Title: Establishing a Connection

Part 1

Rating: PG

Author: MacGateFan

Disclaimers: Unfortunately, not mine.

Author's Note: This was written for the lj community, ShepsAtlantis hiatus challenge. Prompt #2 - What if? Pick a moments in season one and alter it, then show the resulting fallout. I chose Brotherhood and I went all out apparently... Way longer than I had anticipated. Enjoy!

"Elizabeth!" Rodney exclaimed the moment he stepped from the event horizon. "We found it!"

Elizabeth stopped in the middle of the staircase and stared at the ZPM in astonishment. She smiled broadly as she continued down the remaining stairs to greet her flagship team. Elizabeth took in their expressions.

Rodney was grinning wildly, happy with the prospect of being able to shield the city against the Wraith if need be, Ford was nearly bouncing with excitement, and Teyla was genuinely happy that her new friends now had a connection with their home.

When she finally took the opportunity to look at John, she was surprised to find he had left the Gateroom. "Where did Major Sheppard go?"

"Ma'am, we had another run in with the Genii while we were there. Kolya to be more specific."

"Was he injured?"

Ford shrugged. "To be honest, I don't really know. He has a tendency to down play his injuries. From what I could tell, he just had a few bruises and a busted lip."

"He was favoring his side," Teyla responded.

Elizabeth nodded. "Why don't you try to track him down, Lieutenant? Besides the fact I want to speak to him, of course, he should have Carson check him over."

"Yes, Ma'am."

Ford was surprised to find John in the infirmary already. He was quietly tucked away in one of the beds. He knew something was wrong at that moment. "Sir?"

"Hey. Looks like Carson found some cracked ribs,"he replied. "Nothing I can't handle."

Carson walked up to them, a small needle in his hands. "Major again you're trying to hide what's really going on. Not only does he have cracked ribs, but it looks like he's developed an infection from a cut on his arm."

"When did you get that, Sir?"

"Fighting Kolya, of course. Now, if you don't mind, I'm going to get some sleep.■

Carson eyed Ford and the pair went into his office. "What happened on the planet, Son? He seems very withdrawn."

"I don't know, Doc. I mean, we got a ZPM, we beat Kolya, and we made some great allies. I just don't see what could have gone wrong."

The physician was thoughtful for a moment. "Perhaps this has to do with Kolya? The last time Major Sheppard dealt with the man, he was forced to kill people defending Atlantis. This may have triggered some kind of delayed post traumatic stress disorder."

"You do realize that if that's the case and Dr. Weir reports that, they're gonna to send him back to Earth."

"Aye, Lieutenant," Carson replied with a sigh. "I know."

Elizabeth was staring intently at the computer screen before her when a knock pulled her from her thoughts. She smiled. "Come in, Carson." Once he was seated, she asked the burning question in her mind. "How is Major Sheppard?"

"Physically he's mending fine, but Elizabeth, I can't seem to get through to him. He's barely eating, barely sleeping. If he keeps this up for much longer, I'll have to feed him intravenously."

"And we still don't know what triggered this?"

"I have a hunch it was Kolya, but since I, nor Dr. Heightmeyer and his team, can't get him to open up, we can't be certain."

Elizabeth nodded. "I can't stall General O'Neill and the IOA much longer, Carson," she said. "If I do, they're bound to figure out that Major Sheppard wasn't just injured in the line of duty. If I don't tell him, someone else just might in their report."

"Aye. I'll go down to see if any of the others have had any luck." He paused. "Perhaps you could come down later? See what you can do?"

"I'll try."

Elizabeth watched him leave the room. She really did need to see him soon anyway. It had been almost a week since they returned from Dagan and she'd only seen him twice since then. Between briefings with the IOA and negotiating with Allina and her people, it had been an exhausting week.

"Major," Teyla said, taking his hand. "Can you hear me?"

John blinked his eyes open and was greeted by a warm smile. "Hi Teyla."

"Hi John. Are you feeling all right?"

"I think I'm a little hungry," John replied, "but..."

"But what?"

"I can't eat knowing what I've done."

Teyla looked at him in confusion. "What you have done? John, you have done nothing wrong. We have a ZPM, a way to protect ourselves from the Wraith and a way for you and your people to contact your planet as well as allies. John, you have done everything right!"

"Those people... They can never contact their families again, why should I... not that I have any family," he added.

"John Sheppard, are you feeling sorry for yourself? That is not something I would ever expect from you."

"Not me, Teyla, them."


"The Genii."

Teyla nodded in understanding. Seeing Kolya again was definitely the trigger for John's mood. She took his hand in hers. "John, look at me! That was not your fault! You did what you had to do to protect the city! No one blames you!"

"Kolya does."

"He did not say that!"

"He didn't have to, Teyla!" John exclaimed, sitting up. He ignored the slight twinge of his healing ribs. "I have to live with it everyday! I have to dream about it and hear the thump of their bodies as they hit the shield!"

Teyla was standing at this point, trying to get John to calm down. Carson rushed in carrying a needle. He quickly injected it into John's IV as Teyla continued to attempt to calm him down.

"Shh... It's all right, John," she said. "Everything will be all right."

John held tightly to her hand as he drifted off to sleep.

Elizabeth arrived in the infirmary to see John playing with the bowl of soup Carson had sent up for him. Shaking her head, she walked over to him. "You do know there are starving children in the Pegasus Galaxy who would love even a sip of that, right?"

John looked up from the bowl. "I've tried to eat it, but it just keeps coming back up. I seem to have these panic attacks and I start keep thinking about those soldiers..."

He trailed off and Elizabeth placed a hand on his shoulder, smiling. "John, you have to realize that you did what you needed to do so we would all survive. We both know there's never a good reason to kill someone, but when you're defending yourself, your friends, I think it's justifiable.

"The reason you're feeling the way you are is that you are nothing like Kolya. You are a caring and thoughtful person. I've seen this demonstrated within the walls of this very city."

John wanted to believe her so badly. Deep down he knew he did, but coming to terms with it was another problem by itself. "I know you're trying to help, Elizabeth, but I think I'm going to be sent back to Earth regardless of how I'm dealing with this."

"What makes you say that?" she asked.

"McKay told me about Colonel Caldwell. That guy always seems to be there when I screw up. He's friends with my Dad and hates my guts. He hated how I disregarded those orders and what it did to his best friend. I'm half surprised he didn't voice his opinion against me when I joined the expedition."

Elizabeth wasn't expecting John to tell her so much information about his past. He must be feeling vulnerable, she thought. "John, you don't have to..."

"It's all right," he replied. "After I received my black mark, my Dad disowned me. I remember packing everything into my car. Caldwell and a few other generals were there to witness and they had a few too many drinks. They kept making comments and throwing empty cans at me. I'm not sure where Dad was through the whole thing, but I just ignored it and left."

"Why didn't you say anything?"

"What was I going to say? And to who? It wasn't like my life was threatened," John said.

"Dr. Weir."

Elizabeth tapped her radio. "Go ahead, Peter," she said.

"The Daedalus has arrived. Colonel Caldwell is requesting permission to land at the east pier."

"Thank you," she replied. ⌠I'm going down to meet them now."

John watched as she hesitated. "Go on, I'll be fine, really. Besides, I'm sure Caldwell is looking forward to meeting his new boss."

Elizabeth shook her head as she headed towards the door. "Very funny."

She arrived on the pier a few minutes later with Sergeant Bates in tow. Elizabeth took a deep breath when Colonel Caldwell finally appeared. She had to make a good impression since he would be the one to report to General O'Neill and the IOA.

"Colonel Caldwell," she said, extending her hand. She eyeballed the man, trying to remind herself to stay objective despite what John said he did. "Welcome to Atlantis."

Caldwell accepted her hand. "Thank you, Doctor." He glanced behind her at Bates, who was saluting him. He returned the salute. "I was lead to believe that Major Sheppard was in charge of the military here."

"He is, Colonel," Elizabeth replied. "He was injured on the mission to recover the ZPM."

He seemed to ignore Elizabeth's comment, then moved over to Bates. "Sergeant, I'd like you to supervise the unloading of personnel and cargo. Report to me within the hour."

"Yes, Sir!"

As Bates moved away, Caldwell turned to face Elizabeth. "Now let's visit Major Sheppard."

John had just finished his soup when Elizabeth led Caldwell towards him. He took a deep breath and tried to sit up as straight as possible. He was giving John that same look of detest from so many years ago.

"Sir," he said with a nod.

Elizabeth noted the slight change in John's demeanor around Caldwell and suddenly the Colonel was looking at her. "Yes?" she asked, almost hesitantly.

"I'd to speak with Major Sheppard in private, please." Caldwell waited until Elizabeth was out of earshot before he spoke up. "I understand you were there when Colonel Sumner was killed. In fact, if I read the report correctly, you are indirectly responsible for his death."

John swallowed around the lump in his throat. He really hated feeling intimidated by people, but the whole situation with Sumner still hadn't left him alone. He still had nightmares about it.

"Surely you didn't travel light years from Earth just to berate me, Colonel."

Caldwell grinned smugly. "Of course not, Major. After a conversation with your Father it was decided I would get your job and you were going back to Earth."

"My Dad..."

"Yes, he knows. The President gave him clearance when he asked about you. He honestly couldn't understand why you came out here, but he realizes the answer now. Dr Weir was just using you for your gene."

John shook his head in disbelief. That couldn't be further from the truth... could it? Now that he thought about it, she was quite insistent that he come. Hell, even General O'Neill was!

"I'll leave you to your thoughts, Major."