Stargate SG-1 and Stargate: Atlantis, the characters and universe are the property of Stargate (II) Productions, Showtime/Viacom, MGM/UA, Double Secret Productions, Gekko Productions and the Sci-Fi Channel. The content of this story is solely for entertainment purposes and no copyright infringement is intended.

A/N: I am NOT in the medical, military, mathematics or science professions so what you read is just 'winging it'. Hope it all sounds plausible. Also in my stories there will always be Dr. Weir and Dr. Beckett.

This is the fifth and final story completing the story arc I've written dealing with Colonel Sheppard's disability. Preceding order: Three for the Price of Two, Conquering Adversities, Unexpected Surprises, Life Altering and now New Beginnings.

The story was beta read and any remaining errors are my own. Enjoy.

New Beginnings

Author: kwillads

"Where's John?"

"Dr. Weir I need you to sit down before I answer that." Carl's voice was smooth and solid like a rock. The same voice she had heard so many times before calming John down.

"I don't want to sit down. Where is John?" She stood with her arms crossed over her chest half way between the bedroom door and the suites door.

"Dr. Weir please, sit down and I will tell you everything." Carl pulled out one of the dining chairs for her to sit in while he pulled out another for himself. He stood there waiting for her to comply.

She was arguing with herself for being stubborn and wasting precious time that Carl could use to tell her where John was. Taking the offered chair she sat down at the dining table. Carl took that as his queue that she was now ready to listen and took the chair he pulled out for himself earlier.

"Colonel Sheppard is in the infirmary." Carl calmly stated putting a hand out to stop her from rushing off. Elizabeth eased back into the chair. "He is stable and currently sleeping."

"Why? What happened? When I saw him at lunch he was going to watch a movie. What happened?" She asked again.

"Nothing happened Dr. Weir. I found Colonel Sheppard resting when I came to get him for his treatment."

"Treatment! Why wasn't I told!" She shouted though Carl was mere inches away.

"There was nothing you or his team could have done. The Colonel wanted it this way. He would not have wanted you sitting in a waiting room. He said as much when he made his two conditions, besides, the procedure came about at an unexpected time. We had no idea how long it would take Dr. Zelenka to make all the necessary calculations. Dr. Zelenka had been working on the calculations for more than two days as you know. When he was sure Dr. Zelenka advised Dr. Beckett who in turn summoned me to get the Colonel that was around 14:30 hours."

"Is he alright? Are his memories back in place?"

"He is stable right now and sleeping that is all we know at this time. He was a bit dehydrated so we started an IV and are taking care of that. As for his memories he fell into unconsciousness at the conclusion of the treatment. We will have to wait until he wakes up to answer that question."

"I want to be with him."

"That will not be possible tonight. Dr. Beckett is keeping him in the isolation room and treating it as such. The only people allowed to be with the Colonel are the doctors and nurses. That is why Dr. Beckett sent me here to explain everything. Once the Colonel wakes you will be allowed to see him. Dr. Beckett said he would personally contact you when the Colonel would be allowed visitors. Now, have you had dinner yet?"

"No. John and I were going to have dinner together." Elizabeth murmured almost silently. She was having difficulty accepting all that Carl had told her.

"All right then, I will get you a tray and bring it to you. I won't be gone long." Carl stood up and left the suite. walking as fast as he could without actually running.

Carl entered the mess hall, filled a tray and turned to leave when his sister whistled from across the room as if hailing a New York cab to gain his attention. Christina had the best, sharpest, loudest whistle in all of New York. It made getting a cab easy whenever they had need of one. Turning about he made his way over to her table ignoring all the stares and surprised looks from the other mess hall diners.

"Sit down Carl and have dinner with us." Christina stated. "I want to tell you how my first day of class went."

"This is for Dr. Weir. I'm afraid I'll have to pass on dinner tonight." Carl replied turning to go.

"Dr. Epson, please what is wrong with Elizabeth? She was to have dinner with Colonel Sheppard tonight. She has been looking forward to it all afternoon from what I have been told." Teyla explained.

"I'm sorry Miss. Emmagan I really can't say. But I need to return." And with that Carl did leave. Leaving three stunned people in his wake.

"Something is wrong. I can feel it." Teyla stood to leave her dinner partners.

"May I come with you? I know I haven't been here long, but Elizabeth is my friend." Christina stated.

"I believe she would like that."

Christina stood and followed Teyla out of the mess hall. Ronon was only a step behind them.

Teyla activated the door chime and waited. Carl came to the door and exchanged a few words before going back to ask Elizabeth if she was up to visitors. Elizabeth allowed them to enter. They were John's friends, hers too, and needed to know what happened. They were not told about the treatment or why Rodney had been sent to Earth. Elizabeth owed them this much.

"Please everyone, come in and sit down." Elizabeth said from the dining table where Carl had placed her dinner. The small group entered and took a seat in the living space.

"Elizabeth, are you all right?" Teyla broached the subject as everyone became seated.

"I am Teyla, thank you for asking."

"We apologize for barging in like this. Please do not let us interrupt your dinner. We will wait." Teyla expressed on their behalf.

"Actually, if Carl doesn't mind he could explain what has been happening."

"I do not mind, as long as you eat your dinner." Carl was firm on the arrangement.

"Better do as he says Elizabeth. Whenever Carl gets that tone in his voice there is no arguing. And if you try, he always wins." Christina informed her new friend.

"Yes I know. I've heard him use that tone with Colonel Sheppard." Elizabeth took a few bites under Carl's watchful eye. "Carl start at the beginning, they need to know everything."

Carl nodded and moved into the living space with their three guests and took a seat on the couch next to his sister. "Three days ago we found out that Colonel Sheppard's memory disorder would become permanent if a treatment was not found. Dr. Heightmeyer, the resident psychologist, contacted her colleagues on Earth and together they came up with a possibly treatment."

"That is good, is it not?" Teyla said.

"It is good Teyla but it comes with risks." Elizabeth stated from her position at the table.

"Dr. Weir is correct, there are risks. Colonel Sheppard agreed to the treatment on the condition that Dr. McKay not be on Atlantis and must never be told or find out. Colonel Sheppard was more concerned with his wellbeing than his own. Not that unusual I know."

"So Sheppard had McKay sent to Earth?" Asked Ronon.

"In a manner of speaking, yes Ronon. Rodney went to Earth under the guise of finding a way to protect John and Dr. Lantis's implants from the EMP's and ARG's. General Brankovik arranged it and made the request sound as if Col. Carter had requested his presence.

Please remember what you are being told cannot get back to Rodney. It is as much for Rodney's welfare as it is for John's." Elizabeth informed them.

"We will keep this to ourselves Elizabeth. Please continue." Teyla gestured to Carl to continue.

"Dr. Zelenka has worked the past two days calculating the necessary requirements for the treatment which he finished around 14:00 hours today."

"Dr. Epson, what is this treatment? Was the time-lining not helping?" Inquired a confused Teyla.

"Colonel Sheppard said the time-line worked but only for those few moments you recounted the situations or missions. Some stayed a little longer but none of them stayed long enough for him to grasp a hold of, to recall later when he needed. When he tried to access them later or put them behind the doors that Dr. Heightmeyer explained about he was unsuccessful. Do you recall what I told you about electroshock therapy in our initial meeting?" Carl waited until he got some sign that the two Pegasus Galaxy natives understood to what he was inferring.

"Barbaric. Is what it was." Loudly voicing his opinion.

"I do not disagree with you Specialist Dex, it is to me as well uncivilized. However, this was our only course of action available to restore Colonel Sheppard's memory."

"By flooding his brain with more electricity?" Ronon seethed between a clinched jaw and balled fists. Teyla squelched her emotional disturbance over what John had to endure to get his memories back in place. Christina looked as outraged as Ronon but because she was from Earth she was more familiar with this practice. Many people had been helped using this therapy. She hoped for Elizabeth's sake it helped Colonel Sheppard.

"Yes. Dr. Beckett performed the treatment just a short time ago by sending an electrical current through Colonel Sheppard's brain at precise points. Colonel Sheppard remains in the infirmary under constant supervision and has not regained consciousness yet. He is stable and in no danger."

"Did it work?" Ronon growled. He'd seen some awful things in his years as a runner but never had he come across such barbaric means like this.

"We do not know as yet." Carl replied.

Teyla needed to know both sides before she could come to terms that this was the best course of action for her friend. It disturbed her greatly to know that John had once again put himself in harms way. "What would have become of Colonel Sheppard had nothing been done?"

"The new memories Colonel Sheppard would make would be tossed in with the old in no particular order. As time moved on he would find it harder and harder to recall faces, places, names, his military training. Dr. Heightmeyer said it would come to the point where he would not be able to recall his own birth date."

"That happened already." Ronon spoke up.

"What did?" Elizabeth and Carl asked in unison.

"Sheppard was in the gym watching me train. We decided to go to the rec room but he didn't remember how to get there. And he had to call me yesterday morning to find out where to meet for our run."

"Carl, are we too late?" Asked an emotional Elizabeth. She'd been aware of it too but thought John was just being funny about not knowing which scrubbie was his.

"I do not believe so. Colonel Sheppard was coherent during the treatment. But I will inform Dr. Beckett none the less."

"Can we see him?"

"No one is allowed to visit the Colonel tonight. Dr. Beckett is treating this like an ICU case, intensive care unit, only doctors and nurses will be allowed. We are hopeful that he will wake by morning. At that time Dr. Beckett will determine who can visit."

"I understand Doctor. Please inform us as soon as he can have visitors. Elizabeth, would you like for us to stay? It would be no bother."

"I would Teyla, thank you. Thank all of you for your support."

"We are family Elizabeth. It is what one does for our family."

"You can stay. I need to leave." Ronon growled getting up. He had fury in his eyes.

Elizabeth stepped into Ronon's path making Ronon come to a halt inches before her. She put her hands on his beating chest. "Ronon…" There were a million things she wanted to say. A dozen platitudes she could say to ease Ronon's fury. But everything she wanted to say escaped her. His eyes conveyed the loyalty, protection, friendship and caring he felt for John whether he would admit it or not. Ronon's eyes were very expressive. Elizabeth only hoped that her eyes conveyed what she wanted to express. Ronon wrapped his arms around Elizabeth and held her. In the same way John would. Ronon understood exactly what she said without so much as a spoken word between them.

Elizabeth embraced the warmth and touch of strong arms around her and Ronon allowed her all the time she needed. When they parted he nodded and moved towards the door.

"Specialist Dex mind if I accompany you part way? I need to fill Dr. Beckett in on what you told us. And return these dishes." Carl asked quickly.

"Suit yourself."

oOo

Mary sat in a hard backed chair humming as she watched the monitors, watched over the Colonel and checked the IV drip occasionally. Dr. Beckett hooked the Colonel up to an EEG to record his brain functions and added a pulse/ox clip to his finger. Colonel Sheppard's heart was strong and was in no danger so the heart monitor was pushed to the side. As her training and education informed her, her patient was in a deep form of sleep.

Two hours earlier Mary practically threw Dr. Beckett out of the door of the ISO room to get some rest. He was over doing the mother-henning he was infamous for. When Becky stopped by to check on the two she told Mary that Dr. Beckett was asleep at his desk. Not the best place to sleep but at least he was sleeping. Mary thanked Becky for covering her normal shift in the infirmary so she could stay with the Colonel. In fact, Mary was doing a double shift. She came on duty at 15:00 hours to assist Dr. Beckett and refused to leave. She planned to stay with him through the whole sorted mess. She was the only nurse on staff that had ever assisted an electroshock therapy. Nellie was fresh out of nursing school and ROTC training. Becky and Pasha were trained specifically in OR procedures but since coming here they had both broaden their skills. Colleen had extensive emergency medical training and worked at a hospital in East LA before coming to Atlantis.

Mary continued to hum while she sat watch over the Colonel. John began his road back to consciousness in stages. He found himself in a dark, dark place, his body heavier than normal. He couldn't seem to move a muscle let alone his pinky finger. Far off in the distance in the blackest darkness that surrounded him he thought he could hear a faint noise. He strained to hear it. His muddled brain wasn't able to distinguish if it was a voice or sound. It was too far off in the distance. John's strength was waning. He concentrated on the noise. Was it friendly or harmful? He was hoping for friendly.

The second time he climbed towards consciousness he could feel something soft underneath him. A warm soft feeling covered him like a blanket. John tried to open his eyes but they weren't ready to greet the world. A pleasant sound rang through his ears but the darkness called him back.

On John's third attempt he was successful. Didn't they say 'third times the charm'? He had managed to climb out of the darkness that surrounded him and comforted him all at the same time. Opening his eyes to mere slits taking in his surroundings he discovered he was still in the infirmary. Comforting blankets pulled up to his chest. His left arm rested across his mid-section with one of those finger clips. The sound he heard in the darkness was now recognizable. Mary watched over him humming a merry little melody. It wasn't familiar per se, but he'd heard it before just the same.

Over the years when he found himself waking up in the infirmary there had been many times that Mary was either singing or humming as she performed her duties. It was comforting to say the least when the fog and pain of his injuries tried to consume him.

John relaxed back into the soft pillow supporting his head. He let the melody wash over him in calming waves as if he were sitting on the beach as the lapping waves rolled to shore. The room was still and peaceful. As far as he could determine it was just him and Mary. When John heard the chair leg scratch against the Ancient floor he opened his eyes to see what was going on. Unbeknownst to Mary he watched as she checked his IV, recorded the numbers and readings from the two monitors.

Her humming was interrupted when Mary noticed a pair of hazel eyes looking in her direction. "Don't stop." The craggy voice managed to say.

Mary was at his side with a small glass of water that held a straw. "Small sips Colonel." She reminded taking the glass away before he could over do it. "How are you feeling?"

"Fine." Mary smiled at the familiar remark.

"Colonel we've been over this before many, many, many times. You know I don't like it when you give me one word answers on your condition. You also know the consequences. Now shall we try this again? How are you feeling?"

"I'm fine. That's two words. Although 'I'm' is a contraction of 'I am' so technically one could argue that was a three word answer." John smiled at his little attempt at humor. "In order for Beckett to warrant submitting hazard pay for you I have to give him a reason and giving you a hard time is the only one that works. You. Should. Know. That." He punctuated each word with a silly lopsided grin on his face. "By the way where is Carson? I would have thought he would be here hovering."

"He was hovering until I threw him out a few hours ago to get some sleep. Now honestly, how do you feel?"

"I'm good." He couldn't resist and Mary, all 5'3" of her, was about to strangle her patient she had been worried about for hours.

"Consequences it is then." Smirking back.

"How long?" John changed the subject praying Mary wouldn't follow through with her threat.

"Going on nine hours."

"Only nine hours—wow I think that's a new record. I thought maybe since you were still here it had been a few days." Sheppard explained.

"I could tell you the truth and say you're my favorite patient and I wanted to see this through to the end. And that I volunteered for a double shift just so I could keep an eye on you. Or I could lie." Mary stated.

"I'll go with the lie." He laughed. "I wouldn't want you to ruin your 'tough guy' image. Do you know if Elizabeth, Teyla and Ronon know? I remember there wasn't much time."

"Dr. Epson informed Dr. Weir of your condition. I'm not sure about the others. Oh and before you ask, no, Dr. McKay is not back. Rumor has it he should arrive later today. I heard he's over stayed his welcome at the SGC. Now it's almost 02:30 why don't you get some more sleep and I'll have breakfast waiting for you when you wake up. I can only imagine how hungry you'll be after starving yourself."

John was duly chastised. Now that he had his memory back in check, he knew starving himself was a stupid thing to do. But at the time it was the lesser of both evils. John didn't want a repeat of his captivity. It was bad enough he had to deal with the memory of Stevie a memory that had taken him upwards of a year to compartmentalize. A quick thought passed through his mind to argue with his nurse but decided against it. In all truth he was tired as well has hungry. So instead he gave a polite, "yes ma'am." Snuggling down deeper into his pillows and closing his eyes.

TBC 37/60