Title: Darkness of the mind.

Summary: A mission gone wrong effects John more than anyone realizes.

Paring: Hints of Sheppard/Weir.

Spoilers: Nothing really I don't think, but if there are, odds are if you blink you'll miss them.

Disclaimer: Stargate Atlantis is not mine. Only the story line and any made up characters that may or may not appear in the story belong to me.

A/N: Same story as before I just went back and fixed somethings that got missed during editing the first time.

Also Dr. Kate Heightmeyer is not an OC she is a character that will be appearing on the show in the future but that's all I know about the character.

And we don't know why
The innocent die
Will this world ever find a way to change?
And we don't know why
But we know it's not right
We don't know why so many had to die
We don't know why so many had to die

"The Innocent"
Good Charlotte

Elizabeth stood in the infirmary watching over John as he laid in one of the infirmary beds fighting for his life. As far as Elizabeth was concerned John spent way too much time in the infirmary as it was, but this time it never even should have happened. The mission was supposed to have been a simple straight forward, walk in the park, but then again when did anything ever go as planed when John was involved?

On SGA-1's last mission Aiden had managed to break his arm in a small rockslide, so the team had been put on stand by. Teyla had gone to visit the Athosians on the mainland, Rodney had locked himself up in his lab, Aiden had milked up all the sympathy and attention he could get, and John, out of boredom, had bugged Elizabeth to the point where she had been ready to throw him through an incoming worm hole.

So when the chance came up for Elizabeth to get John off world for a few days she jumped at it. A few of the scientists had wanted to explore some ruins that had been found on a supposedly deserted planet and Elizabeth had seen that as the perfect excuse to get John out of her hair as well as a good way to give some of the junior military officers some more off world experience. Little had she known how wrong the mission was going to go.

The group couldn't have been gone for longer than an hour and a half to two hours before the Stargate activated again and John's IDC had been received. Everyone had watched as John half carried half dragged one of the scientists as well as a young Lt. through the gate and then collapse when they were all through. Elizabeth couldn't believe all the blood she saw covering the three and pooling on the gate room floor as she watched Carson and his team jump into action trying to save lives.

Unfortunately the Lt. had been dead on arrival, Carson estimated he must have died just before John pulled him through the gate, and the scientist had died shortly after arriving in the infirmary. Out of the eight people that had gone off world that day John had been the only one to make it out alive and that wasn't even a positive yet, there was still a chance he might not make it through the night.

It was almost two days before John started to come around. Hearing a slight moan come from John, Elizabeth tightened her grip on his hand a bit and motioned Carson over. Rushing over Carson checked all the machines that were helping to keep the major alive then stood back and watched along with Elizabeth, hoping this would be the time John woke up.

Opening his eyes John was assaulted with the harsh bright light of the infirmary and immediately closed them, not attempting to open them again until after Carson had turned the lights down. Once he could get his eyes to stay open with out his head feeling like it was going to explode John was first greeted with the sight of Elizabeth's worried face followed by Carson's.

"Ahh what the hell was I drinking last night?" John moaned, as he tried to roll over onto his side only to discover how bad an idea that had been when his body was swamped by agonizing pain. Looking down he noticed the bandages on his side and all the wires that's when it all came rushing back; the mission, the ambush, the blood, the death.

"Easy there lad." Carson gently placed his hands on John's shoulders and stopped John trying to move. "I'm afraid you won't be doing much moving for the next few days."

"Major…John I know you're probably in a lot of pain right now, but I need you to tell me what happened." Elizabeth spoke after a moment.

"Ambush." Was, all John said.

"The Wraith?"

"No…I'm not sure who they were, but they definitely weren't the Wraith. They came out of nowhere. One minute every thing was fine then the next thing we know these guys are dropping out of the trees right on top of us. Captain Pak and Dr. Whitmore were the first to go down and I took a shoot in the side, Drs. Newmen and Wingfield along with Sgt. Taylor went down on our way back to the gate. Just as we got to the gate Lt. Brash, who'd been bring up the rear, went down and I ordered Dr. Porter to dial the gate then go through while I went back for Brash. After dialing Porter was about half way to the gate when he was hit, I grabbed him on my way to the gate and dragged the two through. Next thing I know I'm waking up here. How are they doing?"

The looks on Carson and Elizabeth's faces told John his answer: they hadn't made it.

Seeing the look of anguish on John's face Elizabeth decided it might be a good idea to give John some time alone to process every thing before continuing their conversation.

"Get some rest John, we can finish this later."

John didn't argue, he had a lot of thinking to do and didn't really feel like company at the moment, even if that company was Elizabeth's. Giving John's hand one last supportive squeeze Elizabeth walked out of the infirmary leaving John to his own thoughts.

I open my eyes
I try to see but I'm blinded
By the white light
I can't remember how
I can't remember why
I'm lying here tonight
And I can't stand the pain
And I can't make it go away
No I can't stand the pain

"Untitled"
SIMPLE PLAN