Disclaimer: I don't own Stargate Atlantis

Spoilers: Hot Zone

Elizabeth blew out the candle that sat on her nightstand. The Vanilla scent lingered in her quarters as she snuggled down into her sheets. The Vanilla scent usually calmed her after her long days. Not today. Damn John Sheppard. He disrespected her orders, he made her look weak. He'd undermined her authority in front of St Bates
Damn him.

John placed his copy of 'War and Peace' onto his nightstand. He wasn't in the mood for reading. Knowing Elizabeth was pissed off; it made him slightly angry. Damn it, didn't she realise that he was trying to protect her. John moved down into his sheets trying to forget the events of the past day.
Bates sat in the Mess Hall sipping his coffee. The day had given him a migraine. Damn John Sheppard and his order. Not only had Weir been pissed at Sheppard but now she was pissed at him for following the orders. He'd work hard to get Weir's trust back after the situation with the Athosians, in saying that, it'd been Sheppard's fault that Weir had began to distrust him in the first place, his and the Athosians.

Bates finished his coffee, stood up and walked out of the Mess Hall. He needed to see Weir.

Bates made his way through the corridors of Atlantis, meeting Grodin on the way but not stopping long enough to talk, he was a man on a mission.

John left his quarters; he had to see her. Had to tell her why he'd done what he had. John walked through the corridors of Atlantis; he was a man on a mission.

John made his way through the corridors as quickly as possible; he couldn't let her go through another minute thinking that he didn't trust her.

John stood outside her quarters, unsure of what to do. He knocked at the door, gently. A few seconds later, the door opened revealing a half-asleep Elizabeth.

"Major, what's wrong?"

Elizabeth rubbed the sleep out of her eyes.

"Elizabeth, I'm sorry, but I need you to know why I did what I did."

Elizabeth sighed

"Come in"

Elizabeth moved and let John enter her quarters.

Bates entered the corridor where Weir's quarters where situated. When he did, he saw Sheppard outside her quarters talking to her. From his position, he couldn't hear what they were saying but he had a suspicion, a suspicion which became bigger when he saw Sheppard enter her quarters.

Bates felt a pang of Jealousy. Sheppard could have any woman he wanted and here he was going for the one woman Bates wanted. Weir was just as bad, she'd been leading him on for months. Flirting, smiling, touching his arm. The whore. She'd been playing with him. She and Sheppard were laughing at him.

Elizabeth sat on her bed and pulled her covers round her.

"Sit down Major."

She indicated to the edge of her bed, next to her. John sat down and sighed

"I wanted to protect you. I didn't mean to upset you or make you think I don't trust you. Because I do trust you. I trust you more then anyone on this city. I didn't think; all I could think about was protecting you…and everyone."

Elizabeth sighed

"John, I understand what you did and why you did it, but the reason I sealed you in the gym was because I was worried, because I wanted to protect you and Teyla. You put yourself at risk, unnecessarily; you put others at risk…" Elizabeth could see that John was about to talk and she put her hands up to stop him "…No, let me finish. Now some of the people on this base already see you as a leader, a lot of the military personal already think I'm not the right person to lead this expedition, undermining my authority just gave them more ammo against me. I need to know that you're not going to put me in that position again. Don't get me wrong, I'm thankful for all the lives you saved, including mine, but next time, let me give the order."

John nodded

"I understand, but let me make one thing clear, if I think you're making the wrong decision I will tell you so."

Elizabeth nodded

"And I will take your views into consideration, if you take mine into consideration."

John nodded

"Okay, I let you to go back to sleep."

Elizabeth shook her head.

"I'm too wired, want to get some coffee?"

John nodded and smirked.

"Yes. Coffee solves all problems."

Elizabeth picked up some clothes and walked into the bathroom, exiting a few moments later wearing a red top and some black trousers. The two of them left her quarters talking and laughing quietly and made their way to the Mess Hall.

Bates watched from his hiding place as Weir and Sheppard left her quarters, laughing, laughing at him. Bates followed them through the corridors wondering what they'd been doing in her quarters. He had an idea. Bastards. He followed them wondering if they were talking about him, laughing at how gullible he'd been to actually believe that Weir actually felt something for him. That Bitch. One day he'd make her pay, he'd make them both pay. He watched them sit in the Mess Hall and talk over coffee. But not today, he'd take his time and hit them when they least expected it.

Fin…