Disclaimer: None of these characters are mine, I wish they were, but they aren't. This story is has Sparky undertones…..ok Sparky overtones- but if they could do it for Long Goodbye then I can do it for this!


Stargate Atlantis- Sometime in season 3, perhaps the end of the season, maybe a cliff hanger.

A/N: ('thoughts') ("dialogue") ( scene changes). Enjoy!

The Link

Part 1

Rodney McKay and John Sheppard were walking down a deserted hallway in the north pier of the ancient city of Atlantis. Rodney was clearly fascinated in the ancient device, referring to it and then looking around to the dimly lit, damp hallway while John was getting more and more bored.

"So, how much longer?" Colonel John Sheppard asked pulling his P-90 up to his chest looking to Rodney.

"Sheppard I have no idea." Rodney replied with frustration in his voice. "This power source is extremely weak and it is hard to pin down."

"And yet," John countered with frustration in his voice as well, "you saw it in the ancient main-frame."

"Well," Rodney began stopping in the hallway, "even a faint power source coming from the north pier- which I might add- hasn't been checked out fully yet and we've been here for what, two years now and still nothing and-"

"Your point Rodney?" John interrupted.

"What? Oh yes, well, the power source might be faint but it alerted us that something was in this general vicinity because it has always been shut down." Rodney explained starting to walk again.

"Even with the ZPM powering the city?" John asked following.

"Yes Sheppard." Rodney stated with exasperation. "Even with a ZedPM powering the city, it has been shut down."

"Now, why is that again?" John asked, his frustration leaving and enjoyment of tormenting Rodney kicking in.

"Because," Rodney began stopping once more. "If the wraith ever come in greater numbers- like the entire fleet, we will need the full power of the ZedPM to power the shield, maybe even the cloak- or- should it even come to it, submerge the city all together."

"Ah." John replied with a smile. "Of course."

"Honestly," Rodney began turning back to the ancient device in his hand. "I can't believe that-" At the power readings that he was getting, Rodney stopped and began to look around with curiosity.

"McKay?" John asked with some concern, "Have you-"

"Sheppard," Came the voice of Weir over the comm. "How's it going down there?"

"I have no idea Elizabeth," John admitted. "Rodney, how's it-"

"Sh-shush!" Rodney shushed as he continued looking around, referring to the ancient device as well.

"Elizabeth, we're still looking." John responded. "I'll contact you if we actually find something."

"Very well." Elizabeth replied looking around the control room. "Weir out."

"Do you think that McKay will find what he's looking for?" Ronan asked, stepping up to Weir.

"I hope so." Elizabeth replied. "I hope so."

Meanwhile, back in the north pier, John was totally loosing patience with Rodney.

"Now, McKay…" John began but Rodney held up his hand to shut him up.

"This way-" Rodney exclaimed walking down the corridor to his left, John followed however Rodney had only taken a couple of steps when he stopped and turned around and went down the other corridor. "Sorry, this way."

John just sighed and followed Rodney, hoping that soon this litter excursion to the bowls of Atlantis would be over. Lucky for John, they entered an ancient laboratory that was partially functioning. There was a thin layer of water on the floor, but all the equipment seemed to be un-damaged.

"This is amazing." Rodney exclaimed looking at one of the control panels.

"What is this place?" John asked looking around, dropping his P-90 to his side.

"I have no idea, however…." Rodney admitted going directly over to one of the controls at which point his eyes grew wide with excitement. "Oh, my….this is incredible."

"What?" John asked again, "What is it?"

"Rodney to Elizabeth," Rodney began tapping his communicator, totally ignoring John's questions.

"Yes Rodney?" Elizabeth asked back. "What is it? What have you found?"

"You better come down here and take a look at this." Rodney replied, excitement in his voice.

"Why?" Elizabeth asked.

"Because I think that I've found an ancient weapon."

"Really?" Elizabeth asked intrigued.

"Really?" John asked excitedly.

"Yes." Rodney replied to both of them though he was still speaking to Elizabeth. "So you have to come down here, right now."

"I'm on my way Rodney." Elizabeth replied with a smile, then turning to Colonel Caldwell who was waiting around while his crew repaired some of the damage that was taken in the last Wraith battle, she stated. "Colonel, you have the control room."

"Of course."

Meanwhile, back in the control room, Rodney began pushing some buttons and the panel and display began flashing wildly. John didn't take much notice at first, but it was the frantic muttering of Rodney that got him worried.

"McKay….?" He replied with his military nod as he took a position in the middle of the control room, observing everything.

"The weapon is rapidly building up a charge" Rodney admitted turning to face John.

"And that is a problem because?"

"Because if I can't figure out how to discharge it the explosion could potentially destroy Atlantis," Rodney explained, worry evident on his face.

"Well that's just great McKay." John exploded as Elizabeth entered the room and Rodney went back to studying the panel frantically.

"What's going on?" Elizabeth asked, noticing that the tension in the room and the flashing panel.

"Genius here decided to turn the weapon on, and now it's over loading." John explained waking over to Elizabeth

"Shouldn't we get Zelenka down here?" Elizabeth asked, worried now herself.

"There isn't enough time." Rodney stated. "And it's building up a charge," Rodney explained his voice slightly frantic. "It's not critical yet."

"Same thing." John sniped back.

"No," Rodney began not looking at John. "actually there is a- oh no."

"What is it?" Elizabeth asked beginning to move towards Rodney when suddenly a piece of the panel exploded knocking Rodney off his feet and on to his back, knocking the breath out of him.

"McKay!" John exclaimed, running over to his friend to make sure that he was alright.

"I'm alright." McKay stuttered out, trying to draw a breath. "I'm ok."

"John?" Elizabeth stated in fear as she looked over to the machine which was now going critical.

"Elizabeth," John instantly got up and ran to get Elizabeth out of the weapon's range when the display panel turned red and a white light began to shine from a clear crystal ball beside the control panel. "What the-?" John began looking at the light when suddenly there was a bright flash and the light surrounded the both of them. Rodney had to shield his eyes, and prepared for the end to come, however the light died down, and once Rodney realised that he was alive, he breathed a sigh of relief.

"Ok, not a weapon." Rodney muttered to himself as he struggled to get up, at that point he noticed that both Elizabeth and John were unconscious on the floor. "Oh, great," He muttered again. "I am in so much trouble, Rodney to control room."

"Caldwell here, Rodney is everything alright down there? We observed a massive power spike and thought that the weapon had-"

"It's not a weapon Colonel." Rodney interrupted. "I actually have no idea what it was, but you have to get a med team down here right away, Weir and Sheppard are down."

"Of course they are." Caldwell muttered to himself before he tapped his communication device in his ear (his communicator, like all the others) and contacted Carson in the med lab. "Caldwell to Dr. Beckett."

"Yes Colonel." Beckett responded from the med lab in his Scottish accent. "What can I do for you?"

"You can get yourself and a team to the north pier, Colonel Sheppard and Dr. Weir have been exposed to some ancient device and are in need of medical attention."

"On my way." Carson replied, he motioned to the assistants around him and together they geared up and headed down the north pier.

­

Back in the infirmary, Carson was bustling around the two beds which held Elizabeth and John, both were still un-conscious but they seemed to be stable, however the monitors which showed their brain-waves had Carson very concerned.

"What happened?" Caldwell asked, his arms crossed and his demeanour very imposing.

"I don't know." Rodney responded for what felt like the hundredth time as a nurse bandaged up his arm which had been cut when he fell. "At the time, I thought it was a weapon, but when the panel exploded- I have no idea."

"Well at least you are alright Rodney." Carson replied coming over to them, Ronan and Teyla moving closer to Caldwell.

"What do you mean by that?" Ronan asked. "Are Sheppard and Weir going to be alright?"

"I'm not sure." Carson admitted, explaining what he was monitoring to the group. "All the tests but one indicates that nothing is wrong with them."

"And the test that indicates that something is wrong?" Teyla asked moving forward. "What of that?"

"Well, the one test that shows that something is terribly, terribly wrong is their brain-waves"

"What's wrong with them?" Rodney asked concerned.

"They are exactly the same."

"The same?" Caldwell asked, unsure if he heard Carson right.

"Aye, well, they are almost in perfect sync, it will be only a matter of time before they are the same." Carson confirmed. "And I have no idea how to reverse it."

"Of course you don't" Rodney replied jumping off the medical bed. "But I'll go back down there and-"

"I can't let you do that." Caldwell interrupted.

"You don't have a choice." Rodney snapped. "I won't touch the machine again, all I want to do is see if there are research notes. If there are then I will be able to figure out how to reverse the machine."

"And do what?" Ronan asked.

"And undue what ever has been done." Rodney explained. "Listen, I know I've screwed up, so let me fix it. We need them."

"Go." Caldwell stated as he motioned to the door. "Do what you have to do."

"Thank you." Rodney replied appreciatively as he ran out the room tapping his communicator on his way. "Zelenka I want you to meet me…"

For those who were left in the med-lab, they did not hear the rest of what Rodney said to Zelenka, but all of them assumed that he was asking the scientist from the Czech Republic to join him in the north pier. Meanwhile, Colonel Caldwell made his excuse to Carson and went back up to the control room to monitor anything that was happening there. Teyla and Ronan agreed to stay and watch over them while Carson went back to work studying their scans.

It was hours later when the three remaining Atlantean personal left in the med-lab were alerted to Elizabeth and John becoming conscious again. John groaned in pain first and seconds later Elizabeth murmured something an opened her eyes as well.

"Go get Colonel Caldwell." Carson asked Teyla and Ronan before turning back to his patients. "Colonel Sheppard, Dr. Weir?" Carson began as his two patients began to wake up. "Are you both alright?"

"Carson-" Elizabeth began groggily as she sat up.

"What happened?" John finished for her. Carson looked from John to Elizabeth and then to the display that was monitoring their brainwaves and shook his head. "Carson?"

"That's what I was afraid of." Carson muttered looking from one machine to the other.

"Carson," John began looking at Carson with worry. "-what are you-"

"Afraid of?" Elizabeth finished interrupting John. At this interchange they looked at each other and realised themselves what was going on. "You can-"

"Read my thoughts?" John asked looking at Elizabeth and knowing what she was thinking. "How is that-"

"Possible? I have no idea." Elizabeth answered John's unanswered question. "Carson?"

"Your brain patterns are exactly the same." Carson answered looking at his two patients.

"The same?" John asked in disbelief. "How-"

"Is that even possible?" Elizabeth finished again.

"Okay," John stated looking at Elizabeth. "You have got to st-"

"Stop finishing your sentences." Elizabeth finished. "I know, but it's hard to know what thoughts are mine and what thoughts-"

"Are yours." John finished look at Elizabeth and attempting to shield some of his more personal thoughts from her, but from the strange and slightly shocked look on her face, he had the distinct feeling that he wasn't doing so well. "Carson can you fix this?" John asked ignoring Elizabeth for a moment and found that she too was trying to keep her thoughts her own.

"I'm not sure," Carson admitted. "Rodney has gone back to the north pier in hopes to find some ancient research notes that will tell us how to reverse the machine."

"So I guess it wasn't a weapon." Elizabeth began, looking straight at Carson and ignoring John as much as she could.

"Obviously not a weapon." John muttered.

"Obviously." Carson replied with a slight smile.

"Well I feel fine, can't we-" John began when he felt Elizabeth about to speak up. "No- don't say it, we may be linked but I do not want to spend an undetermined amount of time in the infirmary and Elizabeth, I know that you don't want to be cooped up here again." Elizabeth merely sighed and settled back in her bed. "So how about it Carson, can we get out of here."

"I'm sorry, you certainly can-"

"Rodney to Carson." Rodney's voice interrupted over communications.

"Carson here, what is it Rodney?"

"Are the Colonel and Elizabeth up yet?"

"Aye they are." Carson responded. "Why?"

"Because I need to see how far the link goes" Rodney replied.

"Link?" John asked. "W-"

"What link?" Elizabeth finished.

"What link Rodney?" Carson asked.

"The link that is in them." Rodney replied as he sifted through ancient data. "Listen, your scans wouldn't have picked them up, but there is an added energy source in both Elizabeth and the Colonel that is transmitting their thoughts, that's why their bran-waves are the same."

"So, why do you need them?" Carson asked.

"I need them to walk around Atlantis to see how far the link can go." Rodney replied.

"Great." John replied pulling all the equipment off of him and hopping of the bed. "Elizabeth, you stay here and I'll go pay Rodney a visit."

"John-" Elizabeth warned, worried that something would go wrong.

"Don't say it." John interrupted. "I want to get rid of this link as much as you and if Rodney says that this is the only way then-"

"It is the only way," Elizabeth finished again. "I know, but Rodney was completely mistaken when he thought that what it- what ever it was that did this to us- he thought it was a weapon. Do you really want to go back down there?" Elizabeth asked and as John was about to answer she spoke it out loud for him "Of course you do, it's the only way."

"Right." John nodded. "So-"

"Carson, let him go." Elizabeth interrupted looking from John to Carson. "This is the only way to fix this."

"Very well." Carson agreed half-heartedly. "You can go."

"Thank you." John thanked making his leave of the room when suddenly he stopped and turned to Elizabeth and answered her unspoken request. "I will, you know that."

"You know what?" Carson asked looking at Elizabeth as John left the room. "Elizabeth, what do you know?"

"Nothing Carson." Elizabeth replied. "Nothing."

"Alright," Carson submitted. "If you say so."

"I do." Elizabeth replied with a laugh.

Meanwhile, John was making his way to the north pier when Rodney contacted him.

"Ok Sheppard," Rodney began over the intercom. "What I need you to do is talk to Elizabeth, not with words, but with your mind. Keep doing that till you get down here, I have to see how much range this link has."

"I'll keep that in mind Rodney, Sheppard out."

"Colonel." Teyla remarked running to catch up with him. "Wait."

"Hello Teyla." John remarked as Teyla fell into pace beside him. "What sends you down here?"

"Colonel Caldwell asked me to walk you down there," At seeing the look on John's face Teyla explained why. "Just in case there are any ill effects of this link."

"Speaking of," John began. "I'm going to have to concentrate on this link alight?"

"Of course."

"Thank you, now…" John fell silent and began to talk to Elizabeth with his mind.

'Can you hear me?' John asked in his mind.

'Yes.' Came the resonating voice of Weir.

'Can you hear me now?' He asked a couple metres later

'Yes' The voice of Elizabeth answered again. 'I can still hear you John.'

On and on it went until both Teyla and John reached the north pier and the lab that Rodney and Zelenka were working in.

"Can you still hear her?" Rodney asked as John entered the room.

"Just a sec." John stated before thinking to himself. 'How bout now, can you still here me?'

'Loud and clear John.' Elizabeth responded in her mind as her body just stared into space. 'Loud and clear.'

"Loud and clear McKay." John responded with a smile. "Loud and clear."

"Wow." McKay remarked as he looked from the ancient display to his lap top. "I didn't think that the link would travel this far."

"Really?" Teyla asked intrigued.

"Yes, as a matter of fact-" Rodney began when Zelenka cut him off.

"Actually, it makes a lot of sense," Zelenka began. "You see, I believe that the ancients created this link as a means of communicating silently during times of war. They could do it over great distances, like the Wraith, however unlike the Wraith, not just anybody could tap into it, it would only have worked if you had been exposed to that machine as you and Dr. Weir were."

"Then why wasn't I affected?" Rodney asked, trying to poke a whole in Zelenka's theory.

"Because the panel exploded and sent you flying Rodney," Zelenka explained. "You weren't caught up in that light as Colonel Sheppard and Dr. Weir were."

"Ah." Rodney stated in agreement. "Of course."

"Sounds good to me," John stated. 'Hey Elizabeth listen…'

'I know John.' Elizabeth interrupted, her voice resonating through is mind. 'I heard everything.'

"You can hear what I am saying?" John stated in shock out loud.

'Yes.'

"She can hear what we are saying?" Rodney asked in amazement.

"Apparently." John stated. "What does that mean?"

"It means," Rodney began taking a look over Zelenka's notes. "That the link can go further."

"Much further." Zelenka agreed.

"I don't think that this is a good idea." Caldwell stated sitting in front of Elizabeth, John, Carson, Rodney and Zelenka, with Teyla and Ronan sitting beside him.

"Oh come on." John began, not believing that he wanted to test this out.

"Colonel," Elizabeth interrupted. "This could be a valuable tool against the Wraith, think of it, in dangerous situations, plans could be made simultaneously from great distances, mistakes will be minimized in times of battle. Surely you see this."

"Not to mention the scientific value of seeing how the brain works like this." Zelenka put in.

"I don't want to take the risk." Caldwell responded.

"With all due respect Colonel," Rodney interrupted. "Isn't Elizabeth still in charge?"

"No, actually, the moment that she became incapacitated under an alien influence I was put in charge."

"Colonel." John began, his frustration mounting.

"Sheppard, I am in charge here and I say no, it is a matter of health." Caldwell explained.

"Actually," Carson interrupted. "They are perfect health Colonel, the only thing that is wrong with them is that their brains are working on the same frequency, but so far it hasn't done them any harm. I think that you should let them go, as their doctor I don't foresee a problem."

"Thank you Carson!" John replied giving the doctor a thumbs up.

"Well…."

"Colonel Caldwell," Elizabeth began again, her voice much more authoritative. "How can you not take this opportunity to learn more about the ancients how-"

"Very well." Caldwell interrupted, knowing that he would never get a moment's peace until he submitted. "You have a go."

"Great!" John replied with a smile, nearly jumping up from the table. "Who's with me?"

Minutes later, Sheppard, Rodney, Teyla and Ronan were all in a puddle jumper ready to go while Elizabeth, Zelenka and Caldwell were in the control room, ready to monitor things.

"Control room, this is puddle jumper one, ready to launch" Came the voice of John Sheppard over the comm.

"This is the control room, the roof's being retracted and you have a go for launch." Caldwell responded

"Thank you colonel" John replied over the comm.

'John, be careful.' Elizabeth thought, her stomach in knots and her instinct telling her that this was a bad idea.

'Don't worry Elizabeth,' Came the reassuring voice of John in Elizabeth's head. 'I will be, I always am'

'Of course.' Elizabeth responded with a laugh.

"Dr?" Colonel Caldwell asked turning to Elizabeth at the sound of her laughing.

"Yes Colonel?" Elizabeth asked back, a smile still on her face.

"Is there anything that you want to say to Sheppard?"

"Thank you Colonel, but he already knows all I need to tell him and besides…." Elizabeth started, getting slightly distracted by the conversation starting in the puddle jumper. "-we are going to be in constant contact, in fact… he's thinking that it would be nice if the rood would retract." Elizabeth tapped the communicator, knowing that it would be the only way that she would get Sheppard's attention. "John, if you want Zelenka to do something you have to ask him, you can't just think it."

"Sorry." John responded over the comm.. "Hey, Zelenka could you please retract the roof?"

"Right, sorry." Zelenka apologised pushing some buttons. "Sunroof retracting."

"This is puddle jumper one." John replied over the comm.. "We are on our way."

"Very well, good luck, jumper one." Caldwell responded.

"He says thank you." Elizabeth replied with a smile as she turned to face Caldwell.

"Of course he does." Caldwell muttered under his breath before walking away to check on Zelenka. Elizabeth decided to head back to her office and no sooner had she sat down when Carson entered.

"Can I come in?" Carson asked as he hovered in the doorway.

"Of course Carson," Elizabeth replied with a smile, indicating with her hand that he could sit down in the chair opposite her.

"How do you feel?" Carson asked as he took a seat worried that the experiment would backfire.

"Fine." Elizabeth replied with a smile. "In fact…"

"What?" Carson asked worriedly as Elizabeth's sentence trailed off and her eyes grew wide. "What is it?"

"I can see what he sees." Elizabeth whispered in wonder as she moved her hand and stared intently at it.

"Excuse me?" Carson asked, thinking that he had misheard her. "What did you say? You can see what he sees?"

"Well, not really," Elizabeth explained turning her attention back to Carson. "I see my office and you with my eyes and yet I can see- no sense what he sees. It's like a transparent image in front of my mind."

"What does it feel like?" Carson asked, half intrigued and half concerned.

"I don't know." Elizabeth answered her voice soft and distant. "It's hard to explain, but it is- wow- the beauty of our planet- John's awe…wow….this is incredible" Elizabeth stopped and just sent a thought out to John in the puddle jumper. 'Isn't it?'

'Yes it is.' John agreed as he flew the puddle jumper. He could sense the emotions from what Elizabeth saw. Her comfort in her surrounding, her deep respect for Carson, it was truly amazing.

"Colonel?" Teyla asked noticing that John seemed to be spacing out.

"Sheppard?" Ronan asked tapping John on the shoulder and snapping him out of his slight daze,

"What?" John asked slightly confused for the moment. "What?"

"Are you able to fly this ship?" Ronan asked accusingly.

"What do you mean by that?" John asked turning his attention back to flying.

"What Ronan means," Teyla interjected trying to smooth things over, "Is that we were concerned only because you seemed distracted."

"I am not distracted." John insisted. "I am fully focused on flying this ship- it's just that I can see- no sense what is happening around Elizabeth."

"Amazing," Rodney replied looking up from his laptop. "That's amazing."

"It's more then just amazing." John stated, trying to get his team to understand. "And it's more then just sensing what Elizabeth is seeing, I can actually sense the individual energies in the city and on the mainland."

"Really?" McKay asked even more amazed. "Wow, this could actually be something, uh, McKay to Weir." Rodney stated over the comm..

"Rodney, this is Weir." Elizabeth responded in Rodney's ear. "What do you have for me? John and I are still in contact."

"Yes, I know but listen," Rodney explained really excited. "Sheppard says that he can sense the energies of the individuals on Atlantis and the mainland, I want you to see if you can sense our presence."

"Alright." Elizabeth responded back in her office. "Just give me a second Rodney." Elizabeth allowed her mind to travel to the puddle jumper and did indeed sense the individual energies of those in the puddle jumper. "Yes Rodney, I can sense you all. John is flying, you are taking down data, Teyla is just sitting, wondering how her people doing and Ronan, Ronan is fidgeting."

"Really?" John asked Ronan, knowing what Elizabeth said through the link. "You're fidgeting?"

"I am not fidgeting." Ronan responded coldly.

'John' Elizabeth thought frantically as she expanded her senses and realized that something was wrong. 'JOHN!'

'What?' John asked in his mind and then as the alarms went off in the puddle jumped and he realised what Elizabeth was trying to warn him about, he shot out an initial volley, but it did nothing to the Wraith dart. "Oh, Crap. Hold on you guys." John took the controls aggressively fired a couple of shots at the Wraith dart and then took the puddle jumper in a dive as he tried to elude the wraith dart with Elizabeth's panicked voice in his mind.

"What?" Colonel Caldwell asked running into Elizabeth's office at Carson's call. "What is it?"

"It's a wraith dart." Carson explained as Elizabeth just sat against a wall, frozen in terror. "Apparently it's disabled the puddle jumpers weapons."

"Then I'll put the Dedalaus in the air." Caldwell offered making a move to the doorway.

"No." Elizabeth whispered in fear, her voice soft and shaky. "There isn't enough time, if he's going to make it out of there, he's going to have to do it on his own-" Elizabeth's voice caught in her throat as John's adrenaline washed over her almost smothering her.

'John watch out!' The voice of Elizabeth cried out frantically into John's mind. "It's coming around for another pass.'

'I know.' John thought back as he took the puddle jumper into a roll. 'I'm trying.'

'John!' Elizabeth cried out as the Wraith dart hit the puddle jumped with another shot.

"One more hit and we're dead." Ronan stated warningly.

"I agree." Teyla chipped in. "Colonel Sheppard we have to get out of here."

"And go where?" John asked in frustration.

"Sheppard's right." Rodney agreed. "We can't head back to Atlantis because of we do, the wraith will know that we're alive."

"They already know that Atlantis survived." Ronan pointed out as John managed to avoid another shot by the Wraith.

"If they knew, don't you think that they would have attacked with something more then a dart Ronan?" Rodney asked. "Don't you think that they would have come in greater numbers a lot earlier?"

"Perhaps." Ronan stated sitting back in his seat. "But how do you explain this?"

"I can't." Rodney shouted in fear just as John spun the puddle jumper.

"Would the both of you shut up?" John shouted in frustration. "I'm trying to..."

But John never got to finish his sentence. The Wraith dart finally managed to get a shot past their shields and the consol in front of John exploded and he was thrown against the side of puddle jumper and knocked un conscious.

"Colonel." Teyla shouted as she rushed to John's side. "Colonel."

"He's out cold." Ronan remarked as he helped Teyla get John out of the pilot's chair and into the back compartment of the puddle jumper. "Can you drive this thing McKay?"

"Of course I can." Rodney replied arrogantly as he sat in the pilots seat. "At least I think so."

"Do not hesitate Rodney," Teyla suggested from the back compartment. "Just act."

"Alright." Rodney replied, his voice tight with fear, but the sudden beeping of the consol in front of him got him intrigued. "Wait, what is this?"

"Elizabeth," Carson asked worriedly as Elizabeth stiffened up.

"What is it?" Caldwell asked as Elizabeth's eyes grew wider. "Doctor!"

"I don't know!" Carson shouted back at Caldwell before taking Elizabeth's hand. "Elizabeth are you alright?" But Elizabeth didn't respond, she just stiffened more and then went limp. "Carson to med-lab, get a team up here right away."

"This is exactly what I was afraid of." Caldwell stated harshly at the people in front of him. "This is exactly, what I was afraid of!"

"Would you keep your voice down," Carson chastised the colonel. "I have two patients who need their rest."

"Yes, well I want her out of here right away." Caldwell ordered.

"She isn't a wraith." Rodney defended.

"She was in a dart." Ronan countered.

"She told you her story." Teyla defended, agreeing with Rodney.

"And you believe what she said?" Ronan asked. "And what about him, since when could we trust him?"

"Why should we not believe them?" Carson asked, trying to calm Caldwell, Teyla, Ronan and Rodney down.

"She attacked out people." Caldwell offered as an explanation. "That's why."

"Oh for heaven's sake," Rodney sighed out in frustration. "She only fired on us, because we fired on her first.

"That doesn't matter." Caldwell countered. "What does matter is them. What about them? Sheppard was hurt, as was Weir. This link Rodney, has gone so far beyond a simple mental connection. What happens to one, happens to the other, isn't that right Carson?"

"Aye." Carson agreed with a nod of his head. "If Rodney hadn't gotten here when he did, we would have lost them both."

"Really?" Rodney asked, not realising that he was a hero. "I saved them?"

"Aye- the moment I got the Colonel stabilized, Elizabeth stabilized as well. If he had-"

"Would you all stop talking about me as if I wasn't in the room?" John croaked out from the bed.

"Colonel," Carson stated as he rushed to his patients side.

"Sheppard." Caldwell noted coming to the other side.

"Are you alright?" Rodney asked coming to the end of the bed.

"Yeah, I think so…" John replied placing a hand on his head, which was still throbbing severely. "What happened?"

"John," Came a weak voice from the bed next to John.

"Elizabeth?" John asked struggling to get up and see Elizabeth, Carson moved aside and allowed the two of them to look at each other.

"What-" Elizabeth began.

"Wraith." John explained, knowing that much.

"And your team-" Elizabeth asked, but left the question hanging, known that John knew what she was thinking.

"Fine." John assured. "We're all fine, I think."

"Yes Colonel Sheppard." Carson interrupted. "You and your team are all fine."

"What happened to the Wraith?" Elizabeth asked the rest of the team knowing that with this question, John would not have known the answer.

"Actually, surprisingly, not a Wraith," Rodney replied.

"What?" John asked in surprise.

"Really…" Elizabeth stated in wonder.

"Then what was it that attacked us Rodney?" John asked the scientist, hoping to catch him.

"Uh, me." Came a small voice from another hospital bed.

"And who is-me?" John asked, his voice changing in surprise as a small, petite and beautiful human stood in front of him. In his mind, he could feel Elizabeth putting up a wall, but for the moment, he didn't care. "Who is she?" John asked turning to Rodney. "Who are you?" John asked again turning to the girl.

"I am Quitha." The girl replied, her soft golden hair around her shoulders and her ice-blue eyes shining with light. "I am truly sorry for shooting at you Colonel Sheppard, but you must understand, you attacked me first and I thought that you were the Wraith in a new type of cruiser."

"No," John replied with a laugh. "No, we are defiantly not the Wraith."

"I know that now." Quitha replied, her voice soft and kind.

"How did you get onto the dart Quitha?" Elizabeth asked, her instincts telling her not to trust this girl, but her mind telling her that it was illogical to doubt her at this time.

"My entire village was culled," Quitha began, her eyes misting up with tears. "-as was I. When I awoke, I awoke on a hive ship. I watched as all I knew were fed upon by those monsters until I was the only one left. When my time came, the Wraith could not feed upon me.' Quitha closed her eyes and pictured the image of the wraith placing his hand to his chest and roaring in anger. "Once he realised that he could not feed upon me, he left." Quitha continued pulling herself out of the horrible memory. "After that, I fled and found someone who could help me."

"And who might that be?" John asked, intrigued.

"Me." Came the voice that John recognised very well.

"Ford?" John asked in surprise as Lieutenant Aiden Ford came into his line of vision. "Ford!"

"Lieutenant!" Elizabeth remarked in surprise.

"Ma'am, Sir." Aiden acknowledged respectfully. "I'm sure that you're wondering how I got off that Wraith hive when it exploded."

"The thought did cross my mind." John replied indicating that he wanted Aiden to continue.

"Well," Aiden began remembering what had happened to me. "I managed to make my way to the dart bay just as the ship was beginning to explode. I got in one and surprisingly it's shields protected me. However, it's auto-pilot engaged, and I found myself entering a new hive ship. They put me in one of those damn cells and tried to get information out of me. Of course, I got too weak to answer, and they finally decided to feed on me. But they couldn't, there was still too much enzyme in my body. They drew it out of me that I had been attacked by a wraith and his enzyme had been sustaining me, that's when they gave me the deal" "We will give you the enzyme you require, as long as you provide us answers for our questions." The wraith's voice haunted Aiden's head, but he continued with his story. "Of course I didn't agree. I would have rather died then given up the secrets that we had worked so hard to keep, but eventually I got to a state of delirium and I agreed. I told them that I was the lone survivor of the Atlantis attack and that I was the only one who had managed to get through the gate as it exploded, with the wraith attached to me. The wraith died, and I got the enzyme."

"And they believed you?" Elizabeth asked in awe.

"Yes ma'am." Aiden replied rather pleased with himself. "I told them that once I got the Wraith off me, I tried to dial Atlantis but that the last chevron wouldn't engage. That convinced them that you had been destroyed. I then told them how I had been a rouge fighter, that I had been killing their kind for their enzyme. This they didn't like, and while they kept giving me what I required to survive, they began to cut down my dosage."

"That's when I found you." Quitha pitched in.

"Yes, Quitha came by and together we made it to the dart bay. I was too weak at this time and told her what she needed to do to fly the ship." Aiden explained.

"Really?" John asked, surprised.

"Yeah," Aiden confirmed. "She got into the ship, beamed me up and we headed to Atlantis."

"And when you attacked me," Quitha continued. "I panicked, I forgot that Aiden had told me that I should expect to be attacked, it was only after you started to run away that I realised who you were and I remembered what Aiden told me and I hailed your jumper and explained who I was."

"That's where I come in." Rodney interjected. "After you were rendered unconscious, I successfully got us back to Atlantis with Quitha and Ford in tow."

"I am truly sorry." Quitha apologised.

"That's quite," Elizabeth began.

"Alright." John finished his voice calm and quiet. "Lieutenant?"

"Yes sir?" Aiden asked jumping to attention.

"Good job back there." John praised.

"Where sir?" Aiden asked, not knowing what John meant.

"On the hive ship, you watched out backs." John explained, with a smile on his face. "Good job, thank you."

"Thank you sir." Aiden thanked. "You're welcome sir."

"Now," John stated, changing the subject "Why-"

"Am I here?" Elizabeth finished. "I remember feeling immense pain, and then- nothing."

"I believe that Carson can explain that." Caldwell interjected.

"Aye." Carson agreed. "The energy that was between you has been stretched to the limit. When Colonel Sheppard was rendered unconscious, it snapped and you Elizabeth felt the result."

"So that's why I fainted." Elizabeth stated, understanding.

"It was my fault?" John asked, slightly taken aback that he had done something to cause Elizabeth pain.

"Indirectly." Carson explained. "The connection isn't gone, it's just immensely weak now- that means that, well, Rodney?"

"Which means," Rodney explained, his voice grave. "that the two of you will need to stay in extreme close proximity for the next little while."

"How close?" Elizabeth asked, curious to know.

"I'd say, that if you get anymore farther apart then you are now, you'll both die." Rodney explained.

"Die?" Elizabeth asked in horror.

"Rodney," John warned. "You have to fix this- not that I don't mind spending time with you Elizabeth-"John stated, putting Elizabeth's objections about being not wanted. "-it's just that we have out jobs to do."

"I know." Rodney stated.

"So fix it." John ordered. "Put us back through the machine, reverse what happened."

"I can't." Rodney denied.

"Why not?" Elizabeth asked, her like John not understanding why Rodney just couldn't put them through the machine again and reverse the connection. 'Not that I actually want the connection gone.'

'Really?' John asked, looking at Elizabeth with confusion in his eyes.

"Are you two listening to me?" Rodney asked, noticing that Elizabeth and John were no longer paying any attention to him.

"Sorry." Elizabeth apologized, closing her mind off to John.

"What were you saying?" John asked.

"I was saying, that this machine was used for long-term reconnaissance between the front line and Atlantis." Rodney explained. "I can't reverse it because the machine wasn't built for that, in fact the Ancients stopped using it."

"Why?" Elizabeth asked, trying to keep her mind off John.

"Because the ancients found that the device was addictive." Carson explained for Rodney.

"Addictive?" John asked in horror.

"Don't worry," Rodney eased. "The ancients found that to keep the connection, they had to be continually exposed to the machine, that's how they found it addictive, and they began dependant."

"Will we be like that?" Elizabeth asked. "Will we be dependant?"

"No." Rodney confirmed. "From everything that I've read says that one dose will wear off in about twelve more hours at the most. The point is, we should permanently lock that room to prevent anyone getting addicted"

"Agreed." Elizabeth replied nodding.

"Agreed." John replied as well.

"Colonel Caldwell," Elizabeth stated changing the subject. "You are in charge until we are back to normal."

"Of course." Caldwell agreed. "Come on everyone, we have to get back to duty, the wraith might be headed our way"

"What?" Elizabeth asked in alarm.

"The Wraith are headed our way?" John asked, in horror. "How?"

"They aren't," Aiden insisted. "Jeez how many times do I have to say this, they think that Atlantis was destroyed."

"Yeah?" Ronan asked, "And how do you know that?"

"Well, I was their captive for months," Aiden stated. "I think I would know, you believe me sir, don't you?"

"Of course I do Ford," John agreed. "But just suppose for a moment that a hive ship followed you and Quitha here,"

"They didn't." Quitha insisted.

"Yeah," Aiden agreed. "I think we would have known if the Wraith had followed us."

"All I'm saying is that if –"

"Actually, you were saying suppose." Rodney interjected.

"Rodney-" John warned.

"Sorry." Rodney apologized.

"What the Colonel is saying Lieutenant," Elizabeth interjected trying to keep the situation calm. "-is that we should let our people do the jobs that have been assigned to them in order to keep us all safe."

"Our people ma'am?" Aiden asked, slightly taken aback.

"Well," Elizabeth began with a smile. "You are Lieutenant Aiden Ford, are you not?"

"Uh, yes ma'am." Aiden agreed.

"Well then, the personal of Atlantis are your people as well, after all-" Elizabeth continued with a smile. "You did come here from Earth with the rest of us three years ago, therefore you belong here with us."

"Yes ma'am." Aiden replied with a smile. "Thank you ma'am."

"Oh!" Carson interjected moving towards Elizabeth and John. "You'll both be pleased to know that the Lieutenant is almost completely weaned off the drug."

"Really?" Elizabeth asked intrigued.

"How?" John asked.

"Well, the Wraith were cutting down my dosages of the enzyme." Aiden explained. "They wanted to kill me and be fulfilled knowing that all Atlantis personal was destroyed, but they couldn't feed on me how I was. They were patient, and they gave me smaller and smaller dosage until Quitha saved me." Aiden looked over at the young beautiful women and smiled and was pleased when she smiled back.

"What Enzyme I have left will be more than enough to wean him off the rest." Carson responded with a smile.

"Excellent." Elizabeth commented. "Colonel Caldwell-?"

"Yes Doctor?" Caldwell asked coming up beside Elizabeth.

"With our sensors out of commission due to that virus, how are you going to determine if the wraith are coming or not?"

"I think it would be best if we took the Orion and the Dedalaus to check it out." Caldwell suggested.

"That'll leave just a few personal on base." John pointed out.

"That's right," Rodney pointed out, worried now. "What if something happens while the two ships are out there."

"Rodney, what are the odds that the Wraith or another enemy will attack when they're gone?" Elizabeth asked, trying to calm her own fears as well as Rodney's.

"Uh, quite slim actually." Rodney stated, knowing that he would be defeated.

"Alright," Caldwell assured getting everyone's attention. "Let's go people, we've got work to do."

"Uh- Zelenka and I will remain behind," Rodney began. "There are a few things that will need doing from this end."

"Very well." Caldwell agreed before motioning to everyone to leave.

"Come on Quitha," Aiden replied taking Quitha by the hand. "I'll show you the rest of the city."

"I'd like that." Quitha responded with a smile and followed Aiden out of the infirmary.

"There's something about Quitha that I just don't like." Elizabeth muttered to John once Ford and Quitha were out of the room.

"Oh, come one Elizabeth," John stated with an exasperated sigh. "She doesn't seem that bad."

"Seem?" Elizabeth asked with a hint of hurt in her voice. "Or look."

"Elizabeth," John replied, his voice a mixture of apologetic shock. However Elizabeth didn't respond she just rolled over and attempted to fall asleep, all the while praying that John couldn't hear her thoughts- which for the moment, he couldn't.

"And this is the control room." Ford stated as he lead Quitha into the control room.

"I know." Quitha stated with an evil look in her eye as she pulled out a mini gun and shot all who were around her. Rodney was first and he managed to hit the lock out button before he was hit. Quitha hit a button on bracelet that she had around her wrist and the clear jewel began glowing purple and green. She noticed Rodney and with a growl, Quitha shoved Rodney off the consol and attempted to get it up and running. After several moments, she growled again and left to get the only people still awake that could help her complete her goals.

They had been silent for what seemed like hours, however John knew that it had only been thirty minutes or so. Carson had disappeared on what was called a medical emergency and he ordered Elizabeth and John to stay put while he left. Elizabeth and John were now alone, and he was still feeling guilty over what he said, and he got up the courage to bring up the subject with Elizabeth.

"Elizabeth?" John asked sitting at the edge of his bed, looking at Elizabeth's back.

"Yes?" Elizabeth responded, not turning to face John.

"Listen, I just wanted to-" John never got to finish his sentence because it was cut off by the sound of an explosion.

"What was that?" Elizabeth asked with a start as she sat up in her bed and looked frantically at John.

"I have no idea." John admitted reaching for his radio. "But I'm going to find out….Sheppard to Caldwell, come in Caldwell." John waited for a moment but only got static. "Sheppard to Rodney." John waited for another few moments but again got nothing but static. "Teyla? Ronan? Zelenka? Ford?" Each name he called he waited, but received nothing but static. "This is Colonel Sheppard to any Atlantis personal, please respond."

"Sir," A lieutenant whom Sheppard knew was new responded; his voice frantic and gunfire going off in the background. "It's the-" The Lieutenant was cut off by more gunfire and the line went static.

"Oh, this is not good." John muttered to himself getting out of his bed and as he turned towards Elizabeth. "I'm going to see what is going on."

"Not with out me your not." Elizabeth responded as she too got out of the bed.

"Elizabeth, it's too dangerous, I'm not about to-"

"John." Elizabeth soothed. 'The link.'

'Oh' John thought, slightly embarrassed. "Well we'll hit the armoury first. But stay close." John ordered as they headed towards the door. "I don't want you too- Quitha! What a pleasant surprise, we were just going to see what the explosion was- um"

"Stay where you are." Quitha interrupted as she moved forward with a hand gun, causing John to bump into Elizabeth. "And be silent."

"John," Elizabeth stated warningly, hearing the change in Quitha's voice. "She's a-"

"Wraith." John finished, feeling completely stupid because Elizabeth had sensed something wrong and he hadn't. "I figured that out."

"You are observant." Quitha responded, her voice changing even more into a Wraith, and her features changing too. "Now, you-" She began, pointing to Weir. "-will come with me. And you," Quitha continued pointing to John. "Will go with them."

"And who might-" John began but stopped when he saw two large Wraith soldiers come up behind Quitha with large stunners in their hands. "Never mind." John muttered looking back at Elizabeth.

"Be silent." Quitha ordered. "And come with me." She moved to grab Elizabeth but Elizabeth jerked away just as John intercepted them.

"She can't." John stated moving Elizabeth behind him.

"And why is that?" Quitha asked, looking most displeased.

"We are linked together." Elizabeth explained standing beside John. "Our minds our linked together and if we are separated we will die."

"How is this possible?" Quitha asked looking from John to Elizabeth.

"It wasn't intentional." John defended, not liking the look that Quitha was giving them.

"No, it wasn't." Elizabeth agreed. "We were exposed to a device that was created by the Atlanteans. That is what caused the link."

"Very well." Quitha stated, not looking happy. "You both shall come with me." Quitha exited the door frame and allowed her two foot soldiers to pull Elizabeth and John into the hallway. Quitha then took the lead and they began walking.

"If I may ask," Elizabeth began shortly after leaving the infirmary. "Where are we going?"

"To your control room." Quitha answered not looking back at her two prisoners.

"And why are we going there?" John asked catching up to Elizabeth and walking beside her.

"Because we are locked out of the system, and I need the two of you to get us into the Atlantean mainframe." Quitha answered.

"And if we don't do what you ask?" Elizabeth asked, hoping that the consequences wouldn't be too dire.

"Then I will kill all of the personal left on this base," Quitha explained. "After which I will feed upon one of you, and watch as the other dies."

John and Elizabeth just looked at each other worriedly and knew that they would need a miracle to get out of the situation that they found themselves in.

A few minutes later, John and Elizabeth were heading towards the control room and they were silently trying to figure out a plan to regain Atlantis from the Wraith.

'John," Elizabeth thought.

'Elizabeth,' John responded, keeping his head straight like Elizabeth was doing.

'The link is getting stronger.'

'Yeah,' John agreed. 'I noticed that- why do think that is?'

'I have no idea,' Elizabeth admitted.

'This could come in handy. We could-' John thought excitedly

'We have no idea if we will be able to test this- us dying will not be a good thing for us or Atlantis. We defiantly do not want the wraith to get to Earth.' Elizabeth thought back quickly.

'Right,' John agreed, mentally kicking himself for being so stupid. 'But he have to something.'

'I know.' Elizabeth agreed.

'Maybe if we-' John began when suddenly there were shots fired at the wraith. 'What the-?' More shots were fired and John pulled Elizabeth to the ground to protect her.

"Are you two alright?" Came a familiar voice.

"Ford?" John asked looking up.

"Are you alright Colonel?" Aiden asked again watching as John and Elizabeth shared a look.

"We're fine." John replied looking from Elizabeth to Aiden and then to Elizabeth again, who in turned looked at her.

"Good," Aiden stated relieved. "-let's go."

Minutes later John Elizabeth and Aiden were still making their way through the city.

"What happened?" Elizabeth asked as they were walking away.

"Why didn't you kill the wraith?" John asked, thinking that his question was more pressing.

"It wouldn't have made a difference Sir," Aiden explained. "They culled an entire planet before coming here, nothing short of blowing them up will stop them now."

"I see." John stated, not liking where this was going.

"Lieutenant, what happened?" Elizabeth asked, wanting an answer to her question.

"It was Quitha ma'am." Aiden explained. "She tricked me, I thought that she was a human, but she's a-"

"Wraith." John interrupted. "Yeah, we kinda figured that out."

"Yeah," Aiden agreed. "I did not see her coming, she knocked me out."

"The question is," Elizabeth began. "- how are we going to stop her?"

"Oh, we are going to have to stop a lot more then just her ma'am." Aiden replied solemnly and let John and Elizabeth to a window that over looked the city where they saw the most horrible sight. There above Atlantis were about twelve hive ships that they could see and both John and Elizabeth knew that there were probably many more around the city.

"Dear God." Elizabeth whispered walking towards the window.

"This could be a problem." John whispered joining Elizabeth at the window.

"A big problem." Elizabeth confirmed.

"Come on," Aiden interrupted. "We have to keep moving."

"Right." John agreed and slowly he led Elizabeth away from the window and they followed Aiden through the city.

While John, Elizabeth and Aiden walked around the city trying to get weapons, the rest of the senior staff awoke in the cell that they had held their Wraith prisoners in.

"Rodney, Rodney?" Teyla called shaking Rodney and trying to get him awake.

"McKay." Ronan shouted which caused Rodney to jump up.

"Huh-? What?" Rodney asked jerking awake.

"Are you alright?" Teyla asked concerned.

"No-" Rodney admitted putting a hand to his head. "Ugh- what happened?"

"The Wraith." Ronan explained helping Rodney to sit up.

"Really?" Rodney replied in shock, having a moment of temporary amnesia.

"Yes," Carson agreed. "It was defiantly the wraith, the marks on Lt. Tannis were un-mistakable."

"But who-?" Rodney asked in shock and fear. "How-?"

"I believe it was Quitha." Teyla replied solemnly.

"Or Ford," Ronan suggested.

"No," Zelenka interrupted. "It was defiantly Quitha."

"And how do you know that?" Ronan asked.

"No," Rodney interrupted. " Zelenka's right- Ford had nothing to do with this."

"And you know this McKay because….?" Ronan asked.

"Because I was in the control room when she turned on us, I was able to lock out the mainframe before I was hit- and Quitha attacked him first, then all of us." Rodney explained clearly quite proud of himself that his memory had returned.

"Then what happened to Lieutenant Ford?" Carson asked.

"I have no idea." Rodney admitted. "But I do know that Ford look absolutely shocked when the Wraith stunned him, he can't be working for her."

"Hey Ford," John began as they left the armoury. "Can I ask you a question?"

"Go ahead sir."

"I assume that everyone on Atlantis has been locked up?" John asked, trying to piece together what was happening and how it had happened.

"I think so sir," Aiden explained. "They are either in the cell or locked up in their rooms, before I found you I went through the personal quarters and heard some banging but neither I nor those inside could get the doors working….the senior staff seem to be in the cell because non of them were in their rooms."

"Alright," John began, trying to put things together. "So how did you escape?"

"Well sir," Aiden began, "-when Quitha stunned me, it didn't completely work. I was totally conscious when I fell, but I was almost totally paralyzed, but it wore off quickly and while Quitha started dragging people away, I managed to drag myself under a control consol where I waited while she was letting Wraith come into the city. When she finally left the gate room unguarded, I was able to escape."

"But that doesn't explain how the hive ships were able to circle Atlantis in such a short time." Elizabeth began. "I mean our sensors were damaged, but even in their damaged state they would have picked up that many ships."

"Actually it does," Aiden began again. "See- last time they attacked, they sent meteors to disable our mines, which also affected our sensors, now McKay said that every 100 years or so, Atlantis gets hit with a severe meteor show, the Wraith would know that because of the first siege with the Atlanteans, so they just waited till this meteor shower came and waited till it had passed through our system then, knowing that our sensors would down not only from the shower, but the virus which I hear was from a wraith module- they must have banked on the fact that we would have problems getting it up and running again so they've been waiting."

"But that was weeks ago." Elizabeth pointed out.

"I know, that means that the Wraith have been planning this for a long time ma'am" Aiden finished.

"We have to finish them off once and for all." John stated as they kept on walking.

"Yes," Elizabeth agreed. "But how? Our drug doesn't work- we can't get it to spread fast enough though their systems- and it's not like we can do anything now especially with the Orion and Dedalaus out there."

"What about the Orion and Dedalaus," John thought, speaking aloud. "What if we could get a message to them?"

"Sir, I doubt that even they could take out that armada." Aiden pointed out.

"Really?" Elizabeth asked shocked. "I thought that the Orion had a whole arsenal of drones."

"True," John agreed. "But most of them are in the lower sections of the city along with the ones that we brought from the planet with the tower for the chair…."

"The chair!" Elizabeth exclaimed excitedly.

"What chair?" Aiden asked confused.

"We have a chair like the one in the Antarctic base." Elizabeth began.

"And now, with a ZPM," John continued.

"We'll be able to power it up and save the city." Elizabeth finished.

"Now we're talking." Aiden said with a laugh.

"Come on," John interjected. "We need to get down to the chair room as soon as-" John was cut off by the sounds of the city alarm system going off. "Now, what?"

Meanwhile, the control room was swarming with wraiths who were trying to unlock the cities main-frame when suddenly they found themselves trapped.

"Oh no…" Elizabeth whispered, listening as the bulk heads around them started to close.

"Run!" John ordered and led the way to the chair room with Ford right behind him and Elizabeth bringing up the rear when suddenly the bulkhead behind them separated them.

'John' Elizabeth cried in horror, watching through the glass of the door as Aiden and John got stuck in a small room with stairs leading down.

"Elizabeth.' John thought in horror as he ran towards the bulkhead.

'John, now what are we going to do?' Elizabeth thought worriedly.

Meanwhile, down in the cell room, those trapped in there were beginning to react to the alarms that were sounding.

"Oh, now what?" Rodney asked standing up.

"I-" Zelenka began, only to be cut off by Rodney.

"Shhh!" Rodney ordered and everyone fell silent and heard the horrible sound of bulkhead doors closing. "Oh no…"

"What is it?" Ronan asked confused.

"The city is locking down." Rodney admitted putting his hands to his head trying to think.

"What?" Teyla asked in horror.

"How is it doing that?" Carson asked.

"Listen," Rodney interrupted. "Zelenka and I planned for this- in the unlikely eventuality that the Wraith would get this city intact, we created a virus to act like a contagion, so if the Wraith started messing around with Atlantean controls-"

"Atlantis would think that a contagion has been released into the city." Zelenka finished.

"Exactly." Rodney stated.

"And what will this do exactly?" Ronan asked.

"This will ensure that all the wraith in the city will be trapped where they are and that no wraith will be able to beam in." Zelenka explained.

"And how is this a problem?" Ronan asked again.

"This is a problem because Elizabeth and Sheppard, who are our only hope of getting out of here will be trapped as well." Rodney explained.

"If they haven't been culled yet." Ronan stated as he sat down on the bench.

"Let's think positively shall we?" Carson interjected.

"Oh they're alive." Rodney stated grimly.

"How can you be sure?" Teyla asked.

"Well I can't-" Rodney admitted. "But the Wraith seem to want us to actually see the destruction of Earth, which is probably why all of us here are still alive- and besides with the computers locked out Quitha will need them to override the system."

"Right." Carson agreed. "But what if they were separated?"

"Oh this is a problem." Rodney muttered. "Oh, this is so not good!"

"So what do we do?" Ronan asked standing up again.

"Nothing." Rodney stated fear and anger lacing his voice. "Absolutely nothing! We are trapped in here and Elizabeth and Sheppard are out there! If they have been separated by more than a single bulkhead then it is only a matter of time until they die and then our only hope of sending a message to Caldwell, taking back the city and saving earth will be gone. Completely gone."

After Rodney's outburst everyone in the cell was deadly quiet.

"If that is so," Teyla stated after a few moments of them all looking at each other. "Let us pray to the ancestors to ensure that they are alright."

"Elizabeth!" John called pounding on the door.

"John!" Elizabeth replied, pounding on the door as well.

"Sir," Aiden interrupted. "We've got to-"

"Ford just go." John ordered. "Try to contact our ships, or even better go find Rodney so he can fix this damn door which I know is his problem."

"Sir I-"

"Go Ford!" John ordered again. "That's an order."

"Yes sir- but" Aiden began again.

"Aiden!" John exploded causing Elizabeth to jump back slightly at the emotion in his voice and his mind. "I can't leave her."

"Understood sir." Ford replied and after a salute, he scurried down the stairs to find Rodney.

"Elizabeth?" John asked turning his attention back to the door. "Are you alright?"

"Yes," Elizabeth confirmed. "I think so…..but how am I going to get out of here?"

"I don't know," John admitted placing his hand on the transparent coloured glass and watched as Elizabeth did the same. "Ford's either going to contact our ships or he's going to go bust Rodney's butt out of where ever he is and get him here to help us."

"John, we have to get me out of here." Elizabeth stated. "We have to go stop the wraith, if they manage to override the lockdown…"

"I know," John interrupted thinking the same thing as Elizabeth. "I just don't know how."

"I know that you have to arrange the crystals in the panel beside the door in a certain order." Elizabeth offered.

"Do you know what order?"

"No." Elizabeth admitted. 'But I should, I've been in Atlantis for three years now.'

'Don't blame yourself.' "Do you know if we have to do this on my side or yours?" John asked again.

"No," Elizabeth admitted again.

"Well then-" John began stepping back to look at the panel beside him. "Let's see if I can…." But Elizabeth never heard what John had said because his words were cut of by the sound of Wraith stunners and P-90 bullets being fired.

"John?" Elizabeth asked in fear when suddenly she jumped because there were shots being fired at her. Elizabeth quickly ducked and managed to kill the two Wraith that were struggling to get though the partially open bulk head. Once they were sufficiently dead to Elizabeth she shoved them back into the other sealed section, closed the bulkhead and shot the panel with the crystals to stop them from sneaking up on her again. Once that was done she was back at the other door that separated her from John in a heart beat. "John? John?" Elizabeth asked out loud fear gripping her heart each moment that he didn't reply to her, she pressed her face to the glass in an attempt to see him, but she couldn't see much of anything- which greatly worried her.

'JOHN!' She cried out frantically with her mind but met nothing. 'I'm not dead, He can't be dead, unless-' Elizabeth stopped that strain of hopeful thought. '-unless the link has worn off.' "Oh my god." She whispered to herself in horror. 'How long has it been? Oh god, JOHN!' Elizabeth cried out in her mind and out loud! "JOHN!" But there was no answer and Elizabeth knew that she was wasting precious minutes but her brain couldn't get an idea together

Meanwhile Aiden was running though the hallways, opening bulkhead doors "Thanks to McKay" he muttered, freeing some Athosians and as the new party was making their way to the main cell they became cornered with Wraith

Meanwhile aboard the Dedalaus and Orion, both of which were badly damaged and dead in the water, Colonel Caldwell was trying to get a bad situation under control

"Get those systems up and running, we have to save Atlantis." Caldwell ordered and nodded grimly as various technicians and scientists replied "Yes Sir". Caldwell then turned back to the task of contacting Atlantis. "Caldwell to Atlantis, come in… Atlantis please respond…."

Meanwhile, Elizabeth was still frantically calling John's name both through the door and over her communicator (neither of which seemed to be working).

"John! John!"

End of Part 1

A/N- Alight, so not the update that I am sure you all wanted, but as I was writing part two, I realised that it would be too long so I went back from my original split point. This is where it was meant to end, here- with a cliff hanger- so enjoy. Hopefully Part II will be up in a week or so I hope you like the new part. Part II will be out soon. I swear