Sheppard's Pi

By Evergreen

SUMMARY: Two years after the first Wraith attack finds Atlantis and her crew in a very different place. The only problem is that John Sheppard doesn't remember any of it!

Major John Sheppard woke up suddenly as if from a bad dream, but he couldn't seem to recall it as he sat up in bed. His eyes quickly scanned his dim surroundings and ascertained that he was, in fact, not in any immediate danger. He was about to roll over and go back to sleep when he noticed that something had moved and was now pressing up to his right leg. He leapt out of the bed, heart pounding, in order to face his "foe". He backed up slowly towards the door and willed the light switch to turn back on. His eyes settled back onto the bed to determine his adversary to see that it was Teyla!

"Teyla?" John exclaimed and he stumbled backward out of the room. How did that happen? He thought he heard Teyla calling after him as the door slid shut. He had absolutely no recollection of asking Teyla to share his bed that evening. He shook his head in an effort to clear it. He also didn't remember, or feel like, he had been drinking heavily enough to warrant his blanking out. He looked down at his state of clothing and noticed that he was only wearing his pajama pants. He walked slowly towards the end of the hallway, desperately trying to remember what had happened last night. His head started to buzz with the effort. He decided to head towards the locker room to score a shirt at least and something to put on his bare feet. As he walked towards his destination, he began to notice his surroundings. The lights in the hallway seemed to glow a little brighter than he remembered. Probably just my imagination. All the electronic displays lit up for him as he passed as usual, so he just sighed and kept walking. No one was in the hallway or in the locker room as he entered. He padded over to his locker and proceeded to enter the combination into the keypad. It buzzed at him several times before he gave up in disgust. Things were getting just a little too "Twilight Zone" for him.

His fingers went up to his right ear to engage his comm., when he realized that he hadn't grabbed it during his hasty exit. He shook his head and decided to head back to his room and talk to Teyla. Perhaps she would understand what was going on. He was hit with his first wave of vertigo about halfway back to his quarters and slammed up against the wall to prevent himself from falling down completely. It passed quickly and he decided to move a little faster to make it back to his quarters before anything else happened. He was about to trigger the door on his quarters when it slid open to reveal a puzzled-looking Teyla. And as if a huge hand shoved at him from the front, John Sheppard was swept to the floor and into darkness.

"Colonel, can you hear me? It's Dr. Beckett. Open your eyes if you can." The Scottish brogue of the station's doctor brought John back to the surface of consciousness.

"Yeah, yeah. It's still Major to you, Doctor." He opened his eyes and started to sit up when the sudden feeling of lightness in his head stopped him. "Whoa. I think that I'll just lie right on back down. Man, I feel like crap."

"I know…John. I'm just glad you're awake again. You've been in and out of consciousness many times over the last couple of days. How do you feel exactly?" The doctor flashed a bright light into John's eyes as he asked the question.

"I feel as if my head is not really connected to the rest of me, like it's floating a few inches above my shoulders, if you know what I mean. I have a roaring headache and my stomach's not very happy with me right now. How's that?" John stared back at the ceiling.

"I ran some tests and I'm still not entirely sure what's going on with you. No one else has presented with the same symptoms and I can't find any evidence of disease. What's the last thing you remember?" Dr. Beckett was making a few notes in John's medical file. A few people wandered around the infirmary, but there didn't see to be anyone else actually requiring medical attention.

"I was just getting ready to deliver the nuclear device to one of the Wraith motherships…then waking up next to Teyla just a little while ago…," he trailed off in an effort to gauge the Doctor's reaction. Dr. Beckett did not flinch, react, or even look up at John's admission. He closed his mouth and waited.

"Wraith attack?…Anything else?" Beckett looked back at John, purposely hiding his emotions at his response.

"No, I think that's about it. Obviously, it went well or we all wouldn't be here. Have all the Wraith been eliminated from the city? Any casualities? Damage to the city?…I need to talk to Elizabeth.." John started to get out of bed and then stopped as he observed the expression on the Doctor's face. "Why? Is there something else I should know?" He looked directly at the doctor, trying to figure out what was wrong.

"It's just a question." The doctor put down his notes gently pushed John back into a supine position on the bed. "John, this may sound like a really stupid question to you, but what year is it?"

"It's 2005, earth time, of course." John closed his eyes and waited for a response against what he was sure was not what he was expected to say. He was also sure that the doctor was hiding something from him. "Are the Wraith gone? I can't seem to recall how things ended with them."

"John, it's 2007, Earth time. The Wraith have been defeated for about a year or so. You were promoted to the rank of Lt. Colonel after the Wraith attack and you had returned to Earth."

"Are you kidding? Promoted…Returned to Earth…You're kidding me. Am I hallucinating again, like on that planet with the mist people? Did McKay put you up to this? Just how much did I drink last night?" John tried to sit up again and valiantly attempted to fight the vertigo that washed over him again. He groaned and closed his eyes.

"Just rest. I will talk to you again in a little while. Try not to think about it too much." Dr. Beckett pressed his fingers to his comm. device and called Dr. Elizabeth Weir to let her know that he was coming to her office with a status report.

"He doesn't remember the last two years, since the Wraith attack, Elizabeth. I'm really quite puzzled by this. He has symptoms of vertigo and headache, and of course, the amnesia." Carson Beckett sat down in the well-worn chair in front of Elizabeth's desk.

"I'm sure you're doing everything you can. He doesn't remember anything since the first Wraith attack?" Elizabeth was incredulous. So much had happened since that fateful attack. The SGC had finally been able to send reinforcements in the form of ships, supplies, and troops to assist them in the defense of the station. The Asgard were also a huge help in containing the Wraith after General Jack O'Neill had reminded them again how Earth helped them with their little 'replicator problem'. All Wraith survivors had been put into stasis until it could be determined what could be done with them. In the mean time, the Pegasus Galaxy had begun rebuilding, for the first time with the knowledge that the culling would finally be over. General O'Neill had decided not to continue as the head of the SGC despite some major reorganizations, had met with Elizabeth before retiring to determine next steps. O'Neill had strongly recommended that Elizabeth be allowed to remain in control of Atlantis. Colonel Sheppard remained on the station as had most of the original staff. Teyla Emmigan had decided to remain on the station as her people relocated back to their home planet. She continued on as a member of the SGA exploratory team and to act as her people's ambassador and advisor to Atlantis. A new leader had been appointed in her stead and she had felt freer to narrow her focus to her goals on the station.

Dr. Rodney McKay and Teyla stood restlessly outside of Elizabeth's office, waiting to be called in for an information update about the Colonel. "You really should be sitting down in your condition. Especially in light of what's going on. The less stress, the better." McKay's uncharacteristic display of concern touched Teyla. Rodney kept himself busy studying the huge caches of information and technology still being discovered on Atlantis and around the galaxy.

"Thank you for your concern, Doctor, but I feel fine. I am not too anxious to sit down." Her hand went protectively to her abdomen, over her growing baby. The door opened and Dr. Beckett stepped out with a look of worry across his features. "Can I see John now?"

"I wouldn't recommend it quite yet, lass. I think that we need to get him comfortable with the fact that he's not back at the time of the Wraith attack before we introduce the idea of your relationship and the impending addition to your family." He patted her stomach gently. "I'm sorry. I will call you as soon as his condition improves." He smiled lightly at her. "Rodney," the Doctor nodded his head at the scientist and strode back towards the infirmary. Rodney nodded back.

Teyla needed more information. "Dr. Weir, what do you think happened to John?" Elizabeth looked up at her.

"I wish I could tell you more, but I know as much as you do about the situation. The Doctor will keep us informed as to his progress. Perhaps you could check with your people and see if they ever had experienced this sort of phenomenon. Or maybe any of the other people you have encountered in your travels. Any information will help." Elizabeth stopped her fingers drumming on the desk as soon as she realized that she was doing it.

"I will, thank you, Dr. Weir." Teyla left with a purpose, at least. Something to divert her from the fact that her husband didn't remember anything about their life together.

Elizabeth organized her stacks of paper for the third time before she realized what she was doing. She didn't enjoy being distracted. She was glad at least that Teyla had something to do to keep her mind off things. Everyone on Atlantis had become such a close-knit family over the last few years that when any one of them was out of action, they all worried. She decided to put together some notes for her discussion with the General later on that day. She thought back to the beginning of this expedition and how Jon came to be part of it. Although Sheppard and General O'Neill didn't know each other very well, they had shared a kinship. They were more alike than either one of them ever wanted to admit. Both of them shared a strong connection to the Ancients. She had met the General briefly who had taken over from O'Neill, but he seemed receptive enough to her ideas and she felt comfortable he would support her in any actions that she felt were necessary.

"I'm sorry to hear about the Colonel's condition. Is there anything you need? Additional medical staff or supplies? I'd be happy to send Daniel Jackson your way and let him study some more Ancient artifacts, perhaps he could find something in the databases. He's been itching to spend more time on Atlantis anyway. I'll send him with the supply run that's coming through the 'Gate tomorrow." Colonel Carter's smile did a lot to cover for her concern, but not quite enough.

"How're the boys, Colonel? Are they 10 months old already?" Elizabeth decided to change the subject. Sam usually loved to talk about her kids, twin boys adopted with General O'Neill. They had been married last spring. "How's the General been?"

"Great, yes, it's amazing they're getting so big, and Jack's fine, too. The boys are keeping him busy. The kids are surprisingly challenging, considering the both of us survived the Go'auld for so long. How's the growing brood on your end? How many new ones do you have now?"

"Well, Lt. Commander Greene and Dr. Johnson had their first child, a girl, about three months ago. Several more additions to Teyla's people, but as there not here full-time, we sometimes forget how many they have now become. And Teyla herself, we expect her to give birth any time now… John had been so excited… He'll be fine soon, I'm sure. And in time for the birth of his child." Elizabeth looked down at her desk.

"We wish all of you the best. Please let us know if anything changes. I'll brief the General. Stargate Command, out." Sam said softly.

"Thanks, Sam." Elizabeth nodded to her. "Atlantis, out." The screen went blank and she heard the "whoosh" of the Gate event horizon blinking out. Elizabeth sat back in her chair and sighed. Nothing was ever easy in the Pegasus Galaxy.

John woke up again, this time feeling a lot more like himself. He sat up slowly, half expecting the vertigo to knock him back down. For now, anyway, it seemed to have subsided. He sat back against his pillows and surveyed the scene in the infirmary. Nothing out of the ordinary seemed to be going on, but things definitely looked and felt different. How or why he just didn't know just yet.

"Ah, Colonel, you're awake." Dr. Beckett came over to his bed and started to take John's blood pressure and pulse.

"Yeah, thanks.,..I did manage to wake up this time. What day is it?" John asked, trying to sound lighthearted, but knowing the answer probably wouldn't be what he wanted to hear.

"How about you tell me? What day is it exactly?" Carson stopped everything else he was doing and looked right at John.

"Where's Elizabeth? I want to talk to her." The set of his jaw showed that he meant business, at least that was the look he was going for. While the Doctor went to call Dr. Weir, John decided to get out of bed and make himself a little more professional looking. He peered into a nearby mirror and attempted to straighten his bed-head. Not much luck there. He couldn't meet Elizabeth looking like a mental patient, so he decided to head back to his quarters to change, maybe grab a shower. He tried to avoid as many people as possible to minimize the strange looks he was getting. He slipped into his quarters and headed for the bedroom. The décor was different from what he remembered, there were women's things around as well. Had they reassigned his quarters to someone else while he was out of commission? No, he did notice some of his own stuff mixed in and a bunch of things he couldn't place at all. He sat on the bed, willing his head not to go all wonky. How could all of this have happened? He couldn't remember the last two years? He put his head in his hands and hoped for some inspiration.

"John? Are you okay?" He heard Teyla's gentle voice sometime later.

"Hmm?" He opened his eyes wider in shock as he saw her in entirety. "Teyla? You're pregnant?"

"Yes, John. The doctor says that I could have our…the baby any time now." She smiled at him lightly.

"How did that happen? Well, I know how that happened…but who? Who's the father?" So many questions swirled around in his head.

"You are, John. We were married last year." She picked up a picture from the dresser showing the two of them smiling while cutting a cake, with everyone from the crew surrounding them. They looked unbelievably happy. She sat down next to him on the bed. "Do you remember anything from the last two years?"

"Nothing. To me, it's the day of the Wraith attack. I'm sure as hell glad that we all survived. I guess you'll have to fill me on the details about that and other things…" He smiled. "Do you mind?" He asked as he held his hand over her belly.

"Of course not, John. Please." She guided his hand to her stomach and placed it on her right side. "Here, the baby's been moving around a lot. If you wait just a minute, you may feel something…there. Did you feel that?"

"Wow, that's amazing! Do you know if it's a boy or a girl?" He asked as he moved his hand around her stomach.

"You said that you wanted it to be a surprise. Athosians never had the technology to determine gender before birth before, so I never considered it. What do you think?" She placed her hand on top of his.

"I think it's one of the best surprises you can get." He looked around again. "Do you know what happened to me the other day that may have caused this?" He turned to see her reaction when he heard his name being called over his comm.

"Colonel Sheppard, this is Dr. Beckett. Please return to the infirmary. Your test results are in."

He touched his comm, "This is Sheppard. Be right there….Teyla, do you want to come? My test results are back." He pulled on his uniform jacket and pants and ran another hand through his hair. "Do I look more presentable?"

"Of course, John." She tried to smooth out his hair again. She gave him a wry smile and gave up.

"Thanks, let's go." He followed her out into the hallway.

John, Teyla, and Drs. Weir, Beckett, and McKay all met in a conference room off of the main infirmary room.

"Okay, Colonel, some interesting things came up in your tests, but I'm afraid they may raise more questions than answers." Dr. Beckett queued up some statistics and charts onto a computer display set up near him. "I ran some diagnostic tests and compared the results to your baseline, which we had gathered when we all first arrived here. I didn't detect any substantial differences as you can see here," he pointed to some charts that didn't mean anything to John. The doctor described more data to the group that to John sounded like another language…. "Your ancient gene seems to have produced much more proteins that are circulating in your blood that we had ever detected in you before. I have compared some of your blood samples from when we first arrived to today and there is over a 400 increase in the proteins now."

"And what does that indicate, Doctor?" Elizabeth leaned forward in her chair.

"I'm not really sure. It doesn't seem to have too much of a physiological effect, except that his brain seems to be assimilating it a little more slowly than the rest of his body. Perhaps that is causing the headaches, the vertigo and the amnesia. I will run additional comparisons over the next few hours and days to see if there is any normalization going. We may have to do a spinal tap to determine protein levels in the cerebral fluid if things don't improve."

Colonel Sheppard sat back in his chair considering this possibility. It sounded just as preposterous as his amnesia. Teyla shook her head slightly, but showed no emotion at this news.

"Teyla, have you heard anything yet from your people?" Elizabeth asked Teyla, who seemed to be thinking very deeply about something.

"Um..I haven't heard back from Holling yet, there is a regional meeting he is attending. I expect to hear from him upon his return. I will report to you as soon as I can." Teyla reported, after regaining a little composure. She began to rise as Elizabeth adjourned the meeting.

"Doctor, please keep us informed. Thanks, everyone." Elizabeth's thoughts were still scattered as she left the room.

The soothing waves always seemed constant and ever changing at the same time. John sighed as he leaned over the railings just a little bit more. He came right out to the balcony after the meeting. Teyla had said something about needing to rest for awhile. He figured he should give her some room. The crisp wind blew right down the back of his jacket and he shivered. He tried very hard to think back to the last thing that made sense, back in the day of the first big Wraith attack on the station. Nothing. For once he was afraid that he would have to rely on his teammates to figure this mystery out. He was just too tired to think about it any more.

His thoughts did slide over to Teyla, he felt for her confusion over this whole situation. He had been committed to her and they were having a baby. How could he not remember that? Not that he was against it, he wasn't, but it was awfully difficult to make the shift from being attracted to her during combat practice to having a family with her. He felt very disjointed with this whole thing. How the hell was he going to get out of this?

He didn't think about how long he had actually been out on the balcony until he began to shiver. Darkness had just started to fall and the last remaining beams of light from the sun stretched very far across the water. The warmth of the day had dissipated and the coolness of the ocean spread beneath him. He had a feeling of being very insignificant all of a sudden and realized how unusual that was for him. He rubbed his upper arms in an effort to warm himself and turned to leave.

Something like an echo formed in his head, "We have a kill. We have a kill. One Wraith mother ship has been destroyed…" A huge cheer swelled up from the group still gathered in the Control Room

"Good news, Rodney…. What about the other two?" Elizabeth turned and faced John with a smile on his face. He did not return the sentiment as he knew what was coming. Elizabeth's face fell slightly at his lack of response.

"Atlantis, the satellite has been destroyed. Grodin was on the satellite. The remaining Wraith ships are pulling back….Het's only bought us some time…."

"Understood, Rodney. Return to Atlantis…."

"Sheppard? Are you okay?"

"Hmm?" The last voice was louder, more real. McKay stood next to him, John had not even noticed until he began speaking. "Yeah, I'm fine. Let's go in, I'm freezing." McKay followed him back into Atlantis.

John walked slowly back to his, no his and Teyla's quarters, not sure if he really wanted to actually get there. The feeling of vertigo he had earlier swept back and made the edges of his vision fuzzy.

"How many of you are in Atlantis?

"What's your name?…Okay, Bob it is. Tell..me…how…many..of..you …are in Atlantis?" He heard himself ask as he shot round after round into a hostile Wraith.

He found himself staring at the door to his quarters, not quite sure what to do next. He breathed out slowly and willed his heart to stop pounding so fast. He knew, desperately knew, that something was wrong with him, with everything. He couldn't seem to figure it out and no one else seemed especially concerned with the fact that he couldn't remember anything of the last two years. He didn't even have any feeling of lost time, like the memories were locked away or something. There was just a blank, a hole. He sighed again and walked into his quarters.

People were concerned, several in fact. Elizabeth sat over a rapidly cooling cup of tea with Carson in the commissary, wondering what to do next. "I suppose we should request another military officer to fill in for the Colonel while he's recovering. Lt. Commander Greene would be a logical choice." Elizabeth was speaking, more trying to convince herself than the doctor that it was the right course of action. He nodded, knowing that she was not actually asking for his opinion on the matter. Those types of issues were what she usually discussed with the Colonel. She paused and swirled the tea leaves that had settled in the dregs at the bottom of her cup.

Carson pored over the sheaf of data that he had brought with him from the infirmary. He had run every test that he could think of, some several times. Nothing much out of the ordinary, besides the level of Ancient protein in his blood and his puzzling symptoms. The doctor and Elizabeth continued in their quiet contemplation of their problems for several more hours.

Carson's barely hidden yawn of exhaustion brought Elizabeth out of her thoughts. "You, to bed. I will see you in the morning." She rose from the table and followed him towards their respective quarters.

John lay next to Teyla, careful not to disturb her. Things were very distinctly weird. He stared at the ceiling in the darkness and wondered how the hell he was going to get out of this. He closed his eyes and let his thoughts wander.

"Major, you stop killing my men and turn yourself in and I may not have to kill Dr. McKay here and the lovely Dr. Weir." John could almost see the grin of self-satisfaction on the face of the Genii General as he held Atlantis hostage.

"Never," he thought, as he ran through the station. "You will never take me alive. I will get us out of this." The sound of a single gunshot ripped him out of sleep and sitting bolt upright in his quarters.

"John, it is alright. It was dream, you are safe." Teyla was rubbing his arm. He patted her hand as he tried to steady his breathing. All of this was happening for a reason. He just had to figure out why.

"I'm fine, Teyla. You go back to sleep. I'm going to take a walk. I'll be back in a little while. I'll have my comm. If you need me." He kissed the top of her head as he slid out of bed. He was amazed how natural it felt to have her here, caring about him. He pulled on a tee shirt and popped his comm. into his ear. He slipped into the hallway, almost in stealth mode, and he really wasn't sure why. He didn't see any reason why, but he couldn't shake the feeling that he needed to be careful. He stopped by one of the armories and convinced the guard that he needed to check something on a log or something. He grabbed a handgun and slipped it into the empty holster on his right side. There, now he felt a little more secure. Can't be too complacent. He acknowledged the guard and made his way down to the Gate room. He surveyed the darkened room and tried to convince himself that nothing was wrong. He had a little niggling in the back of his mind, something… He took his gun out and kept it at the ready as he assessed the room. He walked up to the gate and touched it. The Gate began to activate, the chevrons locking into place with speed he had never seen before, especially here on Atlantis. The activation alarm sounded and several guards raced into the room.

"Colonel, drop the weapon! Sir, please drop the weapon!"

"Unauthorized gate activation! Unauthorized gate activation!"

John did not move until the horizon swooshed past him. He jumped through the Gate as soon as it stabilized.

"General, he's awake! Doctor!" John's eyes blinked open slowly as he saw a bright light being passed into his eyes. "Pupils equal and reactive. Pulse and respiration normal."

John blinked again and shuddered when he saw the face of General Jack O'Neill over his. "What the hell is going on,..sir?" He asked as he tried to sit up.

"I was hoping you'd tell us. You were requested to sit down in the Ancients' chair here after me and you went out like a light. You were out for a few minutes. How do you feel?" Dr. Beckett asked. The General looked at him in the most peculiar way.

"Where is here?" He looked around and saw Rodney, Carson, Dr. Jackson and a few others he remembered seeing only once before. They all were observing him strangely.

Dr. Jackson looked quizzically at John. "The Antarctica base, of course. We were hoping to find information about the location of Atlantis."

"Oh, crap."

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