A/N: Hope I don't step on the canon too much. Now, most of the new personnel I'm going to mention are OFCs and OMCs. Don't worry; there will be plenty of the main cast.

Disclaimer: I don't own John Sheppard (or Atlantis). Because of this, I weep every night.

Beta: J.A.B.

Spoilers: First Season, The Intruder, Runner, Instinct, maybe more

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Chapter 1:

He was tired and realized that the only way he was going to make it was if he got coffee—lots and lots of strong coffee in a nice big cup.

John Sheppard, newly promoted to Lt. Colonel, let himself go on automatic as he shuffled down the maze of halls in Stargate Command in search of his morning jolt. He hadn't slept much and he was sure that he would need to change his clothes soon or they'd send out the hazmat team to decontaminate him.

He scrubbed his hair with his left hand and smiled faintly when he could feel most of it standing up on end. The pilot in him liked it that way. He was pretty sure it gave him the 'I'm cute, take me home' kind of look. In addition, if nothing else, it was a good way to get McKay's goat.

Hell, half the time it also got Dr. Zelenka's goat. The little Czech scientist had his own wild haired thing going on and he didn't like the competition.

By the time John found his objective, he was more alert and his heartbeat was slightly elevated. His right hand had unconsciously gone to rest on the butt of his holstered sidearm as his eyes slid from side to side.

Searching . . . looking . . .

Looking for Wraith.

And Genii.

John snorted softly at himself as he poured out a cup of coffee. He sipped the hot stuff carefully as he turned to go to the conference room he had been using since his promotion.

He didn't notice when his right hand automatically went to his gun as he used his left to hold the cup.

It was strange how his nerves jangled here on Earth. After all the time he spent running from the Wraith, second guessing himself as he tried to be a leader and defend Atlantis, and longing for the former 'quiet' of home, he had thought he would be thrilled to be back.

That feeling had lasted about two minutes once he stepped foot on Earth. Two minutes to find out that Atlantis was his home now, and that he wanted to go back as soon as humanly possible. He missed Atlantis almost as much as he missed flying that month he had spent grounded when he . . . well, he shouldn't dwell on that now.

He had new personnel to help pick for his city.

To be honest, John had flushed a little when Dr. Weir asked him to assist in picking out the new rotation of military members for the Atlantis Expedition. She said she trusted his judgment and that she'd do whatever she could to facilitate pushing his choices through the red tape and past the brass.

Someone saying that they trusted him, and his judgment, and with something this big, was a new experience for him.

Sure, Weir had to trust him the last year they were stuck in the Pegasus. They had been cut off from Earth, so her trust had kind of been forced from her. Now that Earth was in the picture, he had half expected to be replaced or reassigned.

He had never expected more than to be a test subject when he went through the stargate to see what they could find of the Ancients and their Lost City. John was just as shocked as the others were when events conspired to make him the ranking military officer and responsible for the safety of so many.

Knowing it was unlikely that he would have this influence and discretion again, John felt the responsibility press in on him again as he absently retook his seat in the conference room. He turned one of those cheap Bic pens in his hands while he tried to focus his attention on the thick files in front of him on the conference table.

This was a big deal and he was almost afraid he'd blow it by picking the wrong people to help in the rebuilding process.

He reached out his right hand to spread the files out as if they were a deck of cards. He noticed that the neatly typed pages that listed the accomplishments, military career paths and psych evals were for over fifty hopefuls.

Having never been a strict by-the-book man, he had met with as many of the applicants face to face as he could. He was relying as much on his gut feelings of the applicants as he was the pretty words on the piles of paper. Just to see their expressions and their body language as he questioned them.

To feel them out.

John wanted the best for his city—the best possible chance for it to survive and for his people to survive against the choking threat of their enemies.

He wasn't here to get bodies to fill the positions of the dead and missing, he wanted the finest, those prepared both mentally and physically for the challenges that the original members of the Expedition had experienced.

It was a hard concept to convey to the top brass and the applicants but, in the end, he was very satisfied about the people he chose to recommend and was he happy that most of his choices were given the green light.

With his new rank of Lt. Colonel, and his position as the official commanding military officer of the expedition secure, John was ready to return to Atlantis with new hope.

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It was early morning in Atlantis when John Sheppard bounced into Dr. Elizabeth Weir's office as if he were an overgrown puppy with its first chew toy.

It always surprised the expedition leader when she saw the open humor in her ranking military officer's face. After all the Atlantis personnel had been through since they decided to step through the gate and into the unknown, she was glad John still had his basic optimism still in place.

"We're about ready to go to P3M-390." John almost flung himself down onto one of her comfortable white chairs. He settled in with his arms crossed over his chest as he absently bounced his right knee to keep his excitement under control.

"The planet with just rocks and water? How's Rodney taking it?" Dr. Weir let her paperwork go as she leaned in her chair to bask in the Lt. Colonel's enthusiasm for a few moments. Lately, it seemed that hers was in short supply and she was glad to see John's still in action.

John raised his left eyebrow, and for a moment, Elizabeth thought of Spock on Star Trek. She almost laughed to herself as she remembered having the same thoughts when Teal'c of SG-1 had done the same thing during her very brief command of the SGC.

Sometimes, she even caught Teyla doing it.

"McKay is being . . . McKay. Since there is no technology or power source, he wants to leave it up to the new teams to explore the place."

"And you said?"

"Where's the fun in that?" Sheppard did that half nod, half chin lift that made him seem to be even younger than he looked right now in his exhilaration.

Dr. Weir allowed herself a grin. Rodney had always been a little hardheaded and impertinent, even on his best behavior. It amused her to see him butt heads with Colonel Sheppard over the missions, and to hear their running 'war' of words.

She shifted a few things on her piled up desk to find the mission brief John had submitted yesterday. "I see you're going to be taking three of the new teams out on this one. I was wondering when you would finally let them out of Atlantis."

She had wondered when, after months of instruction and practicing had gone by, why the new Atlantis reconnaissance teams were still twiddling their thumbs and still doing light duty in the city.

"Well, they're going to be out there soon . . . on their own. I just want to make sure that they listened when they were going through the training," said John in a bored voice that accompanied a shrug of his shoulders. "Besides, Major Lorne will be around here for a while after his accident in the Jumper Bay. He can keep an eye on things while I'm gone."

She could now hear the underlying tension in his voice. 'I want to make sure that they live when I let them go out without me,' was how she translated his words in her head. In the past, it usually wasn't his own team's missions that Colonel Sheppard worried about the most. It was the teams that he couldn't watch over that gave him the nightmares.

"You all picked good people, Colonel. I'm sure they'll do just fine," she smiled. "And I'm sure Major Lorne can handle whatever military matters that may come up on our end."

He nodded his head and she tried to stifle a snort, as his undomesticated hair didn't budge. Just how did he get his hair to do that so that it stayed in place all day without falling flat?

John raised his eyebrow again at her snort. "What?"

"Nothing. Keep us updated while you're out there."

"Not a problem."

Elizabeth didn't return to her paperwork when Sheppard leapt to his feet and did his patented 'cocky pilot' walk out of her office and down to the main floor that housed the stargate. She moved to the catwalk in front of her office and frowned a moment when she noticed that John's right hand stayed on his holstered gun all the way.

The longer their stay here in Atlantis, the more wary John Sheppard seemed to become. Even with his positive attitude, he seemed to be ready for almost anything at all times. Even when he was 'home' and off duty.

She looked down at her own clenched white knuckled fist on the railing and she revised her thought.

They had all become a little more wary and high strung since meeting the Wraith and the Genii.

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It didn't take long after John left her office for the four teams to assemble near the gate with their equipment. Dr. Weir watched from above as John went to all the new people to make sure that they were ready.

The Lt. Colonel seemed almost like a mother who was sending her children to their first day of school as he checked straps, weapons and supplies. With eleven new soldiers, one field medic and three new scientists for whom he was responsible, John was making sure that everyone was taking what they needed for at least a three-day stay on the alien planet.

Just in case . . .

The new people, including the scientists that Rodney had helped select, seemed excited and eager as John pointed his finger at them and gave them his speech about listening to the veterans and about not straying far from their teams.

Many of the soldiers nodded. Most were not new to combat—many had served in campaigns on Earth and they knew a little of what they would be facing when they went through the stargate and into hostile territory.

They finally moved out with John's teammates Ronon Dex and Teyla in the lead, the new teams in the middle, and John and Rodney bringing up the rear.

John took a moment to raise a hand to Weir just before he stepped through the blue ripples of the gate and onto P3M-390.

She didn't have time to wave as his form disappeared into the light.

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Dr. Rodney McKay had conflicted feelings about being on P3M-390. While he was glad, even happy, about being on the mission since it took him away from being stuck overseeing the teaching projects of his latest people, he wasn't pleased it was to such an unexciting place.

He opened his mouth to complain to the Colonel, but realized that the Colonel was off with some of his new soldiers setting up a sketchy security perimeter.

"Playing soldier," muttered Rodney under his breath as he watched Sheppard, with small gestures and calm words, cautiously position his soldiers.

Rodney finally turned away and huffed. Really, his brilliance would be more beneficial to Atlantis if he could be looking for Ancient technology, instead of looking at the properties of the native water and rocks of a planet that seemed to be at the dawn of its existence.

In the end, Rodney had only agreed to come when Sheppard pointed out that the scientists were part of his responsibility. Well, that and the seemingly contagious excitement that poured off the Colonel whenever he talked about the mission.

Therefore, Dr. Rodney McKay sat on a rock and watched the new scientists as they took samples and as they murmured to each other in low voices.

He could pick out Dr. Jeromy Grant and Dr. Katy Mawyer as they scanned their prized samples and comparing data. Dr. Henry White was carefully taking their sealed samples and placing them cautiously in a shockproof metal case.

"Dr. McKay! I believe we may find single-cell organisms here. Much like what would have been found on Earth almost four billion years ago!" rang out the high and eager voice of Dr. Grant from nearby.

The new man's eyes were shining in the hot sun of the bleak planet.

Rodney shifted to see the radiant face of Dr. Grant. "Oh, gooood," he replied in a singsong voice. "How wonderful for you."

Grant didn't seem to notice the mocking tone as he went back to work.

McKay looked around for his teammates. He really wanted to find someone he could complain to about the misplaced glee of the new people. He looked for Ronon, only to see him joining the Colonel in his guard duty on higher ground. Both were talking to the soldiers now as the Colonel swept his out stretched arm around the area and as he pointed toward the guarded stargate. A few of the soldiers nodded in agreement with whatever he said. Ronon just stood with arms folded and with a faint scowl on his features.

Rodney turned his head toward the gate and saw that Teyla was on guard duty with one of the soldiers from the newly designated Team 11. Rodney turned his body so that he could better make out Teyla. He saw that she was also talking as the new guy pointed to the rocks and the other Atlantis personnel.

Rodney gave a mental sigh. He wondered if all the questions from the new soldiers were making his teammates feel as old as he did when the scientists asked him rookie questions.

Go to Pegasus, see the galaxy, and then age ten years in one when you think your life is about to get sucked out by a creepy energy stealing vampire.

All the new people seemed excited to be in Atlantis, to be in this galaxy. Even after reading the old reports. It didn't help that a scene from The Lost World kept running through McKay's head. He whispered Dr. Ian Malcolm's words as they replayed in his head once again, "Oh, yeah . . . ooooh . . . ahhhh . . . that's how it always starts. But then later there's running and . . . screaming."

Just wait until the new people saw their first Wraith, up close and personal. Bad breath and all.

There would definitely be some running and screaming.

Rodney rolled his eyes at his slightly morbid thought, as he continued looking at Sheppard and his men. As he watched, Sheppard crept closer to the edge of the high rocks, to watch as the scientists dipped sample jars into the greenish waters. He suddenly turned to Ronon and said something. The big man nodded and moved away.

From his pensive look, Rodney could tell that the Colonel was uneasy. He snorted. Really, the man acted as if the new members of Atlantis were five years old and that they needed to have their hands held. Sure, they were new, but they had all survived the training, and the hovering of a certain military CO.

Ronon suddenly jumped down from the rocks above, and he strode over to the edge of the water. His thick rolls of hair swung slightly in the soft breeze, as did the trailing edge of his long coat. It didn't escape Rodney's attention that the former Runner came to within jumping distance of the busy scientists.

Rodney rolled his eyes again and he started rummaging in the pockets of his vest. He made a pleased noise when he found what he was looking for. In no time, Rodney was intent upon hungrily munching his strawberries and cream PowerBar.

That's when everything seemed to go to hell in a hand basket.

TBC