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

Epilogue

"You have a full day of class today, right?" John asked while leaning over the sink in his bathroom brushing his teeth. His wife was in the shower behind him.

"Yes." She called loudly over the running water.

"Okay, I'll get the twins ready I have several mission requests to process so it'll be quiet in my office. Meet you for lunch in the mess hall at noon."

"Okay."

John finished his morning grooming ritual then went to the nursery to feed and dress his two kids. When he walked in Harry was already awake batting at his solar system mobile that Radek made which hung over his crib. Checking on Katie she was still sleeping. John prepared two bottles because he knew his daughter would wake soon enough. Scooping up Harry he began feeding him. Once he was done with breakfast John burped him, changed his wet diaper and dressed him. By the time he completed all that his daughter was finally awoke. Following the same process he scooped up his daughter, fed her, burped her, changed her wet and smelly diaper before dressing her.

Both kids lay in their cribs looking around as they watched their daddy pack up the diaper bag with all the necessities. Diapers, change of clothes, bottles… I should have one of everything in my office. It would make this so much easier…formula, oh and can't forget their favorite toys. He crammed whatever else he could into the bag that he thought he might need for the day. Stowing the overly stuffed diaper bag under the two seater stroller he gently buckled his daughter into one of the seats before buckling his son into the other.

John couldn't believe how fast his kids were growing. Seemed like just yesterday they were born and here they were already two months old.

Elizabeth had taken six weeks leave from teaching to be a stay at home mom so to speak. John divided his time between office and their suite in order to help out. General Brankovik had been most supportive—as long as the work got done. John saw to that. At night, John took care of all the feedings to allow his wife to get some much needed rest.

Pushing the stroller into the living space John met up with his wife coming out of the bedroom. Being new parents, living in the Ancient city and having a boss who didn't mind him taking his kids to work with him was too good to be true.

"All set." John announced. The four of them journeyed to the mess hall. It was time for mommy and daddy to eat before starting their busy work filled day.

After breakfast Elizabeth headed off to class while John and the twins headed to his office to work. John loved the days that his wife had to teach all day. It meant that he got to spend his working days with his kids. John equipped his office with two cribs for when it was nap time along with a playpen. A microwave sat on a table in the corner along with a carafe of water he brought from the mess hall on days like today.

Katie and Harry played in the playpen as any two month olds do while he worked processing his mission requests, updating the schedule and escort rosters. When either of them got fussy he was right there to take charge: changing diapers, feeding or just holding them when it was needed. Having his kids in his office didn't detract from his duty one bit. Anyone who stopped by talked quietly if the twins were sleeping. Played or held them if they were awake while base business was discussed around them. A couple of times in the past month he was caught by his friends and men holding one twin in his arm while he typed away with his free hand. He was getting pretty good at the one-handed typing thing. Not as good as Rodney though.

"Colonel Sheppard the Daedalus has just arrived and landed on the east pier." Announced Mary in his earpiece.

"Understood." He clicked off his connection with Mary opening a radio connection with his second-in-command. "Lorne the Daedalus is here. Call out the troops. Yes, I'm going out there too. I think the kids need to see their grandpa." John was busy shutting down his laptop while he talked. Maneuvering around his desk he gathered his children. "Hey Cadets looks like Grandpa Steven is a day or two early. What'ya say we go see him. Would you like that?"

His two kids were all bright eyed and smiles cooing back at him as if they understood his every word. He loaded them back into the stroller, stuffing the diaper bag underneath making his way to the east pier.

"Colonel I see you brought additional help."

"Yes Sir. Dr. Weir is teaching all day so Cadet Katie and Cadet Harry are spending the day working in my office."

"And just how are my God Children doing Colonel?" Caldwell asked already unbuckling and picking Katie up from the stroller.

"Fine Sir." John bent down to pick up Harry as the two officers made idle conversation. "Dr. Beckett says they are right on target for weight and height. Oh…and healthy as a horse."

Col. Caldwell gave a half-hearted chuckle at the Scottish Doctor's choice of phrases.

Lieutenant Colonel Lorne already had a crew off loading supplies when he and the twins arrived on the east pier. The new military forces reporting to Atlantis gathered off to one side of the pier waiting for further instructions. Colonel Sheppard noticed that they were being escorted into the city along with the few science and medical members joining the expedition. A practice he set in motion years ago when he hadn't known what his fate on Atlantis would be.

"Excuse me Sirs, but we seem to be missing a Lt. Steinway." Lorne reported to his CO.

"What do you mean by 'missing' Colonel?" Asked Caldwell.

"He hasn't been checked off the incoming roster Sir. Everyone else is accounted for."

"Maybe he overslept and is still on board the Daedalus." Colonel Sheppard offered with a knowing grin that his superior officer and XO failed to see. "I'll bet he'll show up soon."

"I'll have his quarters checked. If he's not there we'll start a search. Everyone was accounted for when we left Earth. Do we have a description of the Lieutenant?"

"Yes Sir. As memory serves I recall reading from his personnel file he is 5 feet 10 ½ inches, black, kinda round in the middle, strong build. Not hard to miss for a Marine TBS Specialist. We'll keep an eye out for him out here." Colonel Sheppard replied.

"Very well Colonels if you'll excuse me I'd better get to the bridge." Caldwell gave Katie a kiss on her cheek before setting her back down in the stroller.

"Yes Sir." Sheppard and Lorne said in unison.

As soon as Caldwell was out of earshot he put Harry back into the stroller along with his sister before turning to Evan. "Evan I totally forgot to tell you earlier. Lt. Steinway is not a Lieutenant."

"He's not?"

"No, he's a baby."

"A baby Sir?" Evan's voice raised a bit thinking that his CO had smuggled a baby kitten or puppy to Atlantis for the twins. All kids needed some kind of a pet growing up. He himself had a Golden Retriever growing up.

"A baby grand piano to be exact. I had Novak and Hermiod falsify the ships roster in order to smuggle the piano on board. The crate was so big that it would have drawn attention from Caldwell, so we had to create a false identity and credentials in order for the crate to pass security. Lt. Steinway is a Marine instructor brought in for the live fire exercise with artillery. Part of the TBS training. Lt. Steinway had to bring his own specialized equipment: artillery, pop-up targets that sort of thing. It was all I could think of, of how to get the piano here. I had a few friends at the SGC doctor the crate. We need to keep Caldwell out of the loop. You know how he doesn't like transporting non-essential supplies."

"Understand Sir. Oh look over there, there went Lt. Steinway." Lorne pointed to the east pier doorway that was just closing after someone from the dock had entered.

Colonel Sheppard put a grin on his face. "Evan I need a favor, or rather Lt. Steinway needs a favor. He needs you to take charge of his equipment and handle it with kid gloves."

"Yes Sir."

"Okay, now for Col. Caldwell." John inhaled deeply letting it out slowly to calm his nervousness before tapping his comm link. "Sheppard to Caldwell."

"Go ahead Colonel."

"Sir just wanted to report we located Lt. Steinway."

"Thank you Colonel. I was just about to start a search since he didn't respond from the ship wide hale."

"Yes Sir. See you at the briefing. I need to put Katie and Harry down for their naps. Colonel Lorne will finish up here."

"Understood."

oOo

"Rodney I need to see you on Level 8, North Tower right away."

"Sheppard I can't right now. Zelenka disappeared on me and so has Simpson. The General wants me to get the Re'sal device packed up for Area 51 and Caldwell wants me to track down one of your grunts Lt. Steinway. Since when did I become the only one on this base who knows how to locate people? He's one of yours, surely you know where he is. I don't have time…"

"Lt. Steinway is with me right now on Level 8. It's an emergency McKay or I wouldn't ask. Just get over here and don't say a word to anyone else. It's kind of embarrassing if you know what I mean."

Between John, Ronon, Evan, Pete Buckland and Edward Moore they got Lt. Steinway and his artillery gear set up on Level 8 in the North Tower. It took John three days to find the perfect room. Another day passed as he figured out how he was going to get Lt. Steinway into the room, short of using the Daedalus' beaming technology. The room John found had a wall of glass so they took out two panels, while Jumper One hovered under Sheppard's steady mental control. Ronon, Evan, Pete and Ed carried Steinway from the back of the jumper into the room.

When John arrived after putting Jumper One back in her berth in the jumper bay, Evan was already assembling the legs. The Lieutenant had been uncrated successfully. Pete and Ed were working on the bench. By that evening Lt. Steinway sat in all his polished ebony glory.

The following day John invited a few people up to the North Tower for the grand unveiling. Team Lorne minus one astrophysicist, Radek, Miko and Barbara Simpson from Rodney's department, Carson, Carl, Christina and of course Sgts. Moore and Buckland since they helped with the heavy lifting and assembling. General Brankovik, Elizabeth, the twins and himself rounded out the honored guest list. Now John just had to get Rodney up here.

"Embarrassing? What do you mean by embarrassing? Oh…never mind. You can tell me when I get there. McKay out."

"He's on his way." John stated to the gathered crowd. John went into the hallway to wait for Rodney. He didn't tell him which room to go to. John heard Rodney before he ever saw him. He was still complaining about all the work he had to get done yet mumbling that here he was on Level 8 helping Sheppard out of another embarrassing moment.

"This better be a damn good emergency Sheppard. What has your grunt done this time? And why is Caldwell on his case? What did he do to piss off Caldwell?"

"I'll take care of Caldwell. I need you to take care of Lt. Steinway. He's in there." John pointed to the closed door he was standing in front of.

Rodney moved ahead swiping his hand over the door control expecting it not to open. He assumed that the Lieutenant was trapped in the room and couldn't get out. When the door opened Rodney was shocked to see the room filled with people. He'd only expected to find the stupid Lieutenant and Sheppard on this level. Rodney took in the many faces. "What are you guys doing in here?" Before anyone could form a response he saw Zelenka. "So this is where you sneaked off to. We have work to do. The General is expecting…"

"The General is right here Doctor and you may disregard my last request."

"Wha…disregard? Radek? What is going on here? Sheppard!" Rodney's head swiveled back and forth, he was so confused.

John walked up beside him placing a calming hand on McKay's shoulder. "Sorry Buddy. I needed for you to be preoccupied for a while. I needed time to set this up for you."

"Set what up?"

"This." John pointed to the left corner of the room. Everyone that was standing in front of John and Rodney parted to allow an unobstructed view of Lt. Steinway. "Since you decided to teach my kids about music instead of science I knew I had to find a way to bring one of these to Atlantis. So with a little help from Hermiod and Lt. Novak and a few others at the SGC I would like to introduce you to Lt. Steinway."

"This is for me?" Rodney was awe struck. Didn't know what to say for a change finding himself speechless. The baby grand piano was pristine. Rodney walked towards the piano his eyes wide soaking in the grandeur of what was before him. He allowed his hand to caress the wood. "Do you know what this is?"

"Yes McKay it's a piano." John answered snarkily.

"No…I mean this is solid Sitka spruce with a minimum of eight annual growth rings per inch. Vertical solid maple bridge, nickel-plated blued steel tuning pins to resist rust, which is good because of the salt air we get off the Atlantean ocean. Bass strings wound with solid copper and roslau treble stringwire, brass casters and foot pedals. And oh…"

John interrupted McKay's technical inspection of the musical instrument. John knew it was the top of the line when it came to baby grands. He'd spent two days researching before he e-mailed Jeanie Miller for help. With McKay's sister's advice he contacted the world renowned Steinway & Son's Piano Company. This little 5 foot 10 ½ inch piece of concert quality musical art had cost him over forty thousand dollars along with several I.O.U.'s back on Earth at the SGC and of course on the Daedalus. He was glad that Rodney had picked up on the quality the piano was made from but he still wanted to hear how it sounded when a professional played. All he could play was chopsticks and not well at that. "Play something Rodney."

McKay's head shot up so fast John was sure it caused whiplash. "No I couldn't."

"Rodney you promised to teach my kids music. Katie and Harry are waiting." John pointed to Elizabeth who was holding a fussing Harry while Ronon was bouncing Katie. "Please."

Tentatively and anxiously Rodney sat down on the ebony bench. He willed his mind to not notice the people standing around him. He wiped his hands on his pants to dry them off. Nervous since it had been close to thirty years since he last touched a piano. No time like the present he rested his hands on the white and black keys hammering out a soft melody rendition that had all the Earth people present in the room smiling.

When he finished Katie and Harry started to fuss more. Elizabeth thought it was because it was past nap time, but when Rodney started playing his second selection both children settled down content to listen to the beautiful notes their Uncle Rodney was producing. When he finished both Katie and Harry were sound asleep.

"Rodney that was beautiful. Does the music have a name?" Teyla asked.

"They were both children's songs. 'Brahms Lullaby' and the first one was called 'Twinkle, Twinkle Little Star'."

"Do you know more?" She asked again of her friend.

"Yes Rodney, play us something you wrote." Radek chimed in. The others in the room were shocked to find out that he played the piano, now they were shocked again to learn that he had actually composed.

Rodney began playing.

oOo

"Daddy I'm all packed. Can we go now?" Katie asked.

"In a few more minutes, your mother is still packing. Now what have you packed?" John inquired since his wife assigned him the duty to pack the twins vacation bags. Katie sat her bag down on her bed and opened it for inspection. John started poking around inside. "I see you packed Meer'na's doll she made you, Peter the green rabbit, Tommy the orange cat and Ronon's carved horse Ronni. What I don't see are your clothes, socks, pajama's and shoes."

"They wouldn't fit. I tried Daddy, really."

"I know you did sweetheart. How about I give you some help." Katie nodded with an appreciative smile. "How are you doing son? All packed?" John started to pull Katie's things from the closet and dresser that she would need while he waited on his son to answer.

Elizabeth finished her and John's packing and poked her head in her children's room checking on her husband's progress. She arrived just in time for John to inspect her daughter's suitcase. Smiling as John noted the contents and offered to help. John was an excellent father. When the kids were infants it was John who got up to feed them during the night after Elizabeth was through breastfeeding. He explained his military training had prepared him for just these types of circumstances.

John had taken an active part in the rearing of his children from the moment they were born. He took them to work with him, to meetings, to briefings or wherever his job took him on base that was also safe for his children. He was always patient when it came to answering their questions. John also allowed them to help with his duties when they got old enough.

In fact she had caught him in his office one day, both kids on his lap. They were going through e-mails deciding which to answer, which to save for later, which to pass off to someone else and which ones to delete. Elizabeth stood in the doorway in time to hear…

"Okay this one is from Dr. Deerman. Subject says: M7C-927 Mineral Study. What should we do with this one? Open it, save it, pass it on to Uncle Evan or delete it?"

John looked at both his kids as they pondered the question given to them. For being three and a half they were pretty smart in his estimation. Katie spoke up first. "Save it for later. We have lots to look at."

"Do you agree Harry?" Harry just nodded. "Okay then we'll save it to open up later. Next one is from Dr. Murray. Her subject says: Escort Request – Sub-level 5, Section 25, NW pier. What should we do with this one?"

"Send to Uncle Evan, dad." Harry stated. John looked at his daughter who was shaking her head 'yes' in agreement.

"Okay then Uncle Evan it is. This one is from General Brankovik. His subject just says: Meeting."

"Open." The twins said in unison.

After John opened, read, updated his calendar with the meeting details and filed the General's e-mail he moved on to the next one on the list. Ok here we have one from Dr. Kavanagh. Subject says…"

Before John got any further Harry spoke up. "Delete it Dad. He probably wants to complain again." John was shocked at his son's insight but the three of them had been spending a lot of time with Uncle Rodney and Uncle Radek in the lab. On several of their working-visiting trips Kavanagh had showed up to complain to McKay about this thing or that. John had no idea his kids were sponges, picking up everything that went on around them. He would have to be more careful from here on out.

"What do you think we should do Katie?" John asked trying to hide his smirk before making his final decision.

"Delete." Her giggly voice added.

"It's unanimous! We'll delete it."

Coming back to the present Elizabeth heard her son's answer.

"I got two pants, two shorts, five shirts, five socks, underwear, my good shoes, pajama's and my blue blanket." Harry rattled off with all the confidence of a five year old.

"Good son, that's really good. Just to be clear…was that five socks or five pairs of socks equaling ten socks?"

"Oh Dad…" Harry sing-songed to his father. John couldn't believe that his son was already forming an attitude at such a young age.

The Sheppard's had a two week stay on Earth since David finally got around to asking Julia to marry him. John was asked to be Best Man. How could he refuse? June in Highland Springs, VA just outside of Richmond was the perfect time of year for an outdoor wedding. The family stayed in his father's house which was actually his brother's house now. David even invited Evelyn Weir to come stay with them in the huge white house giving Elizabeth time with her mother and the kid's time with their only living grandparent.

The wedding was held in the garden. The backdrop was rolling green hills, white fences and spotted with beautiful horses grazing. Katie was the flower girl tossing her petals high over her head as she watched them float down in front of her before taking another step to repeat the process. Harry was content to stand by his dad holding the rings. For his age he knew he had the more important job.

Two weeks went by fast with the wedding and John allowing the kids to go horseback riding. They were leaving with twice as much luggage as they'd come with. Between Uncle David, Aunt Julia and Grandma Evelyn the twins were making out like bandits. Two days in a row the three women went shopping. New clothes, books, toys…you name it they had it. So did Elizabeth. She bought herself several new outfits for teaching along with a few surprises she bought her husband.

Stepping into their suite back on Atlantis John had one more surprise for his family. "Kids I have a surprise for you."

"John what have you done now?"

"Nothing bad Elizabeth. The kids are getting older now so I thought it was time they each had their own room."

The twins squealed with joy dropping their bags where they stood before running towards their room. While they were on Earth attending the wedding John had the nursery remodeled, dividing it equally and fairly down the center to make each of his kids their own room. When the door from the living space opened what would have been the large room they shared for the past five years was now a hallway leading to the bathroom. On the left was a wall with two doors in it. Both kids opened the first door to look inside before going to the second door. The rooms were exactly the same. Bed, nightstand, dresser, wardrobe, desk and chair. None of their personal things were in either room.

John could see the confusion on their little faces. "The rooms are the same. You have to decide who gets which one. Then I'll help you move your things into your room. I didn't want to decide for you. So you two think about that while Mommy and I put our things in our room. Okay?"

"Yes Dad." "Okay." Harry and Katie responded. John turned and escorted Elizabeth out of the kid's room. He wasn't kidding about having to put their things away. He picked up three bags from the living space floor while his wife took a fourth.

"John that was nice of you. I had been thinking the same thing and dreaded the thought of having to relocate to larger quarters."

"I know. They're growing up too fast Elizabeth."

oOo

Katherine and Patrick ran into the living space giggling. "I won!" Shouted Patrick.

"Only because you stood at the front of the transporter. Next time I get to stand there." His sister informed him.

Elizabeth walked in a moment later missing out on their conversation. John was sitting on the couch working on his laptop when his two giggling children entered. "How was school today?" He asked after they were through with their own personal discussion setting his laptop down on the coffee table so he could give them his full attention.

Both kids ran around the living space furniture to be the first to jump on their father's lap. Katie won that time. Both seven year olds began talking at the same time about their day. John listened intently to what each one said simultaneously. Elizabeth stood by the dining table in awe. How could John make heads or tails out of what they were telling him.

Katherine explained about her music lesson with Uncle Rodney before moving on to her science lesson with Uncle Radek. Patrick told him of his art lesson with Uncle Evan out on the balcony then he continued to tell his father about his cultural lesson with Miko. Then Katherine began to tell about her tumbling. Together along with the other children that had been born on Atlantis, Aunt Christina gave them all a language lesson in the afternoon.

Six years ago Atlantis' infant population took a surprising climb after John and Elizabeth married and had kids. Once others in the expedition saw how they handled it, how they managed work and family together, more and more expedition members married and began having kids. Atlantis was safe with the shield and with fully charged ZPM's to power it. Teyla was the first to get married. Kanaan, a fellow Athosian she had been seeing finally proposed after nearly two years of courtship. Ronon suspected but no one else ever knew for sure until she came to them after he proposed. They had a son who they named Torren. He was two years younger than Katie and Patrick. Teyla was due any time in the next month with their second child.

Nurse Nellie McGuire married Lt. Connifer and had twin boys; Matthew and Scott. Jinto and his 'special one' Karta, had a boy which they named after her father and Jinto insisted he also be named after Colonel Sheppard so Arundel John he became. Ronon had settled down as well marrying one of Carson's new doctors, Jennifer Keller. They had a daughter that was seven months younger than Torren. Jennifer loved Ronon with all her heart. She insisted that they name their daughter Melena. That was the first time ever that John witnessed his Satedan friend actually cry. Although to this day Ronon denies it ever happened.

Airman Stockard who over the years requested more KP duty than any other Marine on base married Nichelle, one of the cooks and nine months later had a baby girl they named Iris. Sergeant Chu who took care of the armory found true love in the clouds, Meteorologist Llka Sheng. Their baby girl, Zaria, was a premature birth. Llka went into early labor when there was an attempted take over of the base. She feared for her husband's safety and life which caused the early birth.

Gate Team Five had brought back a group of what they thought were refugees from a planet culled by the wraith. Little did the refugees know of Atlantis's security measures. Everyone made it out of that skirmish fine including the hostile refugees. Two weeks later a Re'sal shield device was set up on their planet. They were desperate, yet their religious custom didn't allow them to ask for help. McKay found it odd that their religion allowed for an assault.

Thus, with all the kids the North Tower was now becoming 'education central'. All classes were taught there: language, all number of sciences, music, art, math, history, dance and cultural studies. Ronon and Teyla even set up a room with gym mats, a balance beam and balls so the kids could play to keep in shape. The expedition members took turns teaching the kids their field of expertise from A to Z. Meer'na, the Athosian dressmaker came to Atlantis once a week to teach the kids to sew. She claimed it was never too early to learn a craft. Several other Athosian's whose talents were of tracking, hunting, farming or general craft trades offered their skills as well. Living in the Pegasus Galaxy meant you not only learned Earth values and customs but customs of the people around you, caring for you.

Katherine as she liked to be called now, except by her father, she still allowed him to call her Katie, could now play Brahms Lullaby from start to finish. Seems Katherine developed a photographic memory to go along with her higher than normal IQ for a child of seven and her strong ATA gene.

Patrick also had a higher IQ than a normal seven year old and a gift for math like his father. While his sister talked on and on about her studies Patrick studied his father's open laptop. Reading over the last several equations he found an error. Interrupting his sister, "Dad does Uncle Rodney have you doing his calculations again?"

"Yeah. I told him I could help him out. Why?"

"You answered that one wrong. The correct value for this section here for x is negative 1, not 1." Patrick pointed to the screen where he saw the error.

John slid Katie off his lap so he could reach the laptop to get a closer look. Studying the equation his son pointed out to him. It was wrong. "Thanks son, you saved your father from a tongue lashing from Rodney. Did you see any others that were wrong?"

"Nope. Just that one. But if you want I can check over your homework when you get all done."

John couldn't believe how much his son was like him. Thank God that he ended up with his mother's hair instead of his unruly top. "Don't you have your own homework to do?"

"Not tonight. Got it all done in class. Katie has some though." Katie gave her brother the evil eye look as she wrinkled up her nose to go along with her perfect pouting lips.

"Okay then, after dinner you can check over my answers before I send it back to Uncle Rodney."

As promised John let his son check over his homework before he brought out the gym mat. John had PT tonight. After the birth of his children Carl made him promise to start running ten miles with Ronon in the mornings and do his PT at minimum three times a week. John was never so thankful for making that promise. His body and mind felt better and his kids joined in when they were old enough.

With Katherine and Patrick doing PT with him it made it more fun than just a task that had to be done. The three of them would line up on the mat to do push-ups. When it came to sit-ups John always went first letting his kids do the counting to one hundred. When he was done Katie and Harry laid down toe-to-toe while John kept hold of their feet while they did as many as they could. Moving the mat into the doorway John set the bar across the door frame in preparation of his fifty pull-ups. While his kids rested on the bed he hammered out his pull-ups. Moving the bar down to where it was when he was paralyzed. It was the perfect height for his two seven year olds.

Sometimes his kids woke early and he took them on his morning runs with Ronon. It was never too early to start good habits.

oOo

"Welcome back Colonel…I mean General Caldwell." Colonel Sheppard taking a double take at the silver star on his CO's shoulder. "Congratulations Sir. A promotion well desired and long overdue I might add."

"Thank you Colonel. I have the new kitchen equipment you requested. I'm sure your men will know what to do with the supplies. Your men have always handled the off loading of the Daedalus well. If you have the time I'd like to speak with you and Gen. Brankovik about a matter."

"Of course."

Rose finally collected on her abundant amount of I.O.U.'s Colonel Sheppard owed her from over the years. Six months ago she decided to retire as head chef turning the reins over to Emily her executive chef. Rose wanted to stay on Atlantis but needed something to keep her busy part of the time. With the PX being a success she decided to open up a confectioners shop. Over the years the PX had grew by leaps and bounds. The Athosian's opened up a shop to market their crafts of fine tapestries, pottery, herbal teas, blankets and much more. On the last trade talks with Jibban it was negotiated to obtain the hides of the vacca's which the Athosian's tanned and turned into leather coats, pants, bags and the like. A leather store was added to the growing PX.

John had shipped in what Rose needed for her confectioners shop. She was naming it after her son: Danny Boy's Confections. As soon as the equipment was installed, power was supplied Rose could start work on making sweet treats for the base. Since Rose's announcement, Colonel Sheppard had padded their mess hall supplies so that enough sugar, flour and extracts were in reserve to keep Rose busy for months. Rose, Colonel Sheppard along with Katherine and Patrick when time allowed from their studies worked on the space getting it ready, doing most of the cleaning.

Entering the command deck Colonel Sheppard saw Rodney bent over one of the consoles. John was going to ignore him since Gen. Caldwell's request to speak with him and Brankovik seemed urgent but Rodney had other ideas.

"Sheppard!" Rodney yelled from over the console. "Your kids are doing it again."

"Doing what McKay?"

"They're fixing the problems we've experienced lately in the power distribution system since we opened up the western pier for family living quarters. And that's not all, they're rerouting water for better efficiency. The desalination tanks are now operating at 85 percent up from their normal 70 percent. They've written a new gate diagnostic program that is better than mine: faster and accurate down to the sub-harmonic level. They even initiated a new dialing protocol program. And in general those two are causing overall chaos to my carefully orchestrated system." McKay's face was red with frustration.

"Are they making things worse?" From McKay's tirade it didn't sound like it but better to ask then assume.

"No."

"Then what's the problem?"

"It's my job to fix the …"

"Rodney, give it up." John interrupted with a smile. For a year now Patrick and Katherine have been helping out in the labs. "You, Radek, Simpson, and the rest of your staff have taught them how to do it so let them do it. Unless they are doing it wrong. Otherwise go back to your lab and work on something more important. I got a meeting with the General's here. We can talk over dinner." Giving Rodney the brush off, John had to jog to catch up with General Caldwell.

"Generals?" Rodney muttered but didn't receive a response.

"Ah…Colonel Cal…." The General stopped his salutation mid-sentence as his Second-in-Command was waving and pointed hysterically behind Caldwell's shoulder. "Excuse me…welcome Brigadier General Caldwell."

"Thank you General. Do you have a few minutes to talk?"

"Yes by all means, please sit down. And may I offer my congratulations. What is so important on this trip General, the briefing is not for another two hours?"

"Nothing important General I just wanted to ask if you had room for one more. I'm considering retirement and I thought Atlantis would be the perfect place." General Caldwell announced.

"Retirement?" John questioned.

"Yes. I've been thinking about it for a couple of years now. I don't really have anyone back on Earth and besides the fishing is better here. So I thought if you had room…" He didn't want to add that he missed his God Children. Seeing them every two months or so he realized how much he was missing out on: all the firsts, all the new discoveries about their individual talents.

"By all means. We could use another seasoned officer around here." General Brankovik implied welcomingly.

Colonel Sheppard added his two cents worth to the conversation. "And since Patrick and Katie will be turning thirteen in a few months, your timing is perfect. They could use their Grandfather around more often. I'm told the teenage years are most difficult." John paused a minute taking in Caldwell's face. "Who'll take over command of the Daedalus?"

"If I have a say in the selection I'd like to see Lt. Col. Marks take command."

"Good choice." John agreed with Gen. Caldwell, Marks would make an excellent commander and just maybe he wouldn't have to go to such lengths to bring non-mission items into Atlantis anymore.

oOo

John held Elizabeth while she cried. When there was a pause in the continual sobs he lifted her chin to wipe away the tears that streaked her face. "Come now Lizbeth, we both knew this day would come."

"I know. I'm not ready."

"Who ever is?" John returned knowing he wasn't ready for this either.

Katherine and Patrick had been accepted for advance studies at Harvard University in Cambridge Massachusetts. Katherine was enrolled in advanced engineering and music. Her piano playing was something she liked to do. But it was Rodney who pushed her to study more—become the concert pianist that he would…could never be. Patrick enrolled in mathematics like his father and the ROTC program the school offered. Patrick had to cross-register at M.I.T. which suited him just fine.

The four of them were on Earth last week. Katie and Patrick had to be tested in order to pass all the basics and go right into advanced studies. At seventeen Katie and Patrick whizzed through all the testing that was thrown at them. It had been an exhausting few days for the twins. Their test scores were out of this world. The thought if they only knew crossed John's mind while listening to the registrar. Another thought also crossed his mind. John remembered how his father had wanted him to attend Harvard but in spite John had choose Stanford. David had gone to Harvard and he turned out well. Now it was time for a new generation of Sheppard's to make their marks on the ivy league school and world.

While making arrangements for the fall enrollment at Harvard the Director of the Psychology department heard about the twin geniuses and asked permission to test their IQ's for a study he was conducting. John and Elizabeth already knew that their children were smart so left the decision up their kids.

When the twins were two and a half years old they began causing genetic chaos all over Atlantis with their ATA genes. Everyone's limits were tested on a daily basis while John and Elizabeth did their best to control their twins. Grandpa Steven did his best to help. The Earth phrase, 'terrible twos' held a whole new meaning to the scientific research base. By the time the twins turned five years old and were causing less chaos with their ATA genes Dr. Heightmeyer and Dr. Beckett administered an IQ test which revealed both children as 'gifted'. Katie's score was 131 and Patrick's was 133. Carson knew that John was intelligent and after reading Elizabeth's file he found that she too was gifted. At sixteen when the twins started to be 'show off's' or 'know-it-all's' regarding their intellect Uncle Rodney had them take another IQ test. This time Katie scored 184 while her brother came in one point lower. Still, both kids were in the highest genius level, breeching too close for comfort on John's IQ score of 190.

By the time they had arrived back in Atlantis after stopping to see Dave, Julia and their three kids: John Alan Sheppard II who was now ten, Michelle Katherine Sheppard who would turn eight in two months and Adam Patrick Sheppard who was five. The later two both named for Julia's mom and dad. That's when they found out what Katie's and Patrick's score was from the IQ test the Harvard Psychologist gave them. They were both at 197, thirteen points higher than a year ago and six points higher then their father's. John would keep this little bit of information to himself. No sense in getting Rodney, the self proclaimed genius all riled up.

John credited most of their children's success to the people who lived and worked on Atlantis. They are the tops in their fields. And to be tops you had to have brains no matter what Dr. McKay said on a daily basis. These people with whom he lived, worked and protected over the years gave of themselves teaching his children to be who they were today. It was because of his extended family that his kids would someday conquer all the unknowns this galaxy had to offer.

"Come on, dry those tears and let's go to the going away party. Dave and Julia promised to keep an eye on them. They're only nine hours away by car, two hours tops by plane if they need anything." John explained to his distraught wife.

Carl had him reading and discussing 'empty nest syndrome' lately during his weekly visits. Carl had asked that they talk once a week. John remembered the short talk in the middle of hallway while he helped Carl move to his new quarters.

It was just after his return from Sweden that John started up his weekly visits to Carl. Two months after that the Marines shifted their counseling needs and concerns from Lt. Col. Lorne and himself over to Carl. Guess seeing your boss go in on a weekly basis did wonders for Carl's reputation.

"They're only seventeen John. They're my children."

"They're my children too and I'm sixty-five. So let's go to the party."

Elizabeth wiped away the remaining few tears and nodded. Her babies were leaving her. By the time they reached the gate room the good-bye party was in full swing. Elizabeth stood on the mezzanine balcony just off the conference room watching Katherine and Patrick who were making their way around the room thanking everyone for their support and teachings.

Katherine was tall at 5' 11". Her long brown hair had gentle waves that swept down to the middle of her back. Both kids had hazel eyes like their father. Patrick stood 6' 3" tall two inches taller then his dad and just as lean and muscular. His hair was chocolate brown like his mothers and controllable like his Uncle David's.

John put his arm around his wife pulling her close. "I was going to wait and tell you this later after the kids left, but I think now is as good a time as any. I have forty-five years in of service with the Air Force. I've decided to retire. I'm too old to be doing this stuff. I did what I set out to do Elizabeth: correct my mistake. I woke the Wraith prematurely and I've atoned for that mistake. It's taken a few years but at least the Wraith are no longer a problem to the populated worlds of this galaxy.

The Pegasus Galaxy is safe. Effero is now mass producing shield devices. Since we helped them set up a second facility and because of all the volunteers from all the protected planets who insisted in helping with the assembling processes, we have everything covered so to speak. Earth has six new ships patrolling the Milky Way, as well as their own shield devices which you managed to negotiate for them. Our long range sensors show no hostile acts coming from the Wraith. It's like they might be going back into hibernation. General Brankovik and Lorne can worry about what to do with them."

Elizabeth's jaw dropped at the pronouncement. She didn't know what to think. Her children were leaving to start college. Her husband just declared he was retiring. Where did that leave her? "I thought nineteen years ago we promised not to keep secrets from one another."

"It wasn't a secret. I just hadn't made up my mind until now. I figure now is a good time to call it quits. Will you be okay with this?"

"As long as I have you and the children I'm okay. Do you want to move back to Earth?"

"No. Not unless you do." John searched for the answer on his wife's face and was richly rewarded with the answer he'd hoped for.

"I don't either."

"What will you do? Who'll take over for you?" Elizabeth queried.

"I'm pretty sure the General will agree with me that Lorne will make a good base commander. I've been grooming him eighteen years now. Even since the General made a comment back when I had that memory problem. Heck he does most of my job as it is anyway. Shelley's been on his case for a couple of years now. Actually since they were married and he was promoted to full Colonel. She's urged Evan to further his military career. This would be a great opportunity for them. And maybe a promotion too. As for me…well first I thought I would finish War and Peace. After that who knows. I can still train pilots on the puddle jumpers. My gene is still the strongest until our kids come back from college so I can activate tech. We still have a lot to discover about this place. You said so yourself it could take a lifetime and I'm willing to give it my lifetime to unlock all her secrets. I'll keep busy. I have you and the kids to take care of too."

Elizabeth gave John's statements some thought. From the sounds of it he'd been doing a lot more thinking about his retirement than he led her to believe. "Whatever makes you happy, John also makes me happy."

"Good. Hey…I just had a thought. We could go to S2R-773. I'm King there you know. Zam said he'd keep the place running. And besides, did I ever tell you about the bed? It's fit for a King…and his Queen."

The End.

60/60

A/N: My sincere appreciation to EVERYONE who read 'New Beginnings' and my other stories in this arc. Thank you for your support and comments along the way.