Instinct
Chapter 9: Emotions

A/N: Hey, sorry it took so long. My computer has been giving me problems, grrr…
Also, thanks to everyone who has reviewed, it means so much to me! Oh, and big thanks to my beta, SGAngeL, you rock.

John Sheppard found himself in a familiar place as he stood in front of Elizabeth's office. But this time was different, he knew the minute he saw Colonel Caldwell sitting in her chair. Everything about the image in front of him was wrong. The only person who ever belonged there was Elizabeth Weir. He didn't knock to alert the man to his presence; he just stood in the doorframe, a sorrowful look on his face. For once he was hesitant before entering the office. He couldn't help but imagine seeing Elizabeth sitting there, turning her face upwards and smiling shyly. The vision faded when Caldwell spoke.

"Do you need something, Colonel?" Sheppard cleared his head then entered. Usually he would stand next to the desk or even sit on the edge, but today he stood uncomfortably in the middle of the room.

"I wanted to apologize for my earlier behavior, sir. It won't happen again."

"See that it doesn't."

John nodded as he turned to leave but was stopped when Caldwell caught his attention.

"Relax, Sheppard, I'm not going to redecorate her office or anything." The colonel said, looking up from the computer screen for the first time.

"I know." He said casually.

"You really do hate seeing me here, don't you?"

"No, just dislike immensely." Caldwell let out a small laugh. John Sheppard did have a sense of humor.

"If it means anything to you, I don't like taking Dr. Weir's place. She runs this place exceptionally well, better than I ever could have." John smiled; he didn't have a response. He stood for a second, wondering if Caldwell really meant what he said..

"Was there something else you needed, Sheppard?" After a moment of heartfelt words, it was back to business. Colonel Caldwell couldn't have himself run by emotions.

"No, but, uh, thanks." John left hardly believing he had just thanked him.

Elizabeth had been moved to a private room out of courtesy. John had pushed for it, everyone understood why. By now it was habit now to visit Elizabeth any chance he got. Whenever John wasn't in dire need of defending Atlantis he was at her bedside. He often held her hand, regardless of who might be near; even a certain Colonel's looks didn't bother him anymore. So it wasn't at all strange to find that John was currently stationed next to his top priority in the middle of the night, his hand wrapped around a small, frailer one. As he did every night, he took a few minutes just to look her over, making sure she was exactly the same as when he had left her mere hours ago. Of course nothing was going to be wrong, he assured himself. And nothing was, as always. With his free hand he reached up and gently pushed a loose curl away from her face, making him smile.

"You really oughta' do something about that, it drives me crazy." John joked about almost every thing with her, it eased the tension. He found that more and more of the one-sided conversations had jokes replacing the ever popular, 'you're going to make it,' speech.

"Colonel Sheppard?" A small voice was heard from atop the table, where his radio was resting. Every time he sat with her he took his jacket and radio off. He hated being interrupted, but he knew he couldn't do anything to change that. John had to remind himself that other things were going on in the galaxy and that they never stopped to rest.

"I'm here." He answered the call softly.

"Sir, Mr. Logan would like to speak to you."

"Give me a minute."

"Of course. I'll tell him you're on your way." John sighed placing her hand carefully back at her side. "I have to go, Elizabeth. I'll be back later." Standing, he hesitated for a moment before leaning over and placing a tender kiss on her forehead. He hadn't planned on doing that, it had just happened. He hovered above her for a second, whispering, "Elizabeth, how do you do that to me?" Forcing himself up, he grabbed his radio and jacket before looking back to her once more.

Reaching the well-known infirmary, John stood at the foot of Dimitri's bed with a straight face.

"Colonel Sheppard, I've been waiting for you."

"I was busy."

"I've been meaning to ask you, where is Elizabeth?"

"Dr. Weir is…occupied at the moment. There's a lot of stuff going on, we can't afford to take her away from her work."

"I understand, after all she is the leader here."

"Yes, she is." A small silence followed before John spoke again.

"So, figured out your story yet?" Sheppard asked sarcastically.

"It isn't a story. Many of my people saw you leave, they remembered what symbols you pressed on the device."

"Hmmm...I've got to ask you, why are you trying to be so sincere? When I was on your planet you clearly showed a different side to me."

"I know I was harsh; I didn't really think that we needed anyone's help. But Sheppard, I've realized my mistakes and I ask for your forgiveness."

"I'll have to think about that." He said giving a charitable smile, "Back to the point, what are you doing here?"

"I need your assistance."

"For what?"

"I wish to return to my planet, to search for my people."

"Well that would be a wasted trip. I already told you no one was there."

"You aren't aware of our…secret places, Colonel. If my people are still alive they'd be there and they won't come out until I return."

"If you're just going to retrieve your people why do I need to be there?"

"A simple precautionary measure; I wouldn't want us to be attacked again."

"Of course not."

"I understand your hesitation and distrust, but I assure you that those… tense exchanges between us was just envy getting the better of me."

"Are you trying to say that you're jealous of me?"

"You have quite a lot to be envious of."

"Care to share?"

"Well, Elizabeth for starters." John visibly tensed when he heard Dimitri use her name again. Why was he doing this?

"And what would give you that idea?"

Dimitri smiled, he knew John was playing with him, "The way you were around each other; your protectiveness of her when I was near. The looks, the comments; don't try to deny it Colonel, everyone noticed."

"Look, not that any of this is your business, but Dr. Weir and I are friends. Closer than some, but that's it. And for your information, I'm protective of everyone I care about, no matter what degree."

"I see, no offence was meant. I must have misinterpreted your actions." Dimitri decided to play along.

"Apparently." He hated lying about how he felt about Elizabeth, but there was no way he was going talk about it with this man.

Dimitri moved on, pleading, "Colonel Sheppard, please accept my offer. My people are counting on you."

"I'll see what I can do."

Colonel Caldwell met Sheppard as he was leaving the infirmary.

"What did Mr. Logan have to say?"

"He asked if I would accompany him to his planet when he's out of the infirmary. According to him, his people are there, though in hiding."

"Then I suggest you get ready. I was just informed by Dr. Beckett that he's getting ready to release him."

"Honestly, I'm not sure I should."

"You still don't trust him?"

"No."

"This wouldn't have anything to do with Dr. Weir, would it?" Sheppard looked away for a moment, crossing his arms.

"Well, that's enough of an answer for me. Look, as soon as you take him home this can be resolved. So gear up and let's finish this."

"Yes sir."

Standing in front of the gate, Sheppard's earlier bad feeling returned as he saw Dimitri Logan approach him. They merely nodded to each other, when the wormhole opened up. With his team, John stepped through the gate, none of them expecting what would happen on the other side.