to Sheppard"