A/N: First of all, thanks for the overwhelming response. When I borrowed an internet connection long enough to check the reviews, I was shocked. I'm sorry I can't answer them all, but I'm still borrowing computer and internet time, so it's limited. That's why the delay in posting this chapter. I hope you continue to enjoy.

Inner Connection – Chapter 2

Elizabeth hesitated only a second and then turned to follow her military leader down the corridor. "What do you mean? Atlantis actually asked you for help?"

"Not with words," he said as he walked.

"So it's really still just a feeling?"

John didn't say anything, but continued to walk ahead determinedly. Arriving at the control room a few minutes later, he scanned the room until his eyes landed on Rodney. John walked quickly over to him. "Rodney, you find anything yet?"

Without looking up, Rodney answered. "Not yet, Sheppard, I told you I'd let you know. Did you actually get Carson to let you go?"

"Naturally, McKay, since there's nothing wrong with me. Whatever is wrong with Atlantis is getting worse."

Rodney finally looked up. "How do you know that?"

"I just . . . I can feel it, okay? It's starting to feel different, worse. We need to find the problem."

McKay rolled his eyes and looked back at his computer screen. "That's what I'm trying to do, Colonel, and it would move a lot faster if you weren't standing here annoying me. Now go away and I'll call you if I need you, heaven forbid." McKay looked up at Sheppard. "Why are you still here? Go away."

Elizabeth watched as John backed up a step, almost like he was uncertain about what to do. He looked tired and nervous and just a little bit scared. "Do as he says John. Go back to your quarters and get some rest. We'll call you if anything happens."

John stood clenching and unclenching his fists, before finally nodding and leaving the control room.

McKay turned to watch him leave. "What's wrong with him? He's a nervous wreck and he's never a nervous wreck, not even when facing Wraith."

"I don't know, Rodney, but he's really convinced there's a problem with the city. Get Radek to help you and look at everything, no matter how insignificant it seems."

Rodney looked at her a few seconds. "He's got you spooked, doesn't he?"

"More so than I've been in a while. Just keep looking."

oOo

John had honestly tried to sleep. He'd been in bed for almost two and a half hours and had actually dozed off once, only to be awaked by someone dropping something heavy in the hall outside his room and then cursing said object very loudly. But he'd had enough. Trying to lie in bed was making him crazy, now that he was wide awake again. Getting up, he decided he needed a shower.

After a hot shower, he smelled better, but it didn't ease his tension any. Looking in the foggy mirror, he rubbed the stubble covering his face and decided to shave. He didn't really feel like expending the energy, but he also knew there wasn't much else for him to do. Besides, if he was clean and pressed and professional in his appearance, maybe everyone wouldn't think he was a complete lunatic when he kept insisting something was wrong. He looked at his wild hair and the dark smudges under his eyes. Put that with his unshaven face and he looked somewhat like a crazed derelict. No wonder everyone was looking at him funny.

Thirty minutes later he was dressed in a new uniform, clean shaven, and ready to go. He figured he'd check in with Rodney first. "Rodney, it's Sheppard."

His radio crackled with an annoyed voice. "No, I haven't found anything, and yes, I'm still working on it, and yes, I still need you to leave me alone."

The radio went dead, indicating Rodney was finished. John couldn't help but smile, in spite of the fear gripping him. You could always count on Rodney to be Rodney. Since he'd checked out the rest of the possibilities, John decided to have a look at the uninhabited parts of the city for signs of the problem. Checking his gun and grabbing his pack, he headed out the door.

John took the transporters as far as he could and then struck out on foot. He had a mental plan on how to systematically check the whole city, but he hoped he wouldn't have to actually carry through with it. Realistically, he would never finish. He probably needed help, but he didn't know what to tell people to look for and he was pretty sure Rodney and Elizabeth had just been humoring him so far. And Carson looked at him like he did when John was overly paranoid after a bad mission, meaning the good doctor suspected he was one taco short a combination plate.

John was starting his search with the area being recently explored by combination military and scientific teams. It was possible someone had inadvertently activated something or set off a disastrous chain of events. Stepping into the first lab, he slowly made his way around the room. Nothing seemed to be blinking or bleeping or looked particularly disturbed. After several minutes and two complete sweeps, he was satisfied and moved to the next room. This was going to take a while. While his headache was better than before, it was still making itself well-known. On top of that, he was still wound up and tense, like he was when he was expecting a Wraith to pop out at any minute. This was going to be a long day.

oOo

Elizabeth walked out of her office, stretching her back as she went. Scanning the room, she noticed Rodney sitting at a work station staring at the computer screen. For once he wasn't a flurry of motion. She took a step down to go stand right beside him. "Rodney, are you still here? It's almost six-thirty."

Rodney leaned his head to the right, stretching his neck, and then switched over to lean to the left. Straightening his spine, he reached back and massaged his neck with his hand. "Well, obviously I'm still here, thanks to Colonel False Alarm. I've wasted the whole day and still haven't found anything. There is nothing wrong with Atlantis."

The lights flickered several times in a row before returning to their normal setting. "You were saying?" said Elizabeth.

Rodney was already hitting the keys of the computer pad with lightning speed and muttering to himself.

"Elizabeth, have you seen Colonel Sheppard?"

Elizabeth turned to see Carson walking toward them. "No, not since this morning. I thought maybe he was finally getting some sleep and I didn't want to disturb him."

Carson shook his head. "I've left him alone for the same reason, but I just came from his room and he's not there. I took a look in the mess hall as well, but no one has seen him since this morning."

"Have you tried his radio?" asked Elizabeth.

"No, I didn't. I was hoping I could just run into him so he didn't feel so . . . you know. The Colonel hates it when I check up on him."

"So you wanted to check up on him without him realizing you were checking up on him," said Rodney.

"Exactly."

Elizabeth turned back to Rodney. "Did you figure out what happened with the lights?"

Rodney shrugged his shoulders. "Momentary power glitch. It happens. Everything's okay now."

"And you're sure it's not a sign of a bigger problem?" asked Elizabeth.

"I can't be sure, but everything is fine now. If there's a bigger problem, it's hiding somewhere."

Elizabeth nodded and reached for her radio. "John, it's Elizabeth, please respond."

"Elizabeth? Is there a problem?" No one missed the worried edge to his voice.

"Nothing big, just the lights flickering a few times. Rodney thinks it was a temporary power glitch. Where are you?"

"Looking for trouble. Tell Rodney that's just the beginning."

Elizabeth frowned. "The beginning of what? Have you found something?"

"Unfortunately no. The problem is still there, even if Rodney can't detect it yet. Whatever it is, I think it's buried pretty deep. I can't get to itt and I don't think Atlantis knows what it is either. She isn't feeling the full effects yet, so it'll get worse before it gets better."

Elizabeth sighed. "Look, you must have been out there for a while now and it's getting late. Why don't you meet Rodney, Carson, and I in the mess hall for a late supper. We've all been working and haven't eaten as well."

"Elizabeth, I need to keep looking."

Carson decided it was time to intervene. "Lad, you need to come back and let me have a look at you. If you drop from exhaustion, you won't be able to help Atlantis or anyone else. Now come on back and get something to eat and let me do another exam to make sure you aren't having any long-term effects from the chair."

There was a pause while they all waited on him to argue, but then they were surprised. "All right. I'll need to get cleaned up first. Give me about an hour and I'll meet you in the mess hall."

Elizabeth smiled and nodded at Carson. "Okay, we'll see you in an hour. If you're not there, I'm sending Lorne after you."

"Yeah, I figured. I'll be there. Sheppard out."

"Well, gentlemen," said Elizabeth. "I'll see you in an hour."

oOo

John set his tray on the table and sat down beside Rodney, across from Elizabeth and Carson. "Told you I'd be here." He pushed his still damp hair off his forehead and sat down. The last thing he felt like doing was sitting down and eating, but he knew he had to placate the people at the table before he could go back to his search. So he concentrated on hiding the fact that he was so nervous and jumpy he could barely sit still.

"How long have you been out there searching?" asked Elizabeth.

John shrugged his shoulders and stuffed a bite of turkey sandwich in his mouth to give himself a few seconds. "Uh, since a little after noon. I thought maybe the areas of the city we've been opening up the last few weeks might have a clue, something accidentally set off or activated. Haven't found anything yet, though."

"Did you get any sleep?" asked Carson, watching John carefully.

"Couple of hours," John lied. He thought maybe the fact that he had tried that long should count for something.

Carson didn't look convinced, but let it pass. "How's the headache?"

"Better. Not gone, but better than it was. And no, I haven't had any other problems or dizzy spells." That at least was the truth.

"That's good, but I still want to take a look at you after we finish here."

John nodded. "Okay, no problem. Rodney, have you found anything at all?"

Rodney paused, letting his hand come to rest on the table. "No, not really. I found a few odd power readings here and there, and then the glitch with the lights earlier, but nothing serious. Maybe . . . could you just be picking up minor stuff like that and . . . I don't know, kind of blowing it out of proportion."

John looked at Rodney, making sure they had eye contact. "When have you ever known me to overreact?"

Rodney looked down. "Never. That's usually my job."

"Look," John said awkwardly. "I know you guys think I'm losing it –"

"No one thinks that," Elizabeth interrupted.

John's face broke into a crooked grin. "It's okay. In your position, I would think I'm losing it too. I have no proof, it's all based on what's going on inside me and I know you can't understand that. Just . . . promise you'll keep looking. It will show up eventually and I want to be ready for it."

Elizabeth nodded. "All right John, we can do that. But you can't run yourself into the ground looking for this. You need to get some rest."

John nodded. "I know, I will. When are Teyla and Ronon coming back from the mainland?"

"Tomorrow night," answered Elizabeth.

John nodded. "Good. Maybe they can help if I haven't figured this thing out by then, although I have no idea how." John felt better about things when his team was working together. They had such different perspectives that what one couldn't see, usually another could. Their methods and talents just seemed to mesh together perfectly.

Carson noticed that John had stopped eating, leaving almost half his sandwich. "Colonel, you need to finish that. I'm guessing you haven't eaten all day."

"Hey, I had a power bar this afternoon. Besides, I'm not hungry. Tension does that to me. Help me solve this thing and I'll eat a meal that would fill Rodney up for a while."

Rodney stopped chewing and glared at John. "And what is that supposed to mean? You know, never mind. I'll have you know that I do not eat too much. It's hardly my fault that you barely eat enough to ward off starvation. You should take a page out of Ronon's book of proper nutrition. He can –"

"Rodney, I'm kidding," said John, grinning.

Rodney scowled for a moment, mumbled something under his breath, and went back to eating.

"Well, Colonel, I need to see you for a few moments in the infirmary and then I expect you to go back to your quarters and get some sleep. Is that clear?" Carson was wearing his no nonsense, I expect obedience expression.

John gave a mock salute. "Yes, sir. Just let me grab a cup of coffee."

Carson looked horrified. "Absolutely not! Caffeine is the last thing you need right now. No coffee."

John's expression fell. "But I haven't had any all day."

Carson grinned and leaned forward slightly toward Sheppard. "Buck up, Colonel."

John sighed. Revenge wasn't so sweet when you were on the receiving end.

oOo

John didn't feel too guilty as he entered the darkened and long abandoned lab. He had actually managed to sleep a couple of hours before waking to what he could only describe as Atlantis screaming at him. His headache was flourishing and there was now a constant, almost painful high-pitched whine in his head. H wasn't sure if he was hearing it or feeling it, but it had set his last nerve on edge. There was no way he could sit in his room waiting for it to be a decent hour and if the others couldn't understand that, it was their problem. Carson had given him some Tylenol, which had helped at first. That was probably why he'd been able to get some sleep.

A noise had him jerking around, hands gripping the P90 until his knuckles were white. He relaxed slightly as he realized it was the outer walls creaking in the wind. The older, water damaged parts of the city sometimes did that. He resumed his search, finding the usual frustrating nothing. John rubbed the side of his head, wishing the headache would go away, if only for a while.

When he was back in the hall, he wandered over to a window, letting his P90 sag as he relaxed his arms. This level was just above the water and the rising sun streamed in the window, reflecting off the ocean below. It was a beautiful sight, one he never got tired of. This was a slightly different view that what he normally saw and he was momentarily grateful for the experience. The knotting tension grated away, however, drawing him back to his search.

oOo

"I think Sheppard is at it again," reported Rodney as he sat down beside Carson. "I checked his room to see if he wanted to grab breakfast with us and he wasn't there. On the plus side, his bed looks slept in. Either that, or there was a small tornado in his quarters."

Elizabeth shook her head from across the table. "What should we do, Carson?"

Carson sipped his coffee for a second and then set his cup down. "I guess let him be for the time being. He's wound up tighter than a spring right now and I think we'd not be able to keep him still without sedation. He's exhausting himself, but other than that, I suppose there's no harm. There is always the possibility that he's right, in which case he might find the answer he's looking for."

"The area has been cleared for more investigation by the science department, so he should be relatively safe," said Elizabeth. "Should I send someone to keep an eye on him?"

"Might not be a bad idea," said Rodney. "Of course, on the other hand, it might piss him off that you want to keep tabs on him."

"They could offer to help," said Elizabeth.

"You said Ronon and Teyla are coming back later today?" asked Carson.

Elizabeth nodded. "This afternoon."

"I think I'd wait til then and send them. In the mean time, we can keep tabs by radio, ask him if he's found anything," suggested Carson.

Elizabeth nodded. "All right. I think our first radio check is going to be now." She reached up and activated her radio. "John, I assume you're searching the outer part of the city again."

"Yes, I am. Is that a problem?"

"No, just wanted to check in with you. Find anything yet?"

"Don't you think I would have contacted you if I had?"

Elizabeth smirked. "It's hard to tell with you sometimes. Just check in with me periodically so I know how you're progressing . . . and that you're okay. I can send some people to help you if you'd like."

"I'm not exactly sure what I'm looking for, but help would be good."

Elizabeth raised her eyebrows in surprise. "Okay, I'll get a team together and contact you about where to meet. We'll let you know if we find anything on this end."

"Thanks Elizabeth. And tell Carson I'm fine and yes, I slept a while. Sheppard out."

Elizabeth smiled, grateful that he had accepted help. If anything did happen, he wouldn't be down there alone. She started to reach for her radio again, but stopped when her gaze landed on Major Lorne sitting at a table across the mess hall. "Be right back. I have a major to see about a certain colonel."

oOo

John stood before the console, contemplating the darkened structure. It was getting late and he knew the men helping him were tired. He made a decision to send them back and continue the search alone. Once they were back, Elizabeth or Carson would call and complain about him staying, but Atlantis was getting worse and he couldn't afford to stop now. The pain in his head was almost unbearable and he was pretty sure that was some kind of indicator.

"Colonel, we've finished this section," said Lorne from behind him. John turned to face the major.

"Good. I think everyone's had enough for now. Why don't you take your men and head back. I'm just going to look for a while longer."

Lorne looked uncertain. "Uh, sir, you've been here all day. Maybe you should come back with us and we can start again in the morning. You look tired." Tired didn't even begin to cover Sheppard's appearance. He was dirty from searching derelict, long abandoned labs. The stubble from his lack of shaving that morning combined with the bags under his eyes and the pain lines from the headache to make him look weary beyond his years.

John looked firmly at Lorne. "Major, I'm staying here for a while longer. Take your men back to the city, that's an order. And when Dr. Weir asks, tell her I'm fine."

"Is that also an order, sir?" asked Lorne, an edge of frustration to his voice.

John sighed wearily. "Whatever, Major. Just . . . go." John didn't wait for a reply, but turned and walked out of the room, heading down the hall to the next section. When he reached the next search area a few minutes later, he leaned against the wall. His heart rate had escalated again and he felt like the top of his head was about to blow off. Pinpoints of light danced across his vision for a second and it felt like the room suddenly tilted to one side. John slid down the wall to sit in the floor before he fell. Leaning his head forward, he rested his forehead against his knees.

It was several minutes before the vertigo passed and John felt brave enough to lift his head. Opening his eyes, he looked across the lab he'd stumbled into. A cold shiver that seemed to come from the wall behind him raced down his spine.

"Is this it? Are you trying to tell me this is where the problem is?" John got to his feet, staggering a moment as he got his balance. The lights had vanished, but the headache had not and the screaming in his head was at an all time high. John walked unsteadily over to the console against the far wall. Reaching his hand out, he touched the panel and it flickering, trying to come to life. He found that strange, since he didn't think this area had power. He hit his radio button, excitement now joining the fear that filled him.

"Rodney, it's Sheppard."

"What is it now?"

John ignored the irritation in Rodney's voice. "You and Zelenka investigated some lab last week that you were excited about. Where was it and what did it do?"

There was a pause, making John wonder if Rodney was going to ignore his question. "Oh, okay, I remember. It was . . . Section G8 . . . third level I think. It had all kinds of new information on Atlantis's operating systems we hadn't seen before. It also had some research the Ancients had been working on to increase the efficiency of the ZPMs. Radek and I were excited because we thought it was also going to tell how to build ZPMs. Tthe console was in bad shape and we had trouble accessing the information, so I tried downloading it into my computer. But the data was so messed up, it locked up my computer every time I tried to analyze it."

"Well, I think that's where I am now and I also think this is the where the problem originated. Why is there power in here?"

"It's not much. We just rerouted enough we could bring the database up and try to down load it. I'm surprised it's still working. I should probably cut it off. And what makes you think it's causing problems?"

John ignored Rodney's question, knowing the response he would get if he answered it honestly. "I think it's too late for that, but eventually you probably should anyway. Right now, I'm going to do some investigating and see what I can figure out. Maybe you should look at that data again."

"Can't. I deleted all of it. I told you, Colonel, it was screwing up my computer."

John sighed. "All right, thanks anyway. I may need you later."

"Oh, gee, I'll be waiting with bated breath." There was no missing the sarcasm.

One corner of John's mouth turned up. Rodney could always get him, no matter how rotten he felt or how tense the situation. "That's good to know, Rodney. Sheppard out."

John sat down carefully in an old chair, making sure it would hold up before he relaxed his full weight. When it seemed the chair would stay together, he reached out and touched the panel, causing it to flicker to life with a groan. His headache flared, but he kept his palm planted firmly on the console. I'm working on it, Atlantis, just hang on.

TBC

Well, it seems that I'm more longwinded than I thought, as usual. I really do think I can finish it with one more. I'll try to get it up tomorrow.