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

Things on Atlantis took an unexpected turn two days later when the IOA sent a three member delegation through the gate along with a Russian Military negotiator without any advance notification. As the senior staff assembled in the conference room tensions were running high. No one knew why the IOA was here or why there was a Russian negotiator. This impromptu visit from the IOA had everyone on edge. Once everyone arrived and took their seats the doors were closed and locked.

"Thank you all for coming on such short notice. Let me start by first introducing our four guests. On my right is IOA member Pierre Lafayette. Sitting on his right is IOA member Inez Juarez. Seated next to Ms. Juarez is IOA member Vladimir Petrov and General-Mayor Doctor Priboie Brankovik of the Russian Nationalist Military. On my left let me introduce my senior staff; Colonel John Sheppard Military Commander of Atlantis, Lt. Colonel Evan Lorne Second in Command of the Military, Dr. Rodney McKay Chief Science Office, Dr. Radek Zelenka Chief Engineer, Teyla Emmagan Leader of the Athosians, Specialist Ronon Dex formally of Sateda and finally, Dr. Carson Beckett Chief Medical Office here on Atlantis. Now that introductions are completed I will leave it to our guests to inform us why we are gathered here today." Dr. Weir took her seat and waited.

A stressful and silent two minutes passed before IOA member Inez Juarez stood to address the assembled. "Thank you Dr. Weir. As you might know the IOA and its coalition of countries, who are aware of the Stargate program, carries substantial influence in determining how the Stargate Program is run and funded. The International Oversight Advisory committee decided several years ago to place the weight of their funding into this expedition. Undoubtedly you are all aware of this. It is the IOA's position and strong recommendation that Atlantis be given a new direction. Therefore…"

"Excuse me, Dr. Rodney McKay here, exactly what kind of 'new direction' are we talking about here?" Rodney used his hands to emphasize air quotes. "I for one like the direction Atlantis is going in right now. I don't see a need to change it. Scientific endeavors and breakthroughs are happening on a daily basis around here. Just look at Colonel Sheppard there. A few months ago he had been a two year paraplegic. Now he's walking again."

Vladimir Petrov stood up to address the Doctor's concern. "Dr. McKay the new direction of Atlantis will have no bearing on the scientific community working here. Those of us at the IOA are astonished at the number of…what did you call them…oh yes…endeavors and breakthroughs. We have no desire to change or hinder that. In fact we want to pursue more of that. We feel there is a lot to be learned from the Ancients, therefore…"

"…Therefore…" Inez Juarez stepped back into the conversation. "Therefore, we at the IOA have decided to make only one change. That change will be in the leadership of Atlantis. Dr. Weir has an exemplary record for being a negotiator, both here in the Pegasus Galaxy as well as back on Earth. She has done well here but it is time for a change. The IOA has decided that a military officer would be better suited to lead the Atlantis Expedition against the fight with the Wraith. We've chosen such a person. He has a broad military background along with the credentials of being an excellent negotiator as well. That being said, General-Mayor Priboie Brankovik will assume leadership of the Atlantis Expedition effective immediately." Ms. Juarez finished the announcement, in all her self glory, taking in the stunned looks of the senior staff members. Gloating inside she stared at Dr. Weir before continuing.

The room was silent as each member of the senior staff absorbed the IOA's declaration. Not just any silent, but an eerie silent.

"Dr. Weir, the IOA would very much like for you to remain on Atlantis as a negotiator and as a teacher of Ancient language. We do understand if you choose differently. But we hope that you will consider staying. You are a value to this expedition whether you are in a command position or not." Ms. Juarez stated smugly. The smile creeping across her face was getting harder for her to control and hide.

Gathering all her strength Elizabeth rose, "thank you Ms. Juarez, I will give that some thought. Was there anything else…?"

"No. We will be staying a few days however."

Standing on shaky legs Elizabeth addressed their guests one last time. "I'll see to it that guest quarters are made available. With your permission General," Receiving a curt nod and a wave of hand from General Brankovik, "you are all dismissed."

At first no one moved. Stupefied at the news and even more dazed that it was a total surprise. Usually when something like a change in command was about to happen word leaked out and rumors were started. But this – this had to be the most guarded secret of all.

With her head held high Elizabeth exited the conference room. Just before heading down the grand stairs she tapped her comm to have Zaida make guest quarters available for their unannounced visitors. Duty was duty. She didn't stop moving until she had reached her quarters.

Colonel Sheppard was about to rush out the door after her. It was only the quick response of his second in command that stopped him from bolting. Elizabeth had already received permission but military protocol demanded that Colonel Sheppard make the same request as senior military officer. "General, permission to be dismissed."

"Да. Pa3pewehne xpopwo." The General stated his order in Russian before realizing his mistake. By the time the General restated his comment in English, Colonel Sheppard was already out the door. "Yes. Permission granted."

Jumping down the set of three small stairs to the landing Sheppard caught sight of one of the gate room technicians. "Dr Weir?"

"That way Sir." The technician pointed.

Taking the grand staircase two steps at a time Sheppard ran towards the living quarters. Tripping over his own feet sliding to a stop in front of Dr. Weir's quarters he took a couple of minutes to catch his breath. Passing his hand over the door controls to announce himself he waited taking in deep breaths. He didn't want to still be in panic mode when Elizabeth answered. With no answer he knocked on the Ancient door. He was sure she was in there – positive in fact. Finally he closed his eyes and mentally overrode the door controls with a little help from Atlantis.

When the door whooshed open he found Elizabeth sitting on the edge of her bed. From his spot at the door it appeared she was shaking. It only took him four long strides to reach her. Sitting next to her on the bed he put his arms around her shaking body and pulled her into an embrace. At first she was unwilling but those strong arms insisted. Warmth and comfort surrounded her as she gave into sobbing.

She cried in his arms, clung to his shirt in a tight fist as hot tears mingled with his black shirt. He only held on to her tighter. Some forty minutes later Elizabeth was all cried out. John had not uttered a single word. He just held her, let her cry and comforted her the only way he knew how; with his presence. He wasn't sure if she was awake or had cried herself to sleep. He was too scared to move and look. When the door chimed he thought open from his place on the bed. Elizabeth secure in his safe arms. It was times like these that he really appreciated his natural ATA gene.

"Is she alright?" Carson asked quietly from the doorway.

John was afraid to speak so he just shrugged his one open shoulder. Carson entered the room allowing the door to shut behind him walking quietly towards the pair with doctor bag in hand. Once he was close enough he knelt down to have a look-see.

"She's asleep Colonel. Let me help ya and we'll lay her down proper."

Working together they managed to get Elizabeth in a prone position. John went to the closet to get a blanket while Dr. Beckett checked her over. Carson took out a syringe from his medical bad and prepared it.

"What's that Doc?" Colonel Sheppard whispered pointing to the syringe.

"A light sedative to help her sleep."

"She's already sleeping." John stated the obvious.

Carson motioned towards the door and the two men stepped outside into the hallway to speak.

"Look Colonel, Elizabeth has just been through a very traumatic experience. She'll need lots of rest and reassurance to come out of this okay. This is the best way to ensure she gets enough rest."

"I'll stay with her. If she wakes up I'll call you…or…or you could just leave a couple of pills and I'll make sure she takes them. I don't think Elizabeth would appreciate being drugged without her knowing. I know I don't." Thinking of all the times he had been drugged without his knowledge.

"Aye you're right about that she wouldn't. Okay Colonel we'll do this your way. But if she or you need anything you call me right away."

"Will do Doc. Give me a sec, I just need to contact Lorne and have him take over for me."

Carson went back inside Elizabeth's quarters to check on her once more and to leave the medication she would need if she woke up. Colonel Sheppard tapped his comm and left Lorne in charge along with instructions to advise Teyla that Elizabeth was fine at the moment and sleeping. He knew Teyla would be worried as she and Elizabeth had forged a deep friendship stemming from the burden of leadership they both shared.

John entered Elizabeth's quarters and pulled over a lounge chair to position himself by the bedside while he kept vigil. Carson had placed two yellow pills in a small white paper cup and a glass of water on the nightstand before leaving. He watched her sleep.

Several hours later a note was slid under the door. It was on parchment he had seen the Athosians use on the mainland. Picking it up it had only one word, Hallway. John glanced back over to a sleeping Elizabeth before activating the door and stepping into the hallway.

McKay, Ronon and Teyla were all waiting and wondering. He had expected Teyla and was pleasantly surprised to find Rodney and Ronon there also.

"How is she?" Rodney asked concernedly.

"She's sleeping. Beckett checked her over and he seemed okay about it."

"We could take turns you know…keeping watch. Allow you to get some food. You know you have to stay on your schedule or you…you know…" Pass out Rodney thought and stopped himself from saying anything further. His offer was genuine he cared for Elizabeth too.

"Thanks guys but I promised Beckett I wouldn't leave. I'll be okay. If I need I can always call on you guys later. Right?"

"Of course John." Teyla stated with an unsettled smile.

John took a close look at each of his friends. Concern was etched into each of their faces. "Hey, do me a favor. Keep tabs on the IOA Reps and the new General. I want to be the first to know if something isn't right."

"The General is still in the conference room with those IOA people. I heard them yelling over the way the news was delivered. The General didn't seem too pleased." Ronon reported.

"That's good to know. Keep on top of things for me. I need to get back." John pointed at the closed door behind him.

"Tomorrow." Ronon stated.

oOo

John stayed the whole time with Elizabeth like he had promised Beckett. Teyla brought him a late dinner although he really wasn't hungry. Teyla made him promise to eat and John always kept his promises when he could. Around two a.m. Elizabeth woke dazed and confused. She couldn't remember how she had gotten there. She was still dressed in her uniform. A blanket she kept in her closet for chilly nights was spread over her. Looking around her room her eyes fell on a dark figure slumped in a chair. Startled she inadvertently let out a gasp of panic.

John heard the noise and woke up. He quickly gave himself a personal dressing down for falling asleep. It was his duty to stay awake and keep watch over Elizabeth, be there for her if she needed. Straightening up from his hunched over position in the lounge chair he mentally raised the lighting in the room enough for Elizabeth to see that it was him and no harm would come to her.

"Hey Elizabeth." John spoke comfortingly making no sudden moves towards her. She looked scared enough for the both of them.

"John?"

"Yeah it's me. Go back to sleep now. I'll keep watch. Everything will be fine." He tried to assure her though he wasn't so sure himself how this would all work out.

"I don't think I can."

"Here." Reaching towards the nightstand he handed her the white paper cup with the two yellow pills inside and the glass of water. "Carson left these for you. I think you should take them. We can…talk…in the morning."

Obediently Elizabeth took the medication followed by a sip of water. She handed the mostly full glass back and lay back down. John helped her straighten out the cover and watched as she closed her eyes trying to sleep once more.

John set back in the lounge chair whispering: "Between melancholy and disquiet – a brooding cloud – of the restless soul – pacing the floor, wondering the next steps, on a road less traveled by – when words do not come – 'tween the good and night – a gap to mend – a breach to heal – on the other side – of restful sleep – for miles to keep – and inner peace."

John repeated the poem over and over in a whisper until Elizabeth had fallen back into a restful sleep.

John stood at the window watching the sun make its way into the morning sky. Its golden rays gleaming off the water and spires. Periodically over the last few hours he would steal a glance towards Elizabeth. He gave up on the lounge chair after Elizabeth had gone back to sleep. Pacing the small room kept him more alert he didn't want Elizabeth to wake again startled. When he turned his head this time he was rewarded with soft brown eyes gazing back at him.

"Hey good morning. Sleep well?" John asked walking back to the small lounge chair beside her bed.

"Yes thanks to you." She paused a moment to gather her thoughts. "I'm sorry. I don't know what came over me. I'm not usually this insecure."

"Was nothing. You'd do the same for me…" John added quickly. "…or anyone."

"I would. That poem last night…" Elizabeth started to say but her words were lost in thought.

"Between." When Elizabeth gave a wrinkled brow in return he explained. "The poem is called 'Between' by Raymond A. Foss. It was a favorite of my mothers. She would recite it over and over. I was just a child when I heard it. I think it explained how she felt being a military wife. Moving from one post to another not knowing where her husband was: 'on the other side – of restful sleep – for miles to keep – and inner peace.' It gave her the peace to deal with everything I guess. She said it often and I guess I picked it up too."

"It's beautiful. Thank-you."

"Um…I...I should you know…I should go. Let you get cleaned up."

"No. Please stay." She begged reaching out for his hand.

"I won't go until you tell me." John answered back holding tightly to the frail fingers in his large hand. "Ah…how about I go grab some breakfast for the two of us that way you can…you know…" Pointing in the direction of the bathroom that was behind him.

"Okay," she said quietly. "Don't take too long?"

"Ten minutes tops." He smiled.

She nodded acceptance and John helped her from the covers to stand. "Back in ten minutes, I promise." He said one more time before leaving her.

Once in the hall he contacted Carson and told her that she was fine this morning and he was getting her breakfast. John promised to bring her to the infirmary when she was ready. Stepping into the mess hall he grabbed a tray and started filling it. He knew what Elizabeth liked for breakfast so he grabbed a yogurt, some toast and a piece of fruit. Poured two cups of coffee and for himself he grabbed a bowl of oatmeal. As he was about to leave he ran into Lorne's team. Quickly he filled them in on her condition and they in turn filled him in on the status of the IOA reps and of General Brankovik.

General Brankovik had set up a temporary office in the conference room. At least he had the decency not to bulldoze his way in and take over Elizabeth's office. Lorne said he was scheduling appointments to talk to each department that would be carried out the next day or so. The three IOA reps had been assigned sleeping quarters only and were planning on staying only a few days. Guess they wanted to make sure the change over of command went smoothly. Sheppard advised Lorne to assign a detail to each representative. Give them the grand tour so to speak and to keep tabs on them and report back.

Hustling off after giving instructions and updates to his friends he found himself outside of Elizabeth's quarters. He waved his hand over the door controls to announce that he was back. He didn't want to go barging-in in case she had not finished dressing yet.

Fully clothed and with wet hair Elizabeth met him at the door. She allowed him in and he sat the breakfast tray on the coffee table. Elizabeth curled up on the couch and started on her yogurt. John sat back down into the lounge chair and picked up his bowl of oatmeal. Quiet filled the room.

John patiently waited for Elizabeth to start the conversation. He could be patient when the circumstances dictated it and these were certainly the right circumstances.

Elizabeth started crying. As fast as John could he put his oatmeal down and moved to the couch. He took the almost empty yogurt container and spoon from her quivering hands. Setting it on the table he then pulled her into his embrace; wrapping his strong, warm arms around her like a blanket on a cold winter night allowing her to cry until she was ready to talk.

oOo

"I'm sorry John. I don't know what came over me." Elizabeth stated after a good healthy cry wiping the tears from her cheeks.

John reached up and brushed a few tears away as well. Her skin was so soft under his calloused hands. John marveled at the feeling it produced inside him. He had remained silent throughout her tears and sobs. "Hey…it's okay. Everyone deserves a good cry now and then." He still hadn't released her from his embrace.

"What about you?"

"Me? No…no never." He said with a sheepish smile. "I'm too manly to do something like that. I leave that up to McKay. Besides I would never live it down if Rodney or Ronon—hell if the Marines ever found out."

"Oh John." She smiled and half giggled. John loved that smile. Loved that giggle she made when she was happy. John focused on her face noticing how the morning sun coming through the window brought out the red highlights in her hair. He'd never noticed that before now. Her eyes shined and her smile was infectious. "What should I do?" Elizabeth asked in all seriousness.

Her question brought him back from his exploration of her face. "Take the job." He was a selfish sob. If Elizabeth turned down the job and went back to Earth he would resign from the military and go with her. But he really had found a home here on Atlantis and a family who, although crazy in their own right, accepted him for who he was.

"It's not that simple. What would people think?"

"It is simple Elizabeth. Everyone here on Atlantis would think that you got shafted by the IOA and they would be right. But everyone on Atlantis would benefit from you being here. Think of it this way. No more thirty hour days. No life or death decisions to make. No more lengthy reports or meetings. The fate of the galaxy won't be residing on your shoulders any longer. You can sleep late, stay up as long as you want. Have breakfast, lunch and dinner with your friends. Have some fun for a change."

"I'd rather have breakfast, lunch and dinner with you." She said coyly. "But the other stuff you said is good too." Smiling at him with love in her eyes.

"Then you'll take the job?"

"Да. Pa3pewehne xpopwo." = "Yes. Permission granted." in Russian

TBC 2/60