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. Thanks also go to 's Omnipedia and the World Wide Web for all the research I did. I couldn't have created this story or any of my stories without their aid.

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

"John. John can you hear me?" Elizabeth asked from her chair at his bedside in the infirmary. The lighting was dim around the single bed, curtains drawn. In the background Elizabeth could hear the duty nurses taking care of other patients. It was her fourth day sitting vigil over Colonel Sheppard.

"Elizabeth luv, John is still in a coma." Carson said. He hated watching Elizabeth worry so much. There wasn't anything either of them could do until John decided it was time to wake up.

Previously on Atlantis – 11 months ago

"Knock – knock." Colonel Sheppard called out as he leaned on Weir's office door, ankles crossed and arms crossed over his chest, in his most casual pose he could pull off these days. He stood there watching her for a few minutes before announcing himself. He loved the curve of her face and the soft wave of her brown hair. She moved with such poise and elegance just sitting at her desk. That had been something he noticed from the very start of this mission back in Antarctica; her poise, grace, elegance, and even temperament. His eyes locked on her beauty as he waited to be granted entry.

Elizabeth looked up from her laptop with a stunning smile at hearing that familiar drawl; it was strong, with a hint of mischief thrown in for good measure. With a brief wave she granted her Military Commander permission to enter.

"Hey…" John gave a little stumble as he moved into the office from the doorway. This was the third time his foot had fallen asleep on him. Acting like nothing happened to cover up his uncoordinated attempt at walking he continued his last thought. "I've been working non-stop on fitness reports and I'm sure you've been working hard too. How about you knock off for a while and have lunch with me? They're serving spicy botulus pizza and I know for a fact it's one of your Pegasus's favorites."

Elizabeth gave the luncheon proposal two seconds of thought before making up her mind. She was already entertaining the thought of stopping for lunch; although her idea of lunch was a quick grab sandwich and coffee at her desk. The Colonel was correct in his assumption that she had been working non-stop all morning. First it was the latest mission reports on Michael and his super bugs; reviewing each report from each team member involved and those of Col. Caldwell's staff on board the Daedalus as well. Then she had to write her own AAR on the matter and have it all ready for the data burst to Earth tomorrow afternoon.

"You know that for a fact you say?" Elizabeth queried.

"Do you deny it?" John asked giving her his trademark lopsided grin. He had saddled up to lean his hip against her desk while she debated his proposal. There was no denying it. The truth as evident as the soft pink blush ensconced Elizabeth's facial features. To add more mystery he added, "I know a lot of facts about you Dr. Weir."

"Do tell."

"Nope. Not unless you have lunch with me right now. And even then…you'll have to persuade me to reveal what I know." Colonel Sheppard kept his quirky grin on his face while waiting patiently for Elizabeth to accept his offer.

Elizabeth closed down her laptop. She loved spicy botulus pizza. It was made from a sausage discovered on one of their trade missions and they ended up trading medical aid for it. The added challenge to get information out of John Sheppard made it all worth while. Elizabeth knew he was a private man and let very little of himself show to others. He was Special Ops trained according to his military record and if he didn't want to divulge information there was no hope of getting it. Elizabeth liked challenges. The prospect of getting John to talk was like sweet candy to her lips. There had been many UN negotiations back on Earth where she had had to dig for information between too warring parties. Many more such times here in the Pegasus Galaxy as well. Getting each opposing side to divulge even the smallest fraction of information was her specialty. She wasn't top of her graduating class from the University of Chicago or from Johns Hopkins University for nothing.

The two leaders headed for the mess hall. Dr. Weir gave the tech on duty, Zaida, her whereabouts, out of courtesy, as she passed through the control room. Zaida was new to Atlantis. She was the first Portuguese member to the expedition.


"Good Morning everyone. Morning Chuck." Dr. Weir acknowledged as she passed them on her way into her office taking the computer log Chuck handed to her on the PC tablet. Every one of the six member gate room morning staff was at their stations busily working and monitoring their consoles. Setting down her laptop and the PC tablet Elizabeth prepared for her long day to begin. She noticed there was a small bronze looking flower vase about three inches tall with a single white flower. It was a variety she had not ever seen before but its beauty and simplicity was captivating. The small white flower gave off a heavenly scent; honeysuckle she thought.

She stood back up and went back into the control room, passing John with two cups of coffee. "I'll be right there John." He gave a nod of understanding and kept going. Elizabeth walked over to Chuck's workstation and asked quietly if he had noticed or if the night shift had reported anyone in her office. When the answer was a definite 'no' she went back in to start her hour work session with Colonel Sheppard.

"Morning John." She said pleasantly taking her seat and glancing once more at the white flower with curiosity before picking up her morning cup of coffee.

"Morning. What's on the agenda for today?" The base military officer asked.

It had been three weeks since Michael's super bugs had been destroyed on P6R-114. The last four of the planets on the DHD list that Dr. McKay managed to recover were scheduled to be surveyed today. Over a hundred planets had been surveyed thus far. Four teams were heading out today; Lorne's, Cadman's, Lt. Ruiz's and Mjr. Jacobs. In the previous three weeks, searches of the planets revealed little. Five more labs had been found but no information was gleaned. Sixty-three of the planets lay barren, total wastelands. Forty-two still had survivors though small in numbers. The inhabitants explained that many were taken never to be seen again. When asked if they were culled by the Wraith it was a split answer. It was not a normal culling with darts, but many said they saw what looked like a Wraith. Fourteen of the planets Atlantis could not get a gate lock on. They were scheduled for the Daedalus or the Apollo upon their return to this galaxy.

"The last four addresses from Michael's list are being checked out today. I need you to finish your year end staff evaluations. Promotions are due next month along with salary increases and the SGC is requesting your eval's sooner rather than later. And 'no' you may not give everyone 'Excellent' or 'Above Average' like you did last time. Rodney is still upset with that by the way. I know you hate this part of your job, but John that is what being in a leadership role is; lots and lots of tedious paperwork. We need to decide if we need to find a new location or make more space for the PX at its present location. It has really been well received and everyone on base contributes in one way or another. I have my own staff evaluations to complete along with mediating a disagreement between Coswell and Soon. Seems they both want the same lab space and neither will listen to their section leader. What was on your agenda today, John?" Elizabeth carefully selected her wording when posing that question to her Military Commander.

"Chandler and I have to discuss Section 336 after breakfast. Then ferry Blackwell and Smythers to the mainland. After lunch with you, Lorne and I are going over combat scenarios which will take up most of my afternoon. Then back to the mainland to pick up Blackwell and Smythers. Sparing with Teyla and Ronon until dinner then after dinner I was just going to kick back and relax for a change after a busy work filled day." He was finding it hard to get back into his 'laid back' look slouching further into the guest chair. Wheelchairs hadn't allowed for slouching.

"I see. Well I'm sure Dr. Chandler can find someone else to hit golf balls with. So you'll have plenty of time to work on your performance evaluations before and after you ferry Blackwell and Smythers to the mainland. Col. Lorne will have to find someone else to play Combat Flight Simulator III with…perhaps Captains Overton or Polansky or Lieutenants Ruiz, Manetti or Connifer. I hear they're all really good pilots even if they are Marines. And I'm sure that Teyla and Ronon will understand that duty comes first. Don't you agree Colonel?"

John sat in total shock before uttering stoically changing his posture in his chair. "No." How did she know? I should have picked up on something when she said 'what was on your agenda.'

Smiling like she was the Cheshire cat who had caught the canary, "I'll expect those evaluations first thing in the morning." Taking the last sip of her coffee she sat down her mug and noticed that her white flower had turned a beautiful yellowish-orange color.

Did she really expect to have all 980 military evaluations by tomorrow? It was somewhat of a relief to him that he had started the military eval's three weeks ago but he still had over one-fourth of them yet to complete. "I might not make it for lunch today." He said in passing.

"I'm sure you can take a few minutes to have lunch. Besides the menu for today is Athosian stew. One of your favorite foods I do believe." Still smiling to beat the band she remembered trying to get facts out of John. Over the last several weeks while they had lunch together each one of them gleaned information about the other. Trivial items such as their likes and dislikes in food, movies, books nothing really earth shattering or personal.

Elizabeth liked classic movies, classical songs and romance novels and spicy food, the more spice the better. That was her wild sense of adventure she allowed herself. John on the other hand liked comfort foods, movies with fast cars, fast planes, fast boats and the like. He liked reading the classic books like War and Peace in their original language plus he has a love for football.

"I guess so. But don't blame me if you don't get all the evaluations tomorrow. Pick you up at noon?"

"That'll be fine. And John…have a good day."

John gave her a lopsided grin as he left her office not saying anything more. Although he was thinking it, it would have been a good day; playing golf and video games. It was 08:00 and time to have breakfast with Lorne's team before they went off world for a couple of hours.


"You're busy this morning and you haven't even had your cup of coffee yet." John supplied pushing the cup across her desk for her to reach.

"I know. I know. I'm getting all the personnel evaluations together to be sent out with our data burst today. I have two that I need to finish up before then." Elizabeth informed him.

"Personnel Eval's? Wait a minute you told me that the SGC needed them ASAP. That was two and a half weeks ago. I worked my butt off to get those done and I could have actually had the last two weeks!" John's voice was an octave higher by the time he finished.

"If you wouldn't procrastinate, John I wouldn't have to resort to those tactics." Weir admitted.

"I didn't procrastinate. It looks to me like you might have procrastinated though." John pointed to the grayish colored flower sitting on her desk.

"How do you know about that?" Astounded that he noticed the flower after all these weeks and even knew what the color meant. It was just last week when Dr. Katie Brown was in her office for a meeting that she learned about the mood flower. Animus Flosculus Floralis she called it. And for the next hour Dr. Brown told her of the ten different color changes the flower was capable of.

White was peace and purity. Yellow had mixed emotions; bright yellow was joy and happiness while a darker yellow was deceit and betrayal. Red also had mixed emotions. It could mean passion or it could mean fight or flight. Warmth and balance produced an orange color while green related to envy. Blue reflected harmony and purple wisdom. Black was overworked; brown melancholy and finally gray was strained. Dr. Brown named only a few emotional traits and offered to send Dr. Weir a full list once she was back in her lab.

"Rodney had some repair work to do in the Botany lab a while back and needed my ATA gene to override one of the consoles they were having troubles with. Rodney's wasn't strong enough. So while I waited for Rodney to need me Dr. Brown kept me entertained by telling me about some of the interesting plants they've found. Did you know she named one after McKay? Called it Rodneyana Villosa; it looks like this cactus thing with these prickly spikes sticking all around. It definitely reflects McKay's personality. She also told me about that one. This one is a mood flower of some kind. Animal Floss something or other she called it. It's supposed to pick up on the mood of the individual who receives it and change its color to match their mood. Gray is anxious and hurried I think."

"Yes well I am down to the wire right now so I guess the mood flower is correct in its coloring. So why don't we dispense with our work session this morning so I can finish. I'll see you for lunch later." There were days when being the lead administrator had its draw backs.

"Okay I guess." Dejected by the brush off; he always looked forward to his hour work sessions. That and lunch, of course.

As John got up to leave Elizabeth quickly thanked him for her morning coffee. Turning back to her laptop she furiously typed away.

A single flower like the one Dr. Weir had on her desk only lasted a few days away from the plant body Katie Brown had explained. Elizabeth had had the flower on her desk for almost three weeks. When Katie told her this she asked right away if she was missing any plants from the lab. If the flower only had a life span of three to four days someone had been putting a fresh flower on her desk unnoticed. At minimum—seven times somebody had been in her office without her knowledge or the control room staff noticing. And someone on Atlantis had access to a mood flower plant.

The following day she checked the past three weeks logs, checked with the gate room staff; all three shifts and no one reported seeing or hearing anyone in her office. The next step would be to check the surveillance cameras leading into and around her office. A task she fully intended to follow up on. She shuttered at the thought of reviewing over five hundred hours of surveillance footage.

Mid-morning on the second day Dr. Weir strolled into Lab 1 and found Rodney and Radek working on an Ancient device. By the looks of things, things were not going well. So she he didn't feel too bad interrupting her scientists with a personal matter. First she explained to Rodney what she needed. Then he brought Zelenka in on it since Radek had more knowledge of the Ancient monitoring system. Accessing the requested logs for the past three weeks they downloaded the files to a spare PC tablet and sent Dr. Weir on her way.

Three days later she returned the barrowed equipment. She had given the downloaded files to Chuck to review and in three days he scanned all five hundred plus hours of video. Not once catching any unauthorized personnel entering or exiting Dr. Weir's office at any time of the day when she was not present. Rodney's only response to that was someone must have manipulated the logs. He would write a program to search for anomalies but it would take a while before he had any results. Elizabeth was fine with that. She just needed to know who was entering her office without her knowledge.

She recalled her meeting with Mr. Coswell and Dr. Soon and at how her flower had turned black. She thought that it had died. That was truly three hours where her mood was certainly angered and tense.

Rodney still had nothing to report on his anomaly program and another week had lapsed.


At first when John and Elizabeth started having lunch together they sat by themselves at one of the back tables or one of the balcony tables out in the fresh air. Over the course of the last couple of weeks at least one member's of John's old team approached to have lunch with them. It wasn't an everyday occurrence, just once in a while; well mostly it was Teyla and Rodney. Teyla had no ulterior motives of that John was sure. On many occasions Elizabeth and Teyla would dine together. Sheppard figured their bond of leadership had brought them together over the years. McKay on the other hand, John had to wonder about, so on those occasions when Rodney joined them John made sure the conversation stayed neutral. It might have been due to his off-handed questions about where John was at different times of the day. Evan only joined them when his boss waved him over usually to talk a little military business. Ronon was content to either eat alone, with his teammates or with, John noticed, a particular female member of the medical staff.

Colonel Sheppard turned the last corner heading back to his office. He rounded the corner like he had done a million times over but this time he suddenly found himself on all fours. Without any warning his left knee gave out. "Damn!" Was the not so silent curse that escaped his lips as he picked himself back up from the hard cold floor. John looked around to see if any one had been in the hall or if the Marine assigned to patrol this sector had seen him fall. The hallway in both directions appeared to be void of people to his relief.

Sheppard favored his knee as he took the last remaining few strides down the hall to his office. Sitting back behind his desk he rubbed his sore abused knee a few times before getting back to his 'mountain of paperwork' to coin the phrase.

TBC 1/60