Stargate Atlantis – When Time Is Up (Full Story)

Disclaimer: Stargate Atlantis is not my creation and doesn't belong to me. I merely wish to play around with a few marvellous characters for a while and hopefully contribute with a good story.

Characters: I like to involve as many of the regulars as I can but this one is very Sheppard-centric with OC's.

Genre: Hurt/comfort, adventure, drama

Time/Spoilers: The very beginning of season four/ sort of for the episode Sunday

Summary: After the destruction of the Asuran home world and the death of Dr. Elizabeth Weir, Colonel John Sheppard is ordered to take temporary command of the whole expedition until Colonel Carter has settled everything on earth. Sitting on two chairs, dealing mostly with military and civilian, paperwork Sheppard can't wait to get off world. When opportunity presents itself he takes it. However, will he get back before time is up?

Beta: PuddleJ – I owe you one ;)

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Chapter One – And So It Begins

John Sheppard sighed, then closed his eyes and reached up to rub his forehead. He'd been sitting on his ass most of the day, locked up in his office trying to sort out the mess on his desk. Not a man fond of paperwork he'd let the reports, the duty rosters, the programs for training exercises and the applications of new recruits from Stargate Command wait as long as possible. The result being that he now had a mountain of paperwork to sort out. In all fairness he'd attended other things that demanded his attention, such as the most important debriefings with the SGC and the IOA back on Earth. He'd been writing condolences to families that had lost their loved ones during their last showdown with the Asurans. The hardest one being Elizabeth Weir's considering he refused to accept her death in the hands of the Asurans. However, the SGC had written her off despite his protests.

He sighed in frustration, hands behind his neck as he leaned backwards in his office chair. He cursed himself as he realised that he'd broken his promise to himself never to let anyone get close enough. Yet he'd let Elizabeth come very close, as close as his team if not closer and now it hurt like nothing else. Her MIA status forming a void in his heart, the uncertainty of ever seeing her again was almost worse than knowing she was truly gone.

Carson Beckett was different because, even if he blamed himself for being unable to protect the man, he knew that the charming Scottish doctor was dead, well and truly dead.

Sheppard reached up to rub his temples as a dull headache was threatening to increase in intensity. What he would give to get off world and see something else than the four walls of his office and disappear from the diplomatic meddling between the various teams and departments in the city.

"Sheppard," a very familiar voice came over the radio, swiftly ending his brooding and self-pity.

John smirked as he touched the button in his ear to transmit a reply. "Yes, Rodney," he drawled, managing to sound very disinterested in what the scientist wanted.

However, Rodney McKay seemed oblivious to the response as he plunged into an explanation.

"It's been there all along, right under our noses," he said, sounding like he'd just cracked the code to a safe containing the largest treasure on earth.

"From the beginning, Rodney," John admonished, although with a teasing undertone.

"What? Oh, come on Sheppard," Rodney snapped unamused. "You know what I'm talking about. You do lead the expedition at the moment – civilian and military issues."

John dropped the act. "You've found another Ancient outpost?" He asked with a raised eyebrow as he leaned forward in his chair.

"Even better," the scientist replied jovially. "The address retrieved is not in our database but was hidden away in a separate data storage in Janus's lab."

"Okay," John replied carefully. "Now, why would Janus have that address and not…"

Rodney couldn't contain himself and cut him short.

"I believe it's one of those so called secret worlds where he conducted his experiments. Remember that the council wasn't too amused by what he was doing," the scientist said.

When John didn't reply to his statement Rodney continued. "When do we leave?" He asked.

OOOOOO

/Thirty-Six hours later/

John Sheppard stared at the stargate as it crashed to the ground in front of him. The shockwave reversed his mad dash toward safety in Atlantis to the extent that it hurled him backwards. He staggered and fell as his injured leg buckled, not able to support him any longer. He went down hard, falling backwards, his knee twisting at an agonising angle. He just had enough time to twist around enough so that he could cushion the impact with his hands. Dust and debris swirled around him as he lay panting on the ground and he closed his eyes to prevent the sand from reaching them. He coughed as he involuntarily inhaled a large portion of the air and his nostrils flared.

He didn't know how long he lay there but when he finally lifted his head and glanced around he noticed he was alone. The people who'd been following them, hunting them, as they ran toward the gate had disappeared. Instead an eerie silence had settled over the area. With a groan, he turned on his back and stared up at the ominous sky, searching for the Lantean ship that had roamed above their heads moments ago. As he had expected, it was nowhere to be seen. The only thing that even hinted that it had been there in the first place was the smoke pillars that rose around him as the forest had been set on fire. A million thoughts competed for his attention. Who were they? Where did they find the ship? Why did they fire at his team?

His reverie was broken as rain hit his face and he gazed up at large storm clouds coming in from the east. The rain increased in intensity from a drizzle to a heavy downpour, and with some effort he managed to drag himself toward a large tree, standing not far from where the gate had been standing. Grimacing while breathing heavily, he propped himself up against the trunk, protected from the rain. The heavily built gate lay before him in a heap; cracked in so many places he didn't dare to think what would happen should someone dial it. At least his team had managed to get back in one piece, or so he hoped. He refused to believe otherwise; couldn't accept anything else.

His eyes trailed from the gate to his left leg. A broken arrow protruded from the flesh below the knee, embedded in his calf. He reached down to prod the tender area and gritted his teeth as the frayed nerve ends caused it to sting violently, before morphing into a raging fire as his hand closed around the arrow.

"Way to go, John," he scolded himself. "You're so screwed."

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To be continued