Disclaimer: I don't own any SG-Atlantis characters and do this strictly for R and R. No profits involved!

Author's Note: Hello everyone. This is my first fan fiction ever. I have been reading fan fiction, particularly sci-fi, for five years and am just now getting the courage up to write something of my own. I am in love with SG-Atlantis. Weir and Sheppard are my two favorite characters. I'm best at writing about relationships (all types) so you might not see too much action type stuff from me if I decide to continue. This is all in good fun. I have no aspirations to be a great writer. Here is Ch. 1 with more on the way soon. What I thought was going to be a quick three chapter story turned into a ten chapter monster. Please review. I can use all the help I can get. Enjoy!

Sheppard's Shame

by Saharasia

Chapter 1: The Arrival

All was not well on the City of Atlantis. Major John Sheppard and Teyla Emmagan were overdue from a routine mission and had not reported to the base in over forty-eight hours. Dr. Elizabeth Weir had gotten very little sleep within that time, passing the moments standing like a sentinel in the control room, willing the Stargate to activate and seeing her two lost team members come strolling through.

Dr. Weir smiled to herself as she remembered back to her teenage years when she would wait by the phone for hours until she gave up on the cute football player, or whomever her crush was on that week, to call her. Its not that she wasn't attractive, just smart and she had a knack for sniffing out the B.S. A trait she would come to rely on throughout her political career. As if on cue, the Stargate suddenly engaged pulling Dr. Weir out of her musings bringing her to instant alertness.

She turned to her technician. Not needing to be asked he immediately reported, "Its Teyla's code."

"Open the iris and get Dr. Beckett up here with a med team," Weir ordered. She had a bad feeling about this. Her intuition was screaming at her, the hair on the back of her head standing up. This was not going to be good. Something was definitely wrong.

Suddenly, two weary figures appeared from behind the liquid blue pool of light. One of the figures was leaning heavily on the other who was barely standing erect herself.

Weir went immediately into action, not wasting a second and was down the stairs and into the jumper bay in a flash. Teyla, who was supporting a half-conscious Major Sheppard, was gingerly lowering him to the floor ending up in a heap with the major panting heavily next to her.

Dr. Weir's worst fear had just been confirmed. She reached Teyla's side and helped her lower Major Sheppard the rest of the way to the floor. She knelt in front of the Athosian woman as the Major curled up into a fetal position. Dr. Weir noticed for the first time that the Major was half-naked for the most part, bloodied, and bruised.

"Teyla? Can you tell me what happened? Are you alright?" she asked in the bravest tone she could muster.

"I am fine, Dr. Weir," Teyla lied ignoring her own injuries. "Major Sheppard is in more need of assistance than I."

"What did they do to you?" Weir pressed.

"We were tortured by the Xenatites. Major Sheppard received the worst of it. They did not take the news of the awakening of the Wraith very well," Teyla stammered out. She had a look of shock on her face Dr. Weir had never seen on her before. She placed her left hand on the side of Teyla's face in an effort to simultaneously comfort the young woman and check on what looked like a head wound.

A soft moan brought the two women out of the moment and they turned their attention back to the Major. Dr. Beckett and his team had finally arrived, clambering in with their equipment, going into action attending to Teyla and the Major. Dr. Weir stood up and hung back a little allowing the med team to do their jobs.

Dr. Beckett took in the situation in just a few seconds. He didn't like how the Major was looking. He could tell by the time he crouched down to further examine him that he had been badly beaten and had some broken ribs. The Doctor hoped to hell that the Major hadn't suffered any internal bleeding since that would complicate things a bit.

Dr. Beckett leaned in close to the Major to call his name and received no reply. The Major was barely conscious, trembling, and his half-opened eyes were glazed over and vacant.

"Can I get a blanket over here?" he called to one of his team.

A medic rushed over and helped the Doctor spread a blanket over the Major's shivering, pale body. Upon further inspection of the Major's injuries, he discovered cuts, bruises, and a concussion. Taking his stethoscope, he listened to the Major's heart and lungs. He didn't like what he heard, wincing with his effort. Quickly checking for broken bones, he found several broken ribs and a possible fractured cheek bone. They would need to stabilize him and get him to the infirmary, stat, before proceeding.

Near by, another medic was assisting Teyla. She had a few bruises and cuts here and there but was for the most part, intact. The kindly medic helped her up and walked her over to the infirmary protesting the entire that she preferred to remain behind with Major Sheppard.

In the meantime, Dr. Weir had been doing her own visual assessment of Major Sheppard's condition. His hair was matted with blood, his pale skin had a grayish tint to it, his left eye was blackened, and his lower lip was split. His breathing was coming in low, shallow gasps. He had scared the hell out of her once before in the puddle jumper when he had to be revived after the incident with the bug. But this, this was scaring her in a way she couldn't quite put her finger on.

Dr. Weir put a hand over her mouth as she watched Dr. Beckett and his team gently place the Major on a gurney. She almost couldn't stand it when Major Sheppard let out a small painful cry as they moved him despite their best efforts to be careful of his injuries. She wanted to so badly to cry, scream out in anger, lose her cool, but she had to remain strong in front of her crew. Ever the diplomat.

Before the Major was whisked away, she came forward to get the good Doctor's assessment. "How is he?" she quietly asked.

"It's too early to tell, Elizabeth. We'll have to wait and see. He'll pull through but it may take awhile before he's fully recovered if you get my drift," the Scot reported.

"Take good care of him, Doctor. I want a progress report as soon as you have it on both he and Teyla. I would like to see them when they are able to have visitors."

Dr. Beckett and his team quickly exited with the Major in tow. They had inserted an IV drip, placed hit head and neck in a brace, and were administering oxygen, finally stabilizing him enough to move him.

Dr. Weir thought she saw the major glance in her direction for a brief, lucid moment. His eyes, usually full of mirth, mischief, and cheer, were now vacant and full of pain. "I'll be in my office," was all she could manage to eek out as she walked away from the bay and the floor stained with Major Sheppard's blood.