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

As promised when he woke up breakfast was walking in the ISO room door. Damn that Mary was good. After the tray was set down the head of his bed was raised careful of the wires coming from the electrodes attached to his head. He got his first look at breakfast. He thought for sure it would consist of broth and toast. Needless to say he was pleasantly surprised when he found pancakes, bacon, juice and milk. Without hesitation John started eating vigorously. Mary slowed him down by taking a set of vitals.

John was just swallowing the last of his juice leaving his breakfast tray totally empty when Carson entered. Carson exuded tiredness from every pore, his shirt looked like someone had slept in it, his lab coat's wrinkles had wrinkles, he was unshaven and his hair was a mess. The side of his face was reddened with harsh ridges. He looked just like McKay did sometimes after waking up from sleeping on his laptop keyboard, his face picking up the ridges of the plastic keyboard. But most of all the tell-tale signs of his condition were reflected in his sparkling blue eyes that had lost their sparkle.

"Morning Carson, you look like hell." A chipper, satisfyingly full, Colonel told him.

Carson reached for the data pad to scroll the Colonel's readings that had been taken throughout the night and morning hours. He read the nurse's notes of the early morning conversation and the most recent entry which indicated that the Colonel just ate three pancakes, two strips of bacon, juice and milk. More food than John normally ate in one sitting.

"Carson when can I get out of here? Rumor has it McKay's due back today."

"You'll leave after I've completed all the tests I want and only when I say you can. Does that answer your question Colonel?"

"Whoa…Carson…I think you need to go find a real bed, like say the one in your quarters. You're grumpier than a McKay when he hasn't had his morning coffee yet. Really, why don't you go take a few hours and I'll go back to my quarters, shower and talk with Elizabeth, Teyla and Ronon. I'm sure the tests can wait while you get some proper rest."

Carson stood with his mouth ajar; John was talking almost as fast as Rodney. Mary stood off to the side snickering, though she agreed with the Colonel's assessment of the tired doctor. She had tried last night to get him to go to his quarters for some decent rest.

"Ah…" Carson snapped his self out of his own daze. "Ah…you'll do no such thing Colonel. You're staying right here. For God's sake man you just had one thousand four hundred and twenty-five milliamps of electricity course through your brain just over twelve hours ago. What kind of doctor do you think I am?"

"Well when you put it that way…look I'm fine. Really. I'm back to normal, you did it. All my memories are where they should be: tucked nice and neat away just how I like it. You need rest Carson, Elizabeth is probably going out of her mind."

"No!" Carson firmly put his foot down with his exclamation.

"Well at least let me take a shower and see Elizabeth, Teyla and Ronon while you rest if I have to be stuck here."

"Colonel this is the infirmary. Patients don't get to bargain. Patients do what their doctors tell them when they tell them." Carson remembered the Colonel who was compliant after he woke from his five day coma. During his stay he never complained, never bargained for scrubs, didn't escape, asked please… where was that man now? He wondered.

"Sure we do. You and I bargain all the time: showers, scrubs, removing IV's and catheters, everything can be bargained for. Including getting rid of all these wires you got glued to my head. That alone should prove to you that I'm me again. So what do ya say? Shower first then Elizabeth, Teyla and Ronon."

"Colonel you've…" Carson hung his head down though not in defeat. He was tired—exhausted even. He was physically, mentally and emotionally drained. He'd been the one who held the wands in place as electricity was directed into his friends brain. He'd been the one who couldn't stop mother-henning in the late hours of the night. He should have listened to his nurses. "Fine. You win. I don't have the strength for this. You can shower. I'll call Elizabeth and see if I can find Teyla and Ronon. But you will remain here do I make myself clear?"

Colonel Sheppard felt guilty for cornering the doc the way he did. "Carson I'm sorry. I didn't mean…what I said…it wasn't meant to hurt…"

"Colonel it's alright. I'm not upset at you, you're right, I am tired. I should get proper rest before I start any testing. Goes to show you just how tired I am, I'm not thinking to clearly. Mary can…"

"No! I mean she could, but no." John shouted remembering his two a.m. conversation with Mary. No way was he going to allow Mary to give him a sponge bath. God he hated sponge baths more than he hated having a catheter. "You both need your rest. Mary pulled a double shift, you spent most of the night hovering like you always do and I slept solidly for twelve hours. If I need help, Nellie can help me. And would it be okay after I shower that I rest in my usual bed? If you're keeping me here, McKay's going to wonder why I'm in the ISO room. He's a genius you know."

"That's fine Colonel. I'll inform Nellie. Mary luv, you head onto bed. Becky is taking your shift again tonight…and no arguments. Alright Colonel, go get showered and I'll contact Elizabeth."

"You're not going back to your office to sleep are you?" Asked a concerned Colonel.

"I promise lad, I'll go to my quarters once I know everything has been arranged."

"Okay." John waited for Nellie to come in to remove all the tubes and wires from his person. Then he hopped out of bed and padded his way to the infirmary shower knowing full well when he finished he would find a clean set of scrubs on the counter waiting for him.

oOo

The stargate began dialing in, Chuck was working the gate controls and yelled "unscheduled off world activation" as if no one in the room had figured that out already.

General Brankovik came out of his office and stood behind the console where Chuck was seated watching the screen for an IDC over the tech's shoulder. The General didn't ask premature questions. He knew the people staffing the command center in stargate operations knew their jobs and did them extremely well. Brankovik also knew that when the gate finished dialing in Chuck would advise him if it was friend or foe.

"Receiving IDC. Stargate Command, General. They're requesting we lower the shield. They're sending Dr. McKay back. Seems he's outstayed his welcome… Sir." Chuck snickered at what the SGC had stated in their communication transmission. Chuck and Walter, or rather Chief Master Sergeant Harriman, who normally manned the SGC control center, had developed a rapport over the years. It was not always by the book communication between the two men. Walter would, on occasion, fill the Atlantis tech in on information surrounding the new or returning personnel. This gave Chuck inside information to barter with, bet with or win poker games with. Chuck reciprocated when he could. "They are also sending a few supplies and personnel through."

"Lower the shield and call for assistance to help with the supplies." General-Mayor Brankovik stated moving off towards the stairs down into the gate room. Half way down he heard the slurp of bodies and supplies coming through the opened gate. When he got to the bottom Dr. McKay was waiting for him. Rodney's arms holding a fairly large non-descript white box.

"Ah General…I see you've come to welcome me back. Where is everyone? I'd thought they'd come to greet me."

"Nice to have you back Dr. McKay. It has not been the same around here without you." The General smiled and quickly turned his attention to the new Major and the five men that accompanied him essentially cutting Dr. McKay off from any rebuttal he might have had. "Major, welcome to Atlantis. Is this everyone?" The General looked over their shoulders to view the activity behind them.

Two sleds of supplies accompanied the six new Marines along with Dr. McKay's cases. The Major handed over a manifest of supplies which Brankovik briefly scanned noticing that most of the supplies were medical in nature. From the note that accompanied the supplies it seems that Sergeant Major Pertis was sending along some supplies they had just received that had been on back order. The General had to hand it to Colonel Sheppard for his ingenuity at Quartermaster Supply a few months back.

"Yes Sir." The new Major said with military spit and polish. The five other soldiers stood at attention although their eyes scanned the immediate area. The gate room on Atlantis was impressive and overpowering to first timers.

"Relax Major, we wouldn't want you to pull a muscle so soon after your arrival." The General got on his comm and requested Lt. Col. Lorne to the gate room. "Major when Col. Lorne arrives gather your men and he will escort you to the infirmary for a quick medical check before he finds you and the other men quarters."

"Yes General." This time the Major was not so stiff in his reply.

Men swarmed the gate room and started on the two sleds of supplies. The General saw that everything was being handled and was heading back to his office.

"Hey General! What, no welcoming home fanfare? Where's Sheppard? Teyla and Ronon too."

"I believe they are all in the infirmary Doctor."

"Infirmary…why? What happened? Are they hurt?" Rodney began to panic. He was only gone four days, surely his team mates couldn't have gotten themselves into trouble in that short of time.

"No one is hurt. I believe they are visiting Colonel Sheppard."

"Why didn't you just say that in the first place!? Here! Hold this!" McKay thrust the large box he was holding into the General's arms. As he jogged away towards the infirmary he yelled back over his shoulder, "keep it flat. And for God's sake don't lose it!" Were the last words the General heard before the doctor was out of sight. The staff processing the supplies from the two sleds, the six new arrivals, the six Marine guards and the gate room technicians all were dumb-founded at Dr. McKay's comments and hasty retreat. They couldn't believe he had shoved a box at the General.

Racing to the infirmary Rodney's mind played out disastrous scenarios of what the self-sacrificing Colonel might have done this time. He told him to stay away from EMP's but maybe he should have been more specific about other things too. Like no kamikaze runs in the puddle jumpers, no taking on Genii strike forces, no getting taken hostage by disgruntle Marines, lab fires, surfing the sweet breakers on the southern tip of the mainland and the list went on and on inside McKay's head as he was turning the last corner towards the infirmary.

Rodney came to a slow stop after entering the infirmary looking around to find where the trouble magnet fly boy was. Rodney pondered for just a second as to what his idiot friend could have done this time to land himself in the infirmary he barely left a few days ago. He knew it was a bad idea to leave him though he thought for sure Teyla and Ronon would protect him from himself. Hearing talking and some laughter coming from the expected usual curtained off area he walked that way.

oOo

Teyla's head set beeped. "Yes. I understand I will take care of things here. Thank you for notifying me."

By the time John came out of the infirmary shower all fresh and clean and rejuvenated Nellie was plumping his pillows on his usual bed. The curtains were up like he liked it. He never liked hospitals and the Atlantis infirmary was on that same list. He loved the nurses, knew them all by name, liked most of the doctors as long as they were taking care of his men and not him. He still didn't comprehend why Carson kept him in the infirmary when he was feeling so great. He would have gladly come back after the doctor had a few hours of sleep for any tests. Gladly sat through the poking and prodding—well maybe not that gladly but he would have done it for Carson's own piece of mind. He just wanted to be with Elizabeth, his friends and have everything back to normal including work.

John sat down on the edge of the bed letting his feet dangle above the floor. He wasn't tired at all. He felt pretty damn terrific considering what he had gone through. John found one of the shaved areas, the one above his left ear to be exact and was rubbing a nervous hand through his hair. The nurse was tidying the area or something of that nature. "Nellie do you know if Carson contacted Elizabeth?" John said continually looking at the floor and at his dangling legs.

"He did Colonel she should be here any mo…"

"John!" Exclaimed Elizabeth from the part in the curtains. Her eyes betrayed her surprise at seeing him sitting on the side of the bed, wet hair and all. In her minds eye including her nightmares from last night she had John pale and sallow barely able to hold his head up or grasp her hand. She rushed to him forgetting that anyone else was in the area with them.

John heard Elizabeth shout his name and it was music to his ears. He saw the surprised look that flashed quickly over her beautiful face and he smiled the biggest smile he could. As Elizabeth rushed to him he opened his arms and took her into his loving embrace forgetting that Nellie was still there.

As the two embraced Nellie excused herself though she wasn't sure if either of them heard her or had seen her leave.

John held Elizabeth tight in his arms afraid she might vanish if he let go. All the disjointed memories could not compare to this, the real thing. He was holding her, remembered all the times he held her. At the beach, on the south pier, west pier, in her quarters, in his quarters. All those times came flooding back to him and he didn't want to let go. He breathed in her scent and recalled all the times he'd done that before over the past eleven months. He was seeing her for the first time. Elizabeth had confessed to having feelings for him from their first year here in Atlantis. Now that he had all his memories back and in order he remembered feeling the same. John whispered into her hair how much he missed her taking in her unique scent at the same time. Lavender he remembered was the scent of shampoo she used. John made no mistakes as to how much he loved this person wrapped up in his arms as he placed kisses along her neck.

A deep voice boomed from the end of his bed. "Get a room."

Elizabeth and John parted just a little neither of them wanting to lose the physical touch of the other. John laughed at the comment and rested his forehead on Elizabeth's chest. Taking a couple of moments to pull himself back together before responding. "This is my room. See all the nice white curtains? I should just move my personal stuff here for as much time as I spend here. And where did you hear that from? I know I didn't teach it to you."

"McKay." Ronon answered. Teyla had squeezed herself past the curtain and Ronon to stand beside him rejoicing in how good, how normal John appeared.

"Figures. Come here guys. God I've missed you." John threw out an arm in invitation to Teyla and Ronon. Ronon moved closer first at the invitation to share a warrior's hand shake. Ronon and Elizabeth stepped back and allowed Teyla to greet the Colonel in the way of her people. Bowing heads, "I've missed you." John repeated softly to her.

"And I you." Teyla responded. "However we have not been away."

"I know Teyla, but in here," John pointed to his head. "In here you've been gone sorta. I knew who you were, but I couldn't 'feel' how we connected since all my memories were mixed up. Now you're back. All of you," pulling Elizabeth back into his arms. "Can you stay for a while? Keep me company? Carson's sleeping and he wants to run some tests so he won't let me out of here until he does. I'm basically stuck and bored."

"We can stay…unless you would rather be alone." Nodding in the direction of Elizabeth John understood what she was inferring.

"Do you mind if they stay Elizabeth?"

Smiling at how vibrant and healthy he looked she didn't mind at all. Who was she to interfere with his friends—our friends. "Of course not John."

"Great! Find some chairs and sit down. Here Elizabeth." John powered the head of the bed up to a sitting position he scooted across to take the left side of the bed stretching his legs out in front of him as he coaxed Elizabeth to do the same. Ronon and Teyla pulled chairs from somewhere in the infirmary and made themselves comfortable as well. John clasped Elizabeth's hand as they sat shoulder to shoulder, hip to hip on his small infirmary bed.

The four of them talked and talked and talked some more as the morning marched forward. Even Ronon was joining in on some of the topics adding his two cents worth as it were. Elizabeth explained how Carl had came to tell her and how Teyla and Dr. Lantis stayed with her throughout the night. Ronon fessed up to beating the hell out of the practice dummy. At least John was grateful he hadn't taken his frustration out on the Marines like last time. No apologizing necessary except that he would need to get a new practice dummy…maybe a couple.

TBC 38/60