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Author's Chapter Notes: John learns things are not what they always seem to be.


When General O’Neill and Colonel Sheppard rematerialized they were in the infirmary of Atlantis and were immediately led over to an isolated area by armed guards who then locked the pair into an isolation room and they watched the medical personnel getting into their Hazmat suits. Once Dr. Beckett entered the room he asked who was first and General O’Neill said he would prefer to go first, so he went over to the scanner bed and laid down waiting for the scanner to pass over his body as the guards armed their weapons prepared to shoot if things went wrong. Carson advised the General that he was clean and John walked over to the scanner bed, waiting a few steps away so not to risk possibly infecting the General. Once clear, John got up on the scanner a bit apprehensive about what the scan would reveal.

There were so many thoughts running through John’s head as he lay under the scanner but one thought was prevalent, if Victoria Weir was dead then where was he this weekend. He knew he took an airplane from Colorado Springs to Dulles but didn’t have the airline ticket with him it was back in his flight duffle bag. Other thoughts were flying through his head making him wonder just who he spent the weekend with and then it occurred to him, whoever he had been with was making him dream or believe he had seen Elizabeth and had sex with her, he knew it wasn’t right. All of those images had implanted into his mind probably to distract him so they could extract some other information, but what were they after? He didn’t have any special secrets and if the object was gate codes then they must have known that the SGC would change them right away, so why him and why use Elizabeth because he knew she was dead. It just didn’t make any sense to him.

His thoughts were interrupted by Carson who told him the scan was over and he too was clear and neither of them had any nanites in their system and he doubted if they would because last he remembered they were not programmed to go into people with the ATA gene.

“Well I’m sure that they weren’t originally designed to re-write someone’s mind but they were trying to do that when Dr. Weir was infected with them,” O'Neill said with a stern look on his face.

“That may be true General but Elizabeth did not have the ATA gene so the nanites might have considered her and her body something to be reprogrammed,” Carson said after removing his Hazmat helmet. “Sheila will you please go put this away for me,” he said as he handed his helmet to one of the nurses.

John noticed that she looked at him but not in a way that showed that she was attracted to him but more one of curiosity and then she smiled sweetly at Carson and left with the helmets. John was used to women looking at him and of course he checked out women but the way she looked at him was different and he was beginning to wonder about it until General O’Neill got his attention. John then realized that the General had been talking on his cell phone and he hadn’t heard a word of it, his mind was elsewhere so when the General said his name he did his best to cover up the fact that he wasn’t listening when the General was speaking.

“Now that I have your attention again Sheppard, I just got off the phone with General Carter and she is in agreement with me that for now you should be kept in isolation until we can sort this out,” he said with a grim look on his face.

“What? Come on General, isolation? Can’t you just keep me from going off world or something like that? Anything but isolation sir, please.”

“I know it sucks Sheppard but until we can sort this out we need to keep you out of reach of who ever it is that probed your mind,” Jack replied.

“Well if it has to be isolation why not keep me here on Atlantis, I could help them figure out some of the equipment here and,” he was saying before he was interrupted by the General pulling him aside.

“Sheppard, that’s not possible,” the General stated.

The sad but the look on John’s face indicated that he would need more of explanation so the General stepped around a corner and John followed the General down the hall until he was sure that no one else would overhear them.

“Atlantis is only being manned by personnel involved with the deconstruction of Atlantis and only those persons are allowed to be on the ship,” General O’Neill stated in a way that left no room for questions.

“So we’re tearing it apart,” John whispered with shock evident in his voice.

“I don’t like it any more than you do and believe me when I say that I fought the IOA about it but apparently I was in the minority. Unfortunately I didn’t have a little grey alien to use as an ace up my sleeve since the Asgard are gone now. The IOA are planning on learning how this place operated and hope to combine it with Asgard technology and of course they state that it will only be used to on ships to protect Earth.”

He saw the look in John’s eyes but the look he gave John in return showed that this was a sore subject with the General.

“I’m not done fighting yet Sheppard so don’t give up the ghost just yet.”

“If you don’t mind me asking sir, what is going to happen to Carson, Ronon, Teyla and her son? Are we just going to leave them here stranded on Earth,” John asked in his lowest most controlled voice.

“I’m working on to remedy that situation and soon they will need to make a choice of where they want to live but we’re not at that stage just yet. But for now Sheppard you are grounded and are being transferred out of the SGC because someone knows your routine and was able to get to you so for your safety as well as that of the program you are going to be temporarily reassigned and let me stress that this is only temporary. General Carter is getting someone to gather up some stuff from your apartment and it will be sent to your new location.”

“Sir, there should be an airline stub showing my flight number and airlines in my flight duffle and a receipt from my parking at the Springs airport. At least that’s a place to start on this mystery,” John said.

The two men walked over to the main room where the Stargate and control room were located and there was a look of pain in both of the men’s faces as they looked at what was remaining of the once lovely Atlantis which is now apparently only good for spare parts thanks to the IOA. John looked over at the General and told him this made him sick to his stomach and he couldn’t believe what idiots the IOA were to strip Atlantis. O'Neill’s face softened as he turned to speak to Sheppard.

“They’re all a bunch of political idiots who have their heads so far up their ass they will never be able to see daylight again. Their main concern about Atlantis is only people with the ATA gene can fully control this wonderful city which means that they can’t put one of their puppets in command and I believe that is why they are stripping the city. If they think that they are going to get their hands on Asgard technology or information they are in for a big disappointment because it contains the downloaded information and it was given to us not the IOA. I’ll be damn if I ever let them have that information,” Jack said through gritted teeth.

Thankfully the pair was interrupted by the Hammond who advised they were ready for transport. A light engulfed them and they each went their separate ways away from a dying city.


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