A/N-Hey everyone! So, due to auStraliS23 telling me that the time line is off, which now that it has been pointed out I can clearly see, I've changed a few things in the story, so I urge all who are waiting for the next chapter to read this one again first. But, just in case you don't understand a few things, I'll explain the time line and whats going on.

I've changed it to where Woolsey is in control of Atlantis, but Col. Caldwell has come on the Deadulus, as the Deadulus often visits, and has brought Col. Carter and Kavanagh with him, both for separate reasons, Col. Carter for a mission on a planet without a Stargate that she volunteered to lead, and Kavanagh for things on the Deadulus. I've watched all the Stargate Atlantis episodes at least 2 or 3 times, but I've just started watching them again after a year and I'm still at the beginning, so i completely forgot that Dr. Grodin dies, so, just for this story, we're going to pretend that he's still alive. I'm really sorry for the confusion, hopefully this clears it up a bit!

Disclaimer- I don't own Stargate: Atlantis, MGM, or any of these characters, so please don't get mad or sue me or any other strange legal stuff that would make me incredibly unhappy!

Something wasn't right-that much he could figure out by the fact that there were no lights on in the Jumper, except for the radically blinking lights on one of the crystal boards, and that he couldn't remember how he had gotten on the floor. Actually, he couldn't remember why he was even in the Puddle Jumper. The last thing he remembered was him and Jennifer getting ready to go to the weekly movie, which was in the early afternoon that time. They had just walked out of the room, when he remembered that he had forgotten his ear radio and he had gone back to get it, telling her to go on and that he would meet her in a few minutes, and then…nothing. He groaned as he sat up. His back, both of his sides, right shoulder, head, left wrist, and left lower leg hurt really badly. He tried to stand up by grabbing on to the pilot's chair. He got about half way up when he put weight on his left leg, and fell down because of the pain. He tried to take slow, steadying breaths. He tried to stay calm. But he wasn't usually calm, and the fact that he couldn't remember what had happened made him incredibly anxious, his over-imaginative brain starting to spout out stories, hypotheses, and ideas at a growing rate of ridiculousness.

I wonder where John is. The thought came out randomly, but it made him stop for a moment. For the first time since he had woken up, he really tried to take in his surroundings. The first thing he noticed was that the Jumper was in bad shape. No, it was in worse than bad shape, it was in horrible shape. The front of the Jumper, where the pilot seat, co-pilot seat, and the two independent seats behind them were, had several blown consuls, the co-pilot seat and the one behind it were both missing their upper half's, there were black spots all over the place, and he couldn't see out the main view-point. He looked toward the back to find that the door, also covered in black spots that looked a lot like Ronan's blaster's shots, was closed. He sighed and tried to get up again, this time succeeding in sitting in the seat behind the pilot's. He gasped loudly as the pain in his right side grew considerably. He looked down to see what was wrong and immediately wished he hadn't. There was blood seeping out of a wound that was obviously a knife wound. He grimaced again, but didn't make a sound since there was no one there to complain to or to see him in a weakened state. There were only three reasons he ever complained about a wound. One: To make people understand just how horrible (no matter if it was exaggerated) it was. Two: To distract people from any pain he might be in. Three: To distract himself from the pain. Although, what only certain people had ever noticed was that he only complained on the things that weren't immediately life-threatening. This wound, he could tell, would eventually be a real problem. He would probably complain if there were people around, but would stop when it started to hurt too much.

He slowly staggered forward and cried out in pain. Oh forget it, he thought, I'm going to complain anyway.

"Well, look at that. Can't even stand because of the pain. And look at that-no one's here to even notice. Just going to have to get myself out of this alone. Again. Hope I'm not underwater," He shuddered at the thought, "Where is everyone, anyway?"

He kept muttering to himself as he walked up to the consul beside the doors and pulled out the protective covering. He looked at the crystals. They looked just fine to him. There weren't any visible burn-outs, no signs of being shocked in any sense, no reason as to why they shouldn't work. But he knew better than to just look and decide. He wasn't the head of the science department in the ancient's lost city, Atlantis, or the self-proclaimed, proved, smartest man in two galaxies, for no reason. He pulled out a few of the crystals from different areas and looked at them closely. He really wished he had his handheld computer terminal with him. He looked around the room, just in case. He couldn't see it anywhere. He turned back the crystals and began to examine them one by one.

A while later, he couldn't tell exactly how long, he had examined almost all of the crystals, when he found something that greatly disturbed him. The point of the crystal he was holding was slightly burned, but only slightly. There were only two ways that could have happened. Either someone took it out and electrified or shot the very point of it, or someone shocked the entire crystal board on the other side of the doors. Since he thought that the first one was highly unlikely, his logical mind immediately flew to the other. Someone had shocked the other side, and the shock, most likely electrical or perhaps made by some sort of a blast weapon, had traveled through the system. Some of it had been powerful enough to hit the other side, while the rest just stayed inside the other door-controlling crystal board. That could only mean one thing.

He was stuck.

John Sheppard sat down in one of the conference room seats wearily. They had spent the last ten hours searching for Rodney McKay, the head scientist in Atlantis, and also a member of John's team. It had taken them five hours to realize that he was missing. After the movie, Jennifer had been worried that he had never showed up, but the others just thought that he had found something important to do and had forgotten what he was supposed to be doing. Jennifer had looked disappointed, but had been quickly distracted by a medical emergency in one of the science labs. A consul had blown up, and Groden had gotten some pretty bad burns. As everyone went off to do their usual things, Rodney had been quite forgotten. However, after he didn't come to the conference room for their scheduled meeting with Richard Woolsey, Samantha Carter, and Col. Caldwell, they had radioed him. After getting no response, they had gone to his quarters, he wasn't in there, he wasn't in any of the science labs, he wasn't in the infirmary, gate room, or any corridors that they had looked in. They had mounted a minor search after that, and then a full out search. About two and a half hours later, someone realized that there was a Jumper missing. The gate hadn't been activated, so they got the Dedaulus, which had been in orbit around the planted for the last three days, to check the surrounding area, while John and a few others with the ATA gene went out in other Jumpers to search the mainland and the rest of the planet. The search turned out fruitless, and then they really got worried. They had kept searching everyone, under water being one of the main places they looked, since Rodney had been trapped under water before, but even after all that time, they had still come up with nothing.

Richard Woolsey had called a meeting of SGA1, Col. Carter, Col. Steven Caldwell, Dr. Radek Zelenka, Major Lorne, Dr. Jennifer Keller, Dr. Carson Becket, who was in this week, and Dr. Kavanagh. Col.'s Caldwell and Carter and Dr. Kavanagh had come to Atlantis on the Deadulus three days before, after Carter had gone on a mission on a planet without a Stargate in the outskirts of the Milky Way after the Deadulus, on a previous trip, had detected high readings of Naquada. Both Colonels had volunteered readily to help look for Rodney, and Kavanagh had grudgingly agreed after being stared down by Carter and Ronan. Once everyone had gathered in there, Ronan in excessive annoyance because he believed that they would be better off searching for Rodney, the meeting started.

"Okay, everyone, what do we know so far?" Woolsey started off the meeting.

"Nothing much. We've been searching for ten hours and all we've been able to determine is that one of the Jumpers is missing, Rodney isn't, as far as we know, in Atlantis, on the mainland, anywhere on Lantea, or in the surrounding space." John said his voice calm despite his worry.

"We have run several scans of the surrounding area, both under water and above, but we have found nothing." Dr. Zelenka's accent came out heavier than usual as he spoke due to his greatly enhancing worry and fear.

"How far could he have gotten in the Jumper in five hours?" Teyla asked, her brow furrowed in concern. Dr. Zelenka considered this for a few moments before answering,

"The Jumper he is in is undergoing repairs, and is therefore not up to its top functionality, so he could not have gotten very far, and definitely not farther than the Dedaulus searched."

Everyone looked worried at this proclamation. It was truly puzzling. Where in the world, no, universe, was Dr. McKay? Was he hurt? Had he gone voluntarily? They doubted that. How had someone gotten into Atlantis to force him to leave? Was he…? None of them wanted to finish that unspoken worry that could very well be true.

"Is there any way to find him?" Carter asks, her voice showing only a small amount of her desperation. Everyone turned their heads to the two scientists, hoping that they would have an idea, although they were looking more toward Zelenka than to Kavanagh.

"There may be something we can do. I have been thinking about it, and there is a possibility that whoever took McKay was able to hide the ship from scanners…" Zelenka was cut off before he could continue what he was saying.

"I highly doubt any one would be able to hide it against every scan we've sent. I mean, there are very few people on this base who could perform it, much less in the galaxy." Kavanagh said, rolling his eyes. Zelenka looked annoyed; it was obvious they had had this argument before.

"But it has been done; therefore, there is a chance that they could have done it. Just because you can't do it Kavanagh does not mean that someone else couldn't either." Zelenka bit back before launching into a few quiet insults in his native language.

Kavanagh did not look happy at that statement, but before he could continue with the argument, Woolsey cut in.

"Gentlemen. please!" The two both stopped short and looked at him. "Thank-you. Now, Dr. Zelenka, please continue." Kavanagh looked like he wanted to say something, but a glare aimed at him by everyone, Ronan especially, stopped him.

"Yes, of course. If this person or persons were able to kidnap Rodney from right under our noses," Everyone winced at that Dr. Woolsey and Sheppard especially, "then they must know some of our technology, and that of the ancients, so they could very probably fix the scanners. So, I think that with Hermiod's help, we could reconfigure the scanners, connect them with that of the Dedaulus' and make it to where we could possibly find the Jumper. It's a long shot, I know that, but it is all that we have at the moment." Woolsey nodded at this, thinking it over, before he looked up and locked eyes one at a time with Col. Caldwell and then Col. Carter. The two nodded at him, and he nodded at the others.

"Look, I know you all want to think that McKay is still alive and well, but we have to face fact: he might very well be dead, and the Jumper blown to pieces or something, and then all this hard work would be a huge waste of both time and recourses." Kavanagh said, causing everyone to stop where they were, most either still sitting or just rising from their seats. Those who were starting to get up dropped back down with a loud "plunk!" They all looked at him like they thought he was either incredibly crazy for suggesting such a thing, or incredibly heartless, depending on the person. Jennifer looked just about ready to cry at the thought.

"I'm sure Rodney is just fine. He probably just can't contact us, or the person who took him won't let him." She said confidently, her voice only wavering at the beginning. Kavanagh rolled his eyes at her.

"Yes, of course you'd say that. Everyone knows you two are involved. You're letting your emotions get the best of you, instead of being reasonable." Jennifer looked away at his words, her eyes brimming slightly with tears, while everyone else gaped at Kavanagh, Caldwell included.

"I am being reasonable." Keller started, Kavanagh snorted, "I am. Why would the person who did this go through so much trouble of getting in here undetected and then kidnapping Rodney and stealing a Jumper if they didn't plan on keeping him alive? If they wanted to kill him, they could have easily done it here in Atlantis in his lab, and no one would have found him until two or so hours later, possibly even more. So really, it is logical to assume that they want him alive." She spoke quietly at first, but her voice grew in volume, confidence, and strength as she went on. He looked slightly taken aback at her words, but recovered himself quickly enough. He opened his mouth to say more, but was once again cut off by Dr. Woolsey

"I agree with Dr. Keller. He is most likely still alive. We just need to find him. Dr. Zelenka, I'm giving you full control over this, all the scientist will listen to you, understood, Dr. Kavanagh?" Kavanagh said nothing, "Thank-you. I'm sure Hermiod will gladly help. I've heard he's actually grown quite fond of Rodney's visits." He couldn't help but smile slightly, s smile that looked part grimace. Rodney and Hermiod would often play a few games of Chess when the Dedaulus came over. Caldwell nodded, a light smile gracing his feature. "Okay. Umm, everyone else, we can only continue searching. Col. Sheppard, Teyla, Ronan, go take a nap." The three aforementioned people all started to protest, Ronan more in his body language than anything, Teyla looking worried, and Sheppard looking like he might just resign if he ordered him to. "Listen, you'll all be able to search better once the scanners have been reconfigured if you've been rested." They didn't seem to see the same logic he did.

"No." Was all that Ronan said.

"Look, I get that it would be best for us, but we'll just be laying awake, worrying about Rodney if you send us to a quiet room with nothing there to distract us. It could prove fatal." Sheppard said, his eyes gleaming with unsaid determination. Teyla nodded and put a reassuring had on Ronan's shoulder, trying to calm the large Satedan down.

Woolsey sighed and nodded, knowing that arguing would be a lost cause. Carter smiled slightly. She had a quick flash back of all the times she had stayed up for days, working hard, whenever Jack, Daniel, Teal'c, Cameron, Valla, or Jonas had been hurt, lost, or in danger. Concern, worry, and the un-explainable need to do something was the result of a real, true team, the type of team made of team members willing to do anything for one another, the type of team made of team members who became more than team members after a little while. That was what her old team had been like, and that was what SGA1 was like. She understood, accepted, and admired that. Woolsey had also noticed the friendship that the team seemed to share, and he respected it, knowing that it was sometimes the only thing keeping anyone together, way out there in the Pegasus Galaxy.

"Alright." Was all he was able to get out before John, Teyla, and Ronan were out the door, quickly followed by Radek, Carson, Jennifer, Caldwell, Col. Carter, and, slower and less enthusiastically, Kavanagh, who turned and offered her a last, disapproving glance before heading out.

Woolsey walked out after them, passing Carter, who was standing at the door.

Samantha sighed sighed for what must have been the hundredth time that day, straightened up, pushed back a few free locks of hair, and walked out into the gate room, ready to resume the search of Atlantis' top scientist, her old colleague, and friend.

Rodney was getting tired, light-headed, hungry, and desperate. He had tried everything he could think of, but nothing was working. The shields were acting up. Whatever had happened in the Jumper had obviously hit the crystals that controlled the Jumper's shields, and now they were going haywire. They were staying on, which Rodney considered a good thing, kind of, but they were at an incredibly strange frequency giving off a type of EM field that they never had before. The scanners and communications were still the same as before, and they were broken, so they couldn't compensate for the change. He had tried to reconfigure the scanners in every way he could think of to see where he was, but to no avail. All they told him was that he was on a flat surface. So basically, they told him nothing at all. Then, he had tried to fix the shields-also to no avail. He was getting tired and annoyed. His leg, right side, wrist, and head were getting worse by the minute.

He had checked the knife wound and found that it went in right above his pelvic bone and under his lowest rib. He was pretty sure it had hit his large intestine and pancreas. He was bleeding severely. He had found the medical kit and had put the largest bandage he had found on the wound and then rapped the gauze tightly around it, after putting some antiseptic on the wound. It had stung like crazy, but he had gritted his teeth, complained loudly, and then gotten on with it.

Almost immediately after finding out he was stuck he had found that his forehead and the left side of his head was bleeding, so he had taped some bandages onto both places after stopping the bleeding as best as he could. There wasn't much he could do for his wrist or his leg except not use either as much as possible; which really wasn't much at all. He needed his left hand to help his right hand work, and he needed his left leg to move. He had quickly realized that he had broken his Fibula and probably sprained his ankle, so he had to hop if he wanted to move at all. He was pretty sure his wrist was only sprained, although a bone or two might have been cracked; he wasn't really sure.

He sighed for what must have been the hundredth time since he woke up, and leaned back into the seat behind the pilot's, where he had been working on a consul. He was incredibly tired, but he was trying his best to stay awake and aware. The Emergency Medical Kit had had two emergency water-bottles and he was already done with half of the first one. He had realized that he needed to drink sparingly, but he had been so thirsty and dehydrated.

He sat thinking for a while, just trying hard to breathe in and out and to calm himself. His thoughts wandered to his team.

They had probably found out that he was missing by now. His clock had said that it had been about fifteen hours since he had been knocked out after he had woken up, and now it had been sixteen hours. Yes, they had definitely noticed. Either Jennifer had gotten angry or worried and had gone to look for him, or something had needed fixing. At the thought of Jennifer his stomach clinched uncomfortably. Would he ever get to see her again? Or John? Or Teyla? Or Ronan? Or anyone?

Stop that! He commanded himself. You don't need to be thinking like that. You need to get out of here, not worry about anything else. Moaning and whining won't make seeing them again come any sooner, so you might as well get up and start working.

But he didn't. His mind just kept wandering. He thought back to a conversation he had had earlier with the team, Jennifer, and Carson.

"MCKAY!" Sheppard's voice broke through Rodney's thoughts, making him jump and almost fall out of his chair. He looked up at the coming group of five, annoyed. But his scowl immediately disappeared as he realized that he had forgotten that he had had a lunch gate with them. Jennifer looked mad and disappointed, John looked annoyed and slightly angry, although amused at the same time, Teyla looked like she was having a hard time trying not to laugh, Ronan looked emotionless, although Rodney thought he could see a slight smile playing on the Satedan's lips, Carson looked like he was trying to decide whether to be disappointed, annoyed, or amused. Rodney had been trying really hard lately to remember to be on time to everything, and to his credit, he had been doing really well, which was probably why they weren't all that annoyed or angry.

"Look, I'm really sorry; I just found this amazing Ancient piece of technology!" Rodney's grin widened as he saw that Carson and John actually looked slightly interested. Rodney didn't say something that happily if it wasn't really good.

"Rodney"- Jennifer started, but Rodney turned to her with a hopeful look, making her stop. She looked at the others hopelessly. Rodney was actually using puppy-dog eyes that seemed to actually work on him. Jennifer sighed, and Rodney took this as a sign that he could continue.

"It's some type of a communication/weapon thing. Basically, what I think it does is it sets of a low-level EM field that renders all communication devices that had been programmed into it inert, while leaving specific ones intact." John looked impress, thinking what an advantage it would be to have. "Unfortunately, I can't seem to make it work." John deflated slightly, but still looked excited, confident that Rodney-fix-it-all would be able to fix it. As though reading his mind, Rodney shook his head.

"I can only fix it half-way, which wouldn't really work. All that the enemy would have to do is figure out what's causing the disturbance and then they could reconfigure their communications and they would be all set." John, Teyla, and Ronan, who all understood how valuable such a device would be, looked down dejectedly, and Jennifer took this as her cue to step in.

"I'm sorry it doesn't work, really, but now you can come have lunch with us, Rodney!" Jennifer looked happy at the thought, and turned on Rodney by using the same puppy-dog eyes he had used on her. He gave the devise one last look before turning around, sighing, and getting up. John, Teyla, Ronan, and Carson all smiled at this.

"Smitten." John "coughed". Rodney glared at his friend before shooting a response back, which started an argument that lasted until they reached the Commissary and Jennifer and Carson verbally made them stop, while Ronan just glared.

Rodney smiled at the memory, thinking about the bickering that he and John often started with each other. He dully wondered if he would ever get to bicker with his friend again. He shook his head violently, causing his head to hurt. It hasn't come even close to that, Rodney. When have you been the type to give up, huh? He asked himself.

He put his head in his hands, trying to calm the nausea that shaking his head had started. Suddenly, his head shot up, and idea forming in his head. His words from that earlier evening came back to him again. They could reconfigure their communications and they would be all set.

YES! He thought to himself as he jumped up, remembering to put his weight on his right leg and hopping up to the pilot's seat. He sat down heavily and began working, knowing a system that he could use that Zelenka would recognize.

Woolsey went racing up the steps to the Gate Control, SGA1, Caldwell, Carter, and Dr.'s Keller and Becket racing up right behind her. Dr. Zelenka had radioed him and the others behind him, saying that he had something very important he needed them to see, and that it was about Rodney.

As they raced up, Dr. Grodin beckoned them over to where he and Zelenka were standing over a large Atlantian consul with two computers resting on it.

"What's happening, Dr. Zelenka?" Jennifer asked, worry etched into her words.

"We are receiving a very strange signal, and we are not sure where it is coming from." He replied distractedly, his eyes on his computer.

"And what does that have to do with McKay?" Sheppard's voice, gruff because of worry, came from behind Carter.

"Because, I believe it might be from Dr. McKay." He said. He looked like he was going to say more, most likely an explanation, but he was cut off.

"I highly doubt it." It was Dr. Kavanagh who spoke. "I know you want to believe it is, but I really don't think that's the case." Both Dr. Zelenka and Grodin sighed and rolled their eyes, clearly annoyed with their fellow scientist. Carter glared at the doctor, and motioned for the other two scientists to continue.

"Like I was saying, I believe it is Dr. McKay, because the signal is sending off strange burst of energy at seemingly random sequences, with loud bleeping noises." Zelenka continued, and then looked at them as though he expected them to know where he was going with this. Blank faces stared back at him, quickly growing annoyed. Dr. Zelenka hurried on with his explanation.

"Dr. McKay and I have been experimenting with the Atlantian form of Morse Code. We have been sending each other random messages. Last week, we got over the longest message yet. The first page of the report sent in by SGA3, of that planet on MTH-466. The signals coming in from this consists of the exact same things. Specifically the third line of the second paragraph. You know, the one about how they sent in a message to here saying that they were stuck and hurt?"

Woolsey and Sheppard nodded, feeling hope build up inside of themselves despite their attempts to stay emotionless. They were hoping beyond hope that it really was McKay.

"I think that if we reconfigure the receivers, we might be able to send a message back through the same signal, and then if it is McKay, he should send in the next line."

"Why the next line?" Surprisingly, it was Ronan who asked this.

"Because that is what we did with the message. We would repeat the same line over and over again until it was sent back to us, and then we would move on to the next line." Radek explained while Grodin started tapping on his computer and working on the Ancient consul.

"Wait a second, why did the Ancients use Morse Code?" Caldwell asked, while Sheppard looked at Zelenka expectantly.

"Well, it was a very good system to use to send secret messages. There was practically no way that the Wraith could read the message, so it was actually quite useful." Dr. Grodin replied this time, since Zelenka was busy at another consul. Woolsey nodded, having already read Zelenka's report.

"Okay, that should do it. I have sent back the sentence. Now, we just have to wait and see if McKay sends back the next line. No one other than Dr. Woolsey knew that we were doing this, so no one else could know to send back the next line except Rodney." Dr. Zelenka said, his eyes hopeful.

The next few minutes were spent in agonizing silence, the entire Gate Room listening for those few bleeps that would mean that Rodney was alive and well enough to be doing the Ancient Morse Code.

Several minutes later, bleeps were heard coming from Radek's computer. Everyone's eyes grew big, and Zelenka started to type furiously on his computer. A moment later, he looked at the anxious group of people in front of him and smiled.

"It is the next line of the report. I believe that this is Dr. McKay."

Almost everyone let go of a breath they did not know they were holding in. Just as Sheppard began to say something, Radek held up his hand, and immediately silence took over.

"Atlantis. Come in …. Stuck…-umper doors won't op-…Hurt pretty bad…Radek if you can hea-….Reconfig-…-unications…reply." Then there was silence.

"What did he say?" Ronan's voice broke the silence and brought Zelenka into action. He started to type furiously and a few moments later, Dr. McKay's voice came in loud and clear.

"Okay Radek, if you've reconfigured the sensors, you'll be able to hear me, but you'll need to do more than that to be able to respond. You'll have to go down to my lab. There's a consul there filled with crystals. On the third row, fourth from the right, is an advanced communications crystal. You know where to put it. Hurry, please. I'll keep repeating this, just in case you haven't caught it yet."

Jennifer made a noise like a happy mouse and then hugged Teyla tightly, which made everyone else, except Kavanagh, smile and look at each other, relieved.

Rodney was alive.

A/N- Okay, hopefully you understand the time-line, and all that other stuff better. I'm sorry it was confusing. I'm not sure if i'm getting Dr. Woolsey right, because i know his character from Star-Trek Voyager better, so I might accidentally mix the two up. There isn't a lot of him in this chapter, and i'm not sure how much of him will be in the others, but there might be a lot, so if i'm getting it, like, really, incredibly, horribly wrong, please tell me! Oh and remember, READ & REVIEW!