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

When Colonel Sheppard woke several hours later he was still disoriented. Carson's warm blues eyes were greeting him when he emerged from his sleepy state. Coaxing John's lips apart with a wet spoon and a promise of relief Carson slid in another ice chip.

"Any better from this morning Colonel?" Asked the physician. "Are you still confused?"

"A little." John whispered. This time when he woke he was more prepared for the fast onslaught of flickers which apparently was a copulation of his life's events. He felt somewhat stronger this time upon waking. When the flashes of memory started playing out in his mind, John did his best to seize control right away. He used his mind to operate doors, lights, water, jumpers, drones and a lot more all the time. Surely he could control the endless loop of what was happening in his own minds eye. As he concentrated the quick moving flashes that barely gave him an idea started to slow. Still not enough to gain understanding but he was getting there. The picture reel was slowing, and slowing.

(flip) Pain (flip) Horses (flip) Rain (flip) Stevie (flip) Mist-fog (flip) Gun fire (flip) Hive Ships (flip) Father's Funeral (flip) Space Gate (flip) A wheelchair (flip) Parallel bars (flip) Captain Holland (flip) Hazmat suits (flip) Physical Therapy (flip) Old Rodney (flip) Blue Jell-o (flip) Two handcuffed Marines (flip) His Mother dying (flip) Johnny Cash concert (flip) Surfing off Malibu (flip) Third grade sleepover (flip) Destroying three planets (flip) Ancient war ship (flip) A carved headboard (flip) Bent knee push-ups (flip) An ornamental chair (flip) Elizabeth holding gun (flip) His custom skateboard (flip) Arguing with Dave (flip) Teyla bowing her head (flip) Hot sand all around (flip) Hitting a home run (flip) Yelling at his father (flip) His Blackhawk taking fire (flip) Tied up in a cave (flip) Giant man sized bugs (flip) Rodney's face on a flag (flip) A drone after his helicopter (flip) Snow and cold all around (flip) Throwing McKay off the balcony (flip) Jumper heading for enemy ship (flip) Falling and rolling in mud (flip) Flying a F-302 towards a sun (flip) Osprey Helicopter trials in Amarillo, TX (flip) Col. Caldwell grilling him on base protocols (flip) Walking on the bottom of the ocean (flip) Getting married, his bride walking down the isle (flip) Dark haired woman talking about a new direction (flip) A girl in a white dress with vibrant red hair (flip) A man in a uniform holding a gun on Elizabeth (flip) His father taking him for a ride in his jet (flip) His side ached as a Marine stood over him with a knife

(flip) "Firing two." John said into the radio as he and Polansky each fired two drones at the Wraith cruiser. The cruiser had no time to react or retaliate.

(flip) "Engage. Jumper Six engage. You have two minutes. If no kill then break off and head for the hanger. Do you understand?" The Colonel exclaimed.

(flip) A General telling a joke in Russian about three men who go into a bar. There was not a dry eye left at the table. Laughter drew many auspicious looks.

(flip) "Hey dude…that was some barrel ride. Been surfin' long?"

"As much as I can." John stated in passing. He only had a couple of hours to get to class.

(flip)Colonel Sheppard was sitting in his office going over his endless logs of reports, reviewing new mission requests, doing his best to put each mission plan into an already busy schedule. He even processed a few leave requests. Business on Atlantis was running smoothly. John looked up from his laptop …

(flip) "Root Vegetables. The best I can equate them to would be the equivalent of radishes, beets, garlic, onions, turnips, yams, jícama, carrots, horseradish, taro roots. The root colors are not what we normally see however. Radishes are green instead of red, yams are white."

(flip) On his walk back to his room he had to stop for a few minutes. His right foot had gone numb on him and it made it difficult to walk when you couldn't feel it touching the floor. But after a few minutes of stretching or shaking it he was good to go.

John was seeing more and more of each flash that flickered by as he kept a tighter rein on his mind. He had shut his eyes as the fast moving pictures played out on his closed eye lids like a movie theater screen. He could sense Carson's confident presence beside him. It took more time, more thought, more self-control to slow down the images.

(flip) John stepped up to a small podium replacing Teyla. "Hi. I'm Colonel John Sheppard. This is Teyla Emmagan of Athos and standing by her is Lt. Col. Evan Lorne. We came to give you a warning. We have reason to believe that a Wraith cruiser will be coming to your planet soon for a culling."

(flip) John and Elizabeth walked into the conference room together showing a united front as it were. Three IOA representatives sat at one table on the left talking amongst themselves while a General sat at a table on the right tapping away on a laptop and ignoring them as best he could being that they were in the same room.

(flip) 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 he would steal a glance towards Elizabeth. When he turned his head this time he was rewarded with soft brown eyes gazing back at him.

(flip) "…your 'no returns' policy is done for as of today. Not just for Atlantis but for the SGC, Peterson AFB, The Air Force Academy and wherever else you ship supplies to. It's over. You're out of business Pertis. If I hear just one person say they were shipped supplies not on their RQ form you will find yourself at a new post.

(flip) "It's not that kind of a reminder. It reminds me to live each day to the fullest and not take my friends or anything for that matter for granted." John said buttoning up his BDU shirt. He glanced at his clock, it was close to 07:00 and he wanted to talk with General Brankovik before breakfast. "Hey I gotta see the General. Give my report. Meet you for breakfast?"

(flip) Summoning all his willpower in order to answer, "was a tie Sir. This…" Moving his hand up and down his painted BDU's. "…this is Ronon getting even." The pain in his head along with the bright light of the gate room was making him nauseous. "Permission to clean up Sir?"

(flip)"In sure and certain hope of the resurrection of eternal life through our Lord Jesus Christ, we commend to Almighty God our sister Katherine Sheppard, and we commit her body to the ground; earth to earth, ashes to ashes, dust to dust. The Lord bless her and keep her, the Lord make his face to shine upon her and be gracious unto her and give her peace. Amen."

(flip) Ronon was a steady three paces ahead of him which had been the case for years. He had never been able to out run, out jog the Satedan since Ronon had decided to stay and join his team. They were almost back to their starting place when John lost his pacing landing hard on the floor. His right knee screamed of the injustice of falling he rolled over from his side onto his back and stared up at the ceiling panting in astonishment.

(flip) "A hole in one. McKay is going to be pissed. He challenged me to play this computerized golf game his sister Jeanie sent him, said it was absolutely impossible to get a hole in one. Something about the way the idiots wrote the program. And look, I finally got a hole in one. See." John turned his laptop around to show his second in command the screen complete with starbursts flashing in the background. "You're my witness Evan."

(flip) "You can't be a pilot!" John shouted.

"Sure I can. Mommy said I could." Dave shouted back.

"No you can't because I'm going as a pilot. Daddy took me for a ride in his plane, not you." Just then a ten year old John punched his little brother in the eye. "Now you can go as a pirate. You won't need a patch."

(flip) "McKay get down and stay down. Ronon you take care of the three at our eight o'clock. Lorne you got the two at four. Teyla stick close to McKay. I got the two hiding in the tall grass at eleven and I'll make a break for the DHD. Once I get the gate open take out your targets and high tail it through the gate. Any questions? Good! On the count of three." Colonel Sheppard instructed stopping McKay flat from arguing.

(flip) This time they weren't just numb. This time he couldn't feel them. John had been ignoring all the signs. He didn't want to believe that something was wrong. He didn't want to be told the implant was failing. He didn't know if he could go back to his wheelchair. He told himself it was just stress or work related that were causing these episodes. Sitting for to long, exertion with all his running and sparring and not enough rest.

What the hell was that? Implant? He thought to himself. He wished he could have seen more of that memory.

(flip) The General chuckled, "I have discretionary funds at my disposal however I wasn't thinking ping-pong. We'll see about air hockey. Now back to business. As I was saying, all changes to the teams, training, schedules or work assignments are completely at your discretion. I see no reason to butt in. These are your men, you know them best. Hota Ao cokp. tbl he?"

"Да cэp я hota Ao." John replied instinctively at hearing the Russian words spoken to him.

(flip) "Good Colonel, keep going you're almost to the end then you have one more lap to do. You're doing great." Carl coaxed as the Colonel put one foot in front of the other. This was his fourth lap down and back on the ten-foot length of parallel bars. Carl set the goal high. He only expected the Colonel to make three laps. Over the past few weeks when Carl set a goal the Colonel easily surpassed it and yet the Colonel still berated himself for being weak and not doing enough. So Carl thought he would try some reverse-psychology and see how the Colonel handled that.

(flip) "Carl, I have something for you. I wanted to say thank you for all that you have done for me this past year and for all the things I know you will continue to do for me." John lifted, with both hands, the box off his lap and handed it to Carl.

Carl accepted the box but before opening it, set it on the bed corner. It was heavier than he expected. Opening the box Carl reached in and pulled the snow globe out. As he held it with both hands and looked over every inch of the scene inside, he said, "thank you Colonel, it's beautiful." Carl reached underneath and turned the small crank to hear what melody it played.

(flip) "Okay Elizabeth, this is the gun you'll be carrying when off world. Here on the left side is the safety. It should be engaged at all times unless you intend to kill. Here is where the munitions clip is inserted. If done correctly, you'll hear a click. You slide the chamber forward and back and that primes the weapon. It will not fire unless the safety is off. This is the trigger, you place your index finger in and when you are ready to shoot pull back firmly releasing the bullet." Elizabeth paid close attention to his thorough explanation and demonstration of the weapon. When he was through he placed the weapon back down on the bench. "Now it's your turn. Pick up the weapon, hold it, get a feel for its weight, notice how it feels in your hand."

(flip) "Mommy why are you fat?" Asked a two and a half year old Johnny.

"Oh sweetheart, mommy is not fat. Mommy is going to have baby. Would you like a brother or a sister?"

"I don't know. Jeremy has a sister and Bobby has one too. I think maybe I would like a brother. But…"

Katie looked at her first born as he sat thinking real hard. "But what John?"

"How'd it get inside you?"

Katie Sheppard smiled at her son. Since the moment he could talk he was always asking questions. She'd hope not to have this talk until much later. Much, much later.

(flip) "John?"

"Yeah." John replied with disinterest. He was working on his calculus homework.

"Would you take me to the prom?"

"I thought my brother was asking you."Not looking up from his math book.

"I know he wants to take me, but I…well…how do I say this nicely…I don't like him. He's too stuffy, not a lot of fun if you know what I mean. It's prom night. I want to have some fun. So will you? Take me?"

"Sure Suzie, I'll take you. Pick you up around seven on Friday."

"Sheppard! You're here to play baseball, not entertain girls. You're on deck."

"Coming coach!" Slamming his book shut and stuffing it back into his backpack.

(flip)John sat anxiously waiting for his row to get the nod to stand. He watched the other graduates walk across the stage receiving their diplomas; red, white, red, white, boy, girl, boy, girl.

"Hi, I'm Amy. You must be really smart." The girl next to him said.

John had on his red robe just like all the other guys graduating, except that he had a white ribbon around his neck that indicated he was graduating with high honors. And of course a gold braided rope complete with tassels indicating he was an ROTC candidate. Graduation at Stanford had the flourish anyone could ever want, John just wanted that diploma he'd work so hard for. He managed to complete a double major: English Literature and Mathematics in his four years of college. Summer school included.

"Not really."

(flip) "Chuck, dial it up." John made his way out of the command center over to the grand stairs to join the two teams. His headache was raging as he descended. White hot pain blossomed inside his head like a bomb going off exploding throughout his extremities. "Arraggghh!" He screamed clutching his head. The painful scream echoed off the walls bringing General Brankovik running out of his office.

Colonel Sheppard stood about half way between the gate room floor and control deck on the stairs when he screamed in agony. Both teams turned but their reactions were not fast enough as they watched Colonel Sheppard fall, collapsing down the stairs to land in a tangled mess of limbs at their feet. Blood trickled down from a laceration on his forehead after striking one of the steps on his way down.

(flip)"Major Sheppard would you and your Council please stand. Article 92 of The Uniform Code of Military Justice: Failure to obey a direct order or regulation, this court martial finds you guilty with extenuating circumstances. The maximum punishment is dishonorable discharge, forfeiture of all pay and allowances and 6 months confinement. However your attorney made a strong case in your defense. Those five serviceman would no doubt not be alive today had you not disobeyed orders. We, the panel, cannot condone such willful disobedience from our officers. Therefore, the ruling of this court will be forfeiture of one-third all pay and allowances for a period of two years. You will remain a Major in the United States Air Force with no confinement. Your chances of promotion are slim. The outcome of this hearing is now a permanent record in your file. You are a good pilot son, therefore, it is the courts ruling that you may continue to fly. Your flight record is impressive Major. You may return to your unit or report to McMurdo. What say you?"

John couldn't believe his luck. He still got to fly. The mere fact that they didn't ground him was testament to his flying skills and ability. That's all he ever wanted to do was to fly. It didn't take long to make his decision. He was tired of the hot sand. Choosing McMurdo would add one more continent: six down and one to go. "McMurdo, Sir. Thank you Sir." John stated still at attention, eyes forward staring over the Judge's left shoulder.

(flip) Hearing the page for him over the PA meant something was wrong. Using the city-wide PA was a last resort at contact. He needed to get to the control room. The pins and needles feeling were creeping into his limbs. He rubbed his legs hoping it would accelerate the process.

John was sitting on the floor in one of the rooms off corridor G in the west pier where he had teams checking out the labs and rooms now that it had been deemed safe by Dr. Chandler. He had been checking up on the teams progress and was on his way back to his office when his legs spasmed pitching him forward to land hard on the floor. The last thing he wanted was for his men to find him like this so he literally dragged himself into the nearest room.

Currently he sat rubbing his legs holding back the fear and panic that wanted to consume him. Five weeks ago he was on his way to talk to Carson about what was happening to him but had gotten sidetracked when he saw Elizabeth limping. Forgetting all about talking to Carson.

(flip) "Colonel, you have a minute?" Asked Dr. Chandler the structural engineer assigned to Atlantis from the open office door. He continued to rap his knuckles on the door frame.

"Hey Bob, sure come on in. If you're looking for someone to hit golf balls I'll have to decline."

"Me too, as much as I would love to hit a few that's not why I'm here. We finished the west pier and it's structurally sound. I'd thought you'd want to know right away instead of waiting for the boring report I'm going to write about it. You can send your teams in to investigate any time."

"Thanks, I appreciate that. I'm already up to my eyeballs with reports so I could do with one less. Anything I should know?" Colonel Sheppard inquired.

"Sub-level five has about three inches of water but the rest is dry and the whole area is completely safe. They're good to go as you military types like to say." Bob laughed at his own little joke then added, "however, I'll take a raincheck on hitting golf balls. I understand you brought back whiffle balls. How do you expect to retrieve them by the way?"

"I also brought back a king sized fisherman's net on a six foot extension rod. I figure I could use a jumper to skim the water with the hatch down while an unknown party, yet to be determined scoops them up with the net. You want to volunteer? I would, but I'm the pilot."

"I'll give that idea some thought Colonel." Bob declared. Maybe even come up with a better plan. You know us engineers, we like to design."

"You do that. I'll let you know when I can find a few hours and we'll give it a try."

"Sounds good. I'd better get busy on that report. Have a good evening Colonel."

"You too Doctor." As Dr. Chandler left his office John glanced at his watch it was almost dinner time.

(flip) (flip) (flip) (flip) (flip) (flip)……

Hota Ao cokp. tbl he? = Do you not? in Russian

"Aa cэp я hota ao." = "Yes Sir I do." in Russian

TBC 21/60