Disclaimer: I don't own Stargate Atlantis or any of its characters just in case someone wants to sue!

Warning: There is strong violence in this story and scenes that some people may find upsetting so ye be warned!

Thank you to my beta The Bog Witch who corrected all my mistakes.

Hey sorry it took so long to get this chapter up. I spent longer researching the medical procedure but there still might be mistakes because I'm no doctor! Thanks for reading my story and thanks for all the great reviews, I have really enjoyed everyone's comments. Here's the last chapter:

Chapter Seven: Mea Culpa

Lorne steadied himself as he exited the gate on the unknown planet. He looked around distrustfully. 'Trees and more trees!' He thought cynically, every planet they went to looked the same. His team came out of the stargate behind him followed by Ronon.

Lorne motioned to his team mates 'Spread out and keep an eye out for unfriendlies.' The two soldiers complied and they headed in different directions from the gate.

Ronon was hurrying down the steps and Lorne was quick to follow, assuming that the Saetadan had seen something. As they got closer Lorne could see the bulk of a body lying on the ground. He frowned slightly as he realised that it was the hostile.

Ronon knelt down and began to heave the body aside, it was then that Lorne saw the smaller figure of his CO.

'Oh thank God!' Lorne muttered. He bent down to help Ronon shift the weight. Lorne then gazed concerned at Sheppard who lay unmoving.

'He is alive.' Ronon remarked. He had his fingers pressed into Sheppard's neck.

Lorne quickly looked Sheppard over, assessing his injuries. Something wasn't quite right, there was a blue tinge to his lips and his breathing was very shallow. He looked at Sheppard's chest again and noticed the uneven rise and fall of his chest.

'Oh crap!' Lorne cursed. He quickly got to his feet and tapped frustrated on his ear piece. 'Atlantis, this is Major Lorne, we need a medical team here ASAP!'

'They're on their way now Major.' Weir's calming voice was transmitted into his ear. 'What's the Colonel's condition?'

Lorne sighed, knowing that this wasn't the news that Weir wanted to hear. 'Not good ma'am, the hostile is dead but Colonel Sheppard took quite a beating in the process.'

'Understood.' Weir replied.

Beckett burst through the open stargate and hurried over to where Lorne and Ronon knelt. 'How's our patient?' Beckett asked. He quickly felt for Sheppard's pulse. 'Weak and thready.' He murmured to himself. He carefully felt his patient's chest and ribcage. He shook his head. 'The things you manage to do to yourself!' He said to Sheppard. 'Nurse, pass me a needle.' He ordered.

'What's the prognosis doc?' Lorne wondered.

'Sheppard's condition is critical, I will try and stabilise him before we take him back to Atlantis.' Beckett tapped on his ear piece. 'Doctor Weir, please have a gurney waiting and have the operating room prepped. Please shut off the gate so that we can dial back.'

'Affirmative Doctor Beckett.' Came Weir's voice, she was obviously extremely worried about Sheppard though she tried to hide it. The gate shut off with a crack and Ronon hurried over to redial.

The nurse handed Beckett a large needle. Lorne noticed that it was empty. 'What's that for?' He asked.

'The colonel has a collapsed lung and his lung had filled with fluid and air, I will insert this needle to draw some of the fluids out so that we can get him back to Atlantis.' Beckett pulled the lid off the syringe. 'Hold him steady Major, don't worry he won't feel a thing, he's unconscious.'

Beckett cautiously inserted the needle into the side of Sheppard's chest that was not rising. There was no reaction from Sheppard, just as Beckett had promised. Beckett pulled the stopper up on the top of the syringe and Lorne flinched as he saw that it was full of fluid. He wasn't a doctor but he was sure that this wasn't a good sign.

'That's all that I can do for him here. Best get him to Atlantis sharpish.' Beckett suggested. He waved two medics over who were waiting with a stretcher. Lorne helped to gingerly move Sheppard onto the board, he was relieved to see that Beckett had improved his CO's condition, Sheppard was now breathing a little easier.

The medics picked the stretcher up and carried it through the gate, Beckett staying close to his patient all the way.

Lorne followed with Ronon and his two team mates, leaving the peaceful planet and the dead body behind. They stepped through the gate into the hustle and bustle of the control tower. Sheppard was being transferred to the gurney and being rushed toward the infirmary, Beckett was running to keep up with the fast moving gurney.

Weir quickly approached Lorne and Ronon. 'What happened to him Major? Ronon?' Her eyes were following the Doctor, she would rather be asking Beckett these questions.

'Sheppard killed the hostile, stabbed him in the heart.' Ronon supplied.

'So crisis over?' Weir asked.

The two men nodded slightly, it had been a close call this time.

'Alright, get checked out at the infirmary and get some rest, debrief in one hour.' The two men nodded again and set off for the infirmary followed by the rest of Lorne's team.

Weir was left alone in front of the gate. She slowly walked back to the stairs; it was time to tell the civilians that they could now leave their rooms again. Her eyes lingered on the pool of blood that was still at the foot of the stairs, it had been the worst day imaginable.

XXXXXXX

'He has a severe pneumothorax.' Beckett yelled to his fellow doctor as they entered the operating room. The doctor was already prepped and Beckett trusted the man trusted the man to keep Sheppard stable until Beckett scrubbed up.

When Beckett came back, Sheppard had an IV line set up and was intubated. 'I think the pneumothorax was caused by the lung being punctured by a broken rib.' Beckett informed his colleague. 'I will open him up to mend his lung. Keep an eye on his vitals.'

A few hours later Beckett walked exhaustedly out of the operating room and was unsurprised to see a crowd of people waiting anxiously outside. Weir was sitting in one of the chairs tentatively probing her neck. McKay was pacing up and down the hallway annoying Ronon, who was leaning against the wall cracking his knuckles menacingly whilst glaring at McKay. Even Teyla was there, resting in a chair next to Weir. Beckett frowned, he didn't remember giving Teyla permission to be out of bed. He decided to let it slide, for the moment anyway. He was sure that they were all waiting with bated breath to find out how Sheppard was doing. 'The operation was successful; I mended the damage to his lung. He is still intubated but I'm sure that he will be able to breath on his own soon. He has a few broken ribs, he has shattered his kneecap and bruised almost every part of his body. I'm sure that he has concussion but we won't know for sure until he wakes up. I also fixed the stitches that he pulled out in his shoulder. I don't know why I bother though I'm sure Colonel Sheppard will manage to get himself in some new trouble before I can even blink.'

'Does this mean that Colonel Sheppard will be alright?' Teyla asked.

'Aye lass, I'm confident that the Colonel will make a full recovery in time. He won't be out of the woods for a while yet.'

'Great so I guess he won't be able to help me fix the north pier? I need someone with a strong ATA gene to help with the repairs on the damages technology. Are we sure that he's not malingering?' McKay asked.

Beckett rolled his eyes. 'No Rodney, it's quite hard to fake a collapsed lung, not even you could fool me.' McKay looked like he was taking this as a challenge so Beckett quickly pressed on. 'Anyway, all go to your rooms to rest, that's an order, especially you Elizabeth, it's been a hard day. I will let you know when you can visit the Colonel. Teyla, you will come with me back to the hospital bed, I don't remember discharging you.' Beckett ordered.

Everyone hastily followed his orders, though McKay turned around and went to his lab as soon as Beckett was out of sight. Ronon set off toward the gym, even though he would have no sparring partner.

The next day Beckett allowed Weir to be Sheppard's first visitor. She walked into the room and was dismayed at the sight she saw. He was still intubated and had tubes coming out of different parts of his body.

'Don't worry lass. I know it looks shocking but John is fine. I set up a chest drain to get rid of the fluid from his lung. I hope to remove them in the next few hours if the Colonel shows signs of consciousness.'

'May I sit with him?' Weir asked hopefully.

'Of course. Call me if there's any change.'

Weir sat quietly with Sheppard, alone with her thoughts for the first time since the infiltration. There had been so much bloodshed today, so much pain for no reason.

Weir sat like this for some time even though there was so much paperwork she could be doing.

She was mid thought when some movement disturbed her in the bed next to her. Shepard was moving restlessly. 'Doctor Beckett!' Weir yelled.

Beckett quickly came out of his office. He checked Sheppard's vitals. 'He's starting to breath on his own, or trying to anyway. I'm going to remove the tubes now. You may not want to look Elizabeth.' Weir hastily looked away and only looked back when Beckett assured her it was safe to do so.

Sheppard looked much less scary without the tubes and Weir began to believe Beckett when he said that Sheppard would make a full recovery. 'He should wake up soon.' Beckett promised, going over to check on Teyla and his other patients.

Weir settled herself back into the chair beside Sheppard's bed. She didn't have long to wait however, within the hour Sheppard began to wake up.

He could feel someone's hand resting on top of his. 'That rules out Beckett, McKay and Ronon!' Sheppard thought dryly. 'Or I hope so; otherwise I have a slight problem!'

He turned his head to look who was sitting in the chair. 'Hey,' he croaked.

'Hey!' Weir softly replied. She picked up the glass of water and put the straw to his lips. He gratefully sipped as much as he could and felt it sooth his raw throat.

'Deja vu!' He said.

'Yes.' Weir responded, remembering doing exactly the same thing for him yesterday. 'Beckett has been threatening to start charging rent because you're here so much.'

'Really?' Sheppard asked. 'Maybe I should start charging for saving the day, again!'

'Alright, alright. Please don't start keeping count like Rodney does.'

'Would I?' Sheppard asked innocently.

'Of course!' Weir remarked. She clasped her hands together nervously. 'John…' She started.

Sheppard immediately became serious. 'What is it?'

'We recovered Sergeant Smith's body from the north pier, I'm sorry it seems that he was caught in the explosion.' Weir had tears in her eyes.

Sheppard took in the news. Another man to die under his command, he would grieve for Geller and Smith later, in private but he could tell that Weir was taking it hard.

'What's the matter, Elizabeth?' Sheppard asked sympathetically. A tear rolled slowly down Weir's cheek. Sheppard took her hand in his. 'Hey, tell me.'

Weir sniffed and wiped her eyes, she hated self-pity but for some reason she couldn't help herself at the moment. 'Mea Culpa.' She said simply. She smiled at Sheppard's confused look. 'It's Latin.' She added. 'For-'

'My fault. I know what it means but what's your fault Elizabeth?' Sheppard asked.

'Geller, Smith, Teyla, you,' she listed.

'That's as much my fault as yours, Elizabeth, I wasn't here to help search which got Geller killed and I ordered Smith to the north pier which got him killed.'

'How do you deal with it?' Weir asked emotionally.

'You just do. What's this about Elizabeth? It's not like you. We have had men die under our command before.'

'I killed a man, John. I pulled the trigger and he died.' She answered sadly.

'Oh.' Sheppard said, remembering what had happened the day before. 'Listen, what you did wasn't pretty but it saved my life. You saved my life and I am very, very grateful.'

Weir nodded, feeling brighter, trying to look at it from a different point of view. 'I know, I will go and get Doctor Beckett, you must be in pain.'

'A little bit, yeah.' Sheppard admitted.

Later on that day McKay came to visit Sheppard. Sheppard grinned when he saw who it was. 'McKay! Can't believe you could tear yourself away from your lab long enough to visit me.'

'Er yeah, well just wanted to see how you were.' McKay replied awkwardly.

Sheppard suddenly saw that McKay was holding an ancient device. 'What do you want McKay?' Sheppard asked threateningly.

'Well er, I thought seeing as how you're on the mend, you could help me out in fixing the north pier, as it's your fault that it flooded.' McKay answered.

'How did you figure that out?' Sheppard asked. 'So you need someone with a strong ATA gene to touch things?'

'Yes I did just say that, why you insist on parroting everything back to me!'

Sheppard ignored his comment. 'I think I may have a solution for you that will make us both happy.

XXXXXXXX

A few days later after Sheppard had first woken up he was released from the infirmary long enough to go to the mainland for Lieutenant Geller and Sergeant Smith's memorial service. He had to promise to stay in Beckett's sight at all times and to eat more food to go but it was worth it to be finally flying again, not that he was the one piloting the jumper, that would be McKay, badly, but flying was flying he supposed.

The service was short, Weir said a few words about how brave and loyal the men were and a simple plaque was put on one of the trees just outside of the athosian village. It was just a gesture; their bodies had been sent back to Earth where they would have a full military funeral.

After the service, Weir came to help Sheppard back to the jumper. Sheppard leaned heavily on her arm and his walking stick to hobble back to where McKay and Beckett were waiting.

'John, do you remember the soldier who was guarding the prisoner when, well you know.' She was rubbing her neck nervously.

'Yes.' Sheppard answered cautiously.

'Well you know I asked you not to punish him.'

'Yes.'

'I was wondering if you kept your word.' Weir continued.

'Elizabeth, I am insulted that you don't trust me.' Sheppard protested, feigning innocence.

'Answer the question John, did you punish the soldier?'

'I may have slightly, but I had to Elizabeth, that's how the military works.' Sheppard explained.

'You didn't demote him, did you?' Weir asked.

'No, nothing like that. I know you didn't want him punished.' Sheppard explained mischievously. 'So I assigned him extra duties instead, helping McKay activate ancient devices, he has a very strong ATA gene, just like McKay wanted.'

'And this has nothing to do with the fact that it was a job you didn't want to do for yourself?' Weir asked thoughtfully.

'Let's just say it killed two birds with one stone!' Sheppard admitted.

The End

Please review one last time I would love to hear what you all thought and if anyone has any ways they think I could improve my writing, you are more than welcome to pm or email me.