A/N: Sorry for the long delay in posting! Life has been pretty crazy lately, but here is a nice long chapter for you in thanks for all your wonderful reviews that keep me going! Oh, and for those of you who celebrate Thanksgiving, Happy Early Thanksgiving!

"John, I'm relieving you of command."

"What?" slurred John as he tried to focus on the stern visage of his commanding officer, despite the fact he felt like he was staked out under the sun in the middle of a desert.

"John you have a history of insubordination and though I chose to overlook that fact when I first brought you to Atlantis, I have come to regret that decision in light of recent events. First, you recklessly and with no regard for my orders crashed an irreplaceable jumper into the city. Not only that, but you showed yourself to be irresponsible, insubordinate, and unfit for command. Due to your actions, if I am to keep my authority on Atlantis I have to show that actions like those will not be tolerated even by the former military head of Atlantis."

"Elizabeth, it wasn't my fault! Something went wrong with the jumper. I wasn't going against you!" John grimaced as he pushed his pain filled body that radiated heat into a sitting position and faced the angry and clearly unbelieving face of his superior.

Withholding a cry of pain as his left side screamed at him, he continued slightly out of breath, "Elizabeth, come on, think about all we've been through together on Atlantis; you have to trust me!"

"But, John, those aren't the only reasons I'm removing you from command. You caused a lab on Atlantis to explode killing Rodney!"

"I just wal…wait what? What are you talking about! Rodney's not dead! He's fine, I mean pretty fine; a little banged up, but definitely alive!" John shouted as his pulse quickened. "He just visited me in the infirmary! There's no way he's dead!"

"Do you remember him leaving the infirmary?" Elizabeth asked in a gentle and calming voice.

"I…no…we were talking…and…I don't know what happened next."

"Oh, John, you're mind must be trying to protect you, though I'm afraid it's just another sign you're unfit for duty," Elizabeth said with a soft sigh. "You were talking with Rodney and then Rodney started having difficulties breathing. Carson rushed over to see what the matter was, but by the time they figured out what was wrong it was too late."

"Wha…what do you mean? He was fine."

"He looked fine, yes, but he had torn his spleen in the explosion you caused in the lab you told him to go to and now thanks to you he's dead.

"I didn't cause that explosion! I just walked into the room and activated the consol like Rodney said to!"

At his words, Elizabeth's expression turned angry, "Oh, so now you're blaming Rodney for his death when you're responsible for it!"

John's mind sought to comprehend the indictment being hurled at him and gasped out, "Wait what? That's not what I meant, I…"

"Why did you do it John? Was the stress of command too much for you? I can't tell you how many times I was told you couldn't handle it. I wish I had listened to them, maybe then Rodney would still be alive!"

"No, it just…"

"So, you couldn't just take out yourself! No, if you're going to commit suicide you have to go out in a big way. You wanted to take out Rodney as well as yourself in—what—a blaze of glory? Well, I can assure you that there is no glory in the explosion you caused; not for you anyways." Elizabeth's voice softened for a moment. "He saved your life you know." Then she clenched her teeth and added, "Of course, he had no clue that you were trying to get both of you killed."

John desperately tried to answer her but found the relentless pounding in his head was keeping him from forming a coherent thought and he was forced to simply endure the continuing barrage from Elizabeth.

"Why is it that you survived instead of him? He deserved to live; you're the one who should have died; deserved to die. No, instead he's dead all because you couldn't handle the stress of being in command on Atlantis; well let me assure you that will no longer be an issue."

John's mouth was dry and he felt his heart racing. Was he responsible for Rodney's death? He couldn't be sure he wasn't. Whether or not he had set it up to explode it was clear that it had responded to his gene. Rodney had even told him that.

John's eyes were drawn back to the cold flint of Elizabeth's eyes as she said, "you're a murderer John! It's not even like Rodney's the first one you killed. You're responsible for so many deaths!" John's muddled and confused mind found no difficulty in accepting the truth in that statement as names and faces flashed through his mind beginning with Colonel Sumner. The guilt crashed over him and seemed to submerge him like an ocean wave in its relentless fury.

"Take him to the brig," Elizabeth's words broke through the haze John found himself in and he saw that two buff marines were standing behind her. She turned to walk away completely emotionless as if it didn't matter to her in the slightest that she had just sentenced John to the same brig they had kept life-sucking wraith.

"Wait!" John called out, "I don't know why the explosion occurred, but I wasn't trying to commit suicide or kill Rodney! Please, just think about this!"

Elizabeth, however, didn't give the slightest sign she heard the desperate pleading from John and exited the infirmary as the two muscular marines made their way to John. John felt himself panicking and struggled to draw in oxygen as two of his own men grabbed his arms to drag him off to the cell in which he had once killed a wraith.

At that idea, John's instincts took over and he found himself fighting with all the strength, little though it was, he could muster. Yet, their grips were firm and John found that he couldn't break away.

"Let me go! I didn't do it! Whatever happened was an accident! Let go!" The grips did not loosen at his cries, but John became aware of voices saying his name over and over again. For a moment, he wondered in confusion why the marine's lips weren't moving as they said his name, but then the world seemed to dissolve around him and instead of the marines there was Carson and Ronon.

"Carson, I didn't do it! You have to tell Elizabeth! I don't want to be put in the cell Steve was in!"

"No one is going ta put ye in a cell. Just breathe. Come on John everything's fine, ye just need ta calm down. I'm sure ye didn' do whatever, and I'll make sure Elizabeth knows that as well. Just take a deep breath. That's it. Now, another. Good!" Ronon and Carson gently pushed John back unto the sweat soaked sheets as he continued to utter soothing phrases.

Exhausted and in pain, John let himself relax against the pillows and took several shuddering breaths before gasping out, "wha…what happened?"

"Ye were having a nightmare and we were having a hard time waking ye up.

John nodded while his mind sorted his memories to determine what had been real and what hadn't been. Abruptly he tried to push himself up saying, "Rodney! Is Rodney really dead! I didn't mean to kill him! It was just that he told me to activate it and I did, I didn't know that it would explode, I…" John talked faster and faster and found himself growing lightheaded.

"Breathe! John ye need ta breathe, come on! Rodney's fine! He's not dead and ye certainly didn' kill him. He's restin' in his room right now, perfectly fine, not that ye'd know that ta here him speak. Come on John! Ye need ta calm down!"

Yet, John was beyond rational thought and Carson's words were swept away without making a dent in the panic that was overtaking John. He began thrashing around as he took in the fact Ronon and Teyla were both there in the infirmary with him, but Rodney wasn't. Rodney always was there!

John realized they must be trying to hide Rodney's death from him, because they didn't think he could handle it in his present condition. Elizabeth had said he was dead and she never lied to him, so if she said he had killed Rodney, he must have, John reasoned as he forgot that it had all been a nightmare.

Suddenly, John's eyes fixed on a figure standing just behind Carson.

"Rodney!" he shouted!

"Why did you want me dead John? Why?" asked the pale figure whose arm was hanging at an awkward angle.

"Rodney, I didn't I swear! You told me to activate it and that's all I did!"

"So, now you're blaming me for my own death!"

"No, Rodney, I just—"

"It's all your fault I'm dead! I trusted you, yet look at what you did! Elizabeth's right! You should be locked in the brig!" After saying that, Rodney's pale form disappeared before John's eyes and he began to struggle to get away from arms pinning him down with a renewed vigor.

All John knew was he had to get away from everyone and the too loud voices that called out things like "hallucinating," "tore his stitches" and "sedatives". It all seemed too much for his battered mind and John desperately wanted to escape it all before his head finally exploded.

Abruptly he felt a sharp pain on his arm and something cool enter his veins. Almost immediately he felt the fight flow out of him and he dropped exhaustedly back on the bed. Though many thoughts still raced through his mind, John found his eyes closing, and he drifted off to the world of nightmares.

…

Carson looked down at all the files, reports, readouts, and data sheets, and felt like throwing something. "It just doesn't make sense. There is no reason for John's body to be acting the way it is," muttered Carson.

John had been recovering with zero complications after the surgery. Everything had been fine, then all of a sudden John' struggling to breathe. Carson recalled his confusion and horror as suddenly John took a turn for the worst and Carson didn't have a proper clue as to why.

It felt like every time Carson checked on him, John was showing more symptoms and no matter what medication Carson gave John to relieve the symptoms it seemed that more just popped up.

Now, John had a high fever and was hallucinating and no matter what Carson or the others said to calm him, John would thrash around. Carson had even been forced to put John's arms in restraints to prevent him from hurting himself further. John had already torn his stitches once and with John's current fragile health, Carson was not about to risk any more injuries; the ones he was dealing with already were quite enough.

It was so frustrating for Carson that no matter what test he did, he wasn't finding what was wrong with John. There was no sign of infection and the symptoms didn't completely support that anyway.

Carson kept thinking of how Rodney, Elizabeth, Ronon, and Teyla had looked when he told them he had no idea what caused John's relapse, but whatever it was; it was killing him. It was almost like the medicines themselves were poisoning John, which was absurd as John had been doing fine on them only hours previously.

Sighing, Carson pushed himself up and walked over to where John was tossing and turning as nightmares robbed him of restful sleep. Gently Carson wiped John's sweaty heated brow with a cool cloth.

"Come on lad, just hold on."

…

Rodney took another delicious swallow of the one cup of coffee the evil voodoo sorcerer, otherwise known as Carson, allowed and studied the readouts on the screen in front of him. Zelenka had finally given in, and gave him all the data on the power spike, subsequent explosion, and malfunctioning transporters. Not that he had had much of a choice.

After witnessing John's sudden and unexplainable relapse, Rodney had been unable to 'rest' or sit still for that matter. His mind was going a million miles a minute, and like always, he had to find something to do. So, he had forced Zelenka to cough up the research, though Rodney knew deep down, that it was more from the desperation and worry in his eyes that got Zelenka to hand it over than the glare on his face or the triad he had uttered.

Rodney set his coffee cup down and clicked on another file, bewailing the fact he could only use one of his arms, which made even the simplest of tasks more difficult. Thinking of his arm brought Rodney's focus to the rest of his body that either ached or throbbed, though of course his arm was doing the best at keeping his attention. The painkillers Carson had given him had worn off, but Rodney was reluctant to get more, as he was afraid that Carson would make him stop working, which was the only thing keeping him sane at the moment. Every time he was still for more than a minute, his mind would flash back to John struggling to breathe as alarms went off all around him.

Rodney, clicked on another file, and forced his mind away from the infirmary were Carson was fighting to figure out why John went from getting better to crashing. While Rodney scanned the data, he reluctantly admitted to himself that Zelenka had done a pretty good job on figuring things out so far. It's just that Zelenka had hit a wall, the same wall Rodney had now encountered and had been banging his head against for the past few hours.

There was something about the explosion that simply was not making sense. The more he looked at the data Atlantis had on the lab, the more he realized there was no reason for it to have exploded, yet it had. Still, what he found even more puzzling was why John's touching the consol had overloaded the system and caused it to explode.

There was no logical reason for events to have played out the way they did, and Rodney hated things that went against logic. Rodney rubbed his tired eyes with his good hand, while wondering if maybe he should give in, and simply work on it later. After all, Carson had forbidden him from doing any work, and he had been at it for the past few hours. Maybe…just maybe…he should take a break…

No, Rodney firmly shook his head as images of John gasping for breath popped in his head. He clicked on another file and scanned it looking for any anomalies that would explain what had happened.

He was about to click on the next one, when he saw it. It was small, easily missed, but Rodney's brilliant mind latched onto it. Typing as quickly as he could with his one hand, he double checked, cross checked, and tore the data apart.

It remained.

"Elizabeth!" Rodney said in a strained voice he barely controlled, "I need to see all senior staff immediately! I think someone is trying to kill Sheppard!"

….

Ronon looked around the room seeing all the senior staff gathered; all except Sheppard that is. It was weird for Ronon not to see him slouching in his chair, for all the world appearing lazy and unaware of his surroundings. Yet, most on Atlantis had learned that John was anything but lazy and unaware of his surroundings. It was an act John liked to put on to catch people off guard. Who would suspect the person leaning against the wall with his hands in his pocket and the 'fly-boy' grin on his face, as Rodney called it, could snap a man's neck with his bare hands.

Rodney entered the room in a rush and Ronon missed Sheppard's snarky comments at Rodney being the last one to arrive at the meeting as he had been the one to call it in the first place.

It was clear to Ronon that Rodney had completely ignored Carson's orders to rest, and he felt a flash of worry for the irritating scientist that had somehow become part of the group of people he cared about. There were dark circles under his eyes and his movements were jittery as if hyped up on caffeine with no actual energy to back it. Teyla, who also noticed this, quickly pulled Rodney to a chair and urged him to sit as everyone else turned to listen to the clearly agitated scientist.

"Someone's trying to kill Sheppard," Rodney began with out preamble. "I've checked the data over again and again and it holds, the power spike was a means to lure Sheppard down to the lab, the consol was set to overload when Sheppard's gene activated it, a virus was activated, so none of the transporters would work after Sheppard had used it to get to the lab, so Sheppard would be the only one in the lab when it exploded, and everyone would be too far out to get him help in time."

Elizabeth interrupted him, "But Rodney, you said that you were the one who told John to activate the consol, so he wouldn't have activated it if you weren't there, right?"

"Actually, the reason I told him to activate the device is due to the main consol making it look like there was a failsafe on it that needed to be activated, and if John had been alone in the room, I would have told him over the radio to check the main consol, and he would have discovered the 'failsafe' and activated the consol anyway; besides, as I said, it was set up to only activate with Sheppard's gene.

"Yet, if I wasn't there I wouldn't have been able to help slow down the build up from the consol and there would have been no chance that Sheppard could have gotten far enough away to survive the explosion. It was only the luck that I was in a nearby section and didn't need to use the transporter to get to him, so I was able to be there and do some brilliant work, delaying the explosion until both of us were far enough from the blast to not be burnt to a crisp."

Rodney was silent for a moment as everyone contemplated how different the explosion could have played out. Ronon, on his part, couldn't stop himself from imagining arriving at lab and discovering his friend blackened, burnt, and dead. It was a far from pleasant thought and Ronon firmly pushed it away for fodder of later nightmares as Rodney began to speak again.

"I'm having Zelenka look over the data from the crash again as I would guess that it was the first attempt on Sheppard's life, which would mean…"

"It's possible John's sudden relapse was the third," interrupted Carson who had a grim and determined look on his face.

"You mean he might have been poisoned or something?" Ronon asked with an angry expression as he imagined beating to a bloody pulp whoever was trying to kill Sheppard.

"Aye," Carson said as he took a deep breath and then said, "I need ta go and test Sheppard's blood for anything that looks like poison."

"Understood Carson. Go."

"Elizabeth, I'd like to go with Carson and stay with John right now," Teyla said as Carson quickly left the room. Elizabeth nodded her agreement and Teyla followed him out of the room while Elizabeth turned to Lorne. "We need to have a marine guarding Sheppard at all times to make sure no one can finish what they've begun."

"Will do and I'll only put people I absolutely trust on it."

"Good, but you need to have the marine watch Sheppard in such a way that whoever is trying to kill John isn't alerted to the fact we're onto him."

Lorne nodded in understanding clearly trying to think of the best way to do that.

"You know," Rodney said with a slightly sickened look, "It probably wasn't a marine who did it. All of the attempts, point to someone who knows what they're doing around a computer. I mean, I almost missed figuring out the lab explosion. Whoever, is trying to kill Sheppard knows how to cover their tracks, it is only because I'm a genius that I found the information that led me to realizing it was a trap to kill John."

"Which means we're dealing with a scientist," Elizabeth said slowly.

"Yeah, most likely, at least I would say a scientist is involved somehow," Rodney said clearly upset at the idea that whoever was trying to kill John was someone he had picked to join the expedition.

"Rodney," Ronon said firmly, "what is happening to John is in no way your fault."

"Oh sure! A scientist I probably picked is trying to kill off one of my best friends and it's not my fault!"

"Rodney, calm down," Elizabeth said firmly, "You are not at fault at all. It's just your exhaustion talking. In fact, Ronon, could you take Rodney to his quarters and ensure that he sleeps."

"Elizabeth! I have so much I need to do right now! There is no way that I can rest right now!"

"Not a problem," Ronon said with a nod to Elizabeth as he began to manhandle Rodney out of the room. "I'll make sure he gets sleep if I have to sit on him."

"What!?"

"Zelenka will keep working, Rodney just go lie down," Elizabeth said with a slight smile at the outraged scientist presently being pushed out of the room towards well needed sleep by Ronon. Ronon, however, noticed that the smile quickly disappeared as thoughts of John passed through her mind as he left the room.

….

Lorne sighed after they were gone. "Dr. Weir, if we have everyone think Colonel Sheppard is under suspicion, it might make whoever is trying to kill him let the guard down. Also, it allows us the opportunity to have a guard watching Sheppard under the guise of you not trusting him, so it will not alert this person that we are on to him."

Lorne's glance at Dr. Weir confirmed the fact she hated the idea as well. Seriously, the idea of making most of the people on Atlantis think that he suspected that Sheppard was a security threat made him sick to his stomach. He was honored to serve under a CO like Colonel Sheppard and it felt like being disloyal to him if everyone on Atlantis began to think that something was wrong with Colonel Sheppard because of his actions; even if the reason he was doing it was to protect him.

"You're right, Major. It might make whoever is after Sheppard let their guard down. Just make sure that the marines watching him know that it's his protection not his escape that they are to be concerned about."

"I most definitely will ma'am."

"Alright, please alert the others of what we have to do. If anyone asks, try to be as diplomatic as possible on the reasons why we are having John guarded. Explain that it is purely precautionary, until a full investigation has been done."

"I will ma-am,"

At Dr. Weir's nod, Lorne left the room and immediately began to radio the marines he wished to have guarding his CO's life. He knew they would be willing and honored to help protect the life of Colonel Sheppard. He just hoped that they'd succeed.

Not long later, several marines were standing in front of Lorne. They were in Sheppard's office as it was bigger than his own, and with such sensitive information he didn't want to use their general briefing rooms.

"…so to make sure that whoever is after Colonel Sheppard fails, I need to have you take turns guarding him, but here's the thing you have to act like your watching him because he's under suspicion."

"Sir, you mean we have to proceed like we believe Colonel Sheppard was at fault in the jumper crash and that he was responsible for the explosion?"

Lorne scanned the faces of the other men and saw the same distaste at the idea on their faces as on the marine who had just spoken. All these men respected Colonel Sheppard, and like Lorne, hated that they needed to act like the Colonel was a security risk.

In fact, pretty much all the soldiers on Atlantis, who had been there for longer than a month, would hate the idea. They respected Sheppard and many of them stopped just short of being in awe of him. However, Lorne thought wryly, Sheppard rarely realized how much he meant to his men, and how hard it was for all of them when he was hurt or in the infirmary.

"I dislike this as much as you do, but we need to do it to keep him safe, and make sure whoever is trying to kill him won't simply disappear and go after Sheppard when we aren't prepared."

The men nodded and Lorne felt a bit better now that he had someone watching Sheppard at all times. He just hoped that Dr. Beckett could figure out what was behind the last attempt; before the last attempt no longer was an 'attempt' and a future one was a mute issue.

…

To Be Continued

A/N: So now you know a bit about why the jumper crashed and such… I hope you liked the chapter and if you did…PLEASE review! ;) You can also review of course if you didn't….