A/N – Apologies if my medical stuff is incorrect. I'm only here for whumpy fun…

Sheppard and Lorne both deactivated the grapple lines and Sheppard noticed there was still one very faint life sign on the HUD.

"Son of a…" he muttered, "We need a medical team to meet us on the South Pier."

Both of the fully functioning Jumpers landed next to the one they had just shot down as a small plume of smoke leaked out from the wreckage and rose into the Lantean sky above.

Chapter 4 – Aftermath

Sheppard rushed out of the back of his Jumper, only pausing on the way to wrench the fire extinguisher from the wall in the cockpit and sling the medical kit over his shoulder.

The Jumper he had just shot down was fortunately resting flat on the pier, as what was left of the drive pods kept it level. Major Lorne exited the back of his Jumper with the same gear as Sheppard.

"Colonel, Sir, there's still one life sign on board."

"I saw it too," Sheppard said as he stepped up to the rear hatch of the damaged vessel.

The engine on one side was still smoking and tiny flames were licking at the side of the Jumper's hull. Lorne walked around and doused the fires as best he could with his extinguisher.

He called out, "We need to put out these fires, or get them out of there."

Sheppard nodded and watched as the hatch slowly opened in front of him. He resisted the urge to cough as thick black smoke billowed out and escaped into the air around him. The atmosphere in the Jumper was soon almost clear apart from sporadic puffs of smoke still coming out of sparking circuitry which was hanging down from the ceiling.

He walked inside and took in the scene before him. Two figures were lying on the floor, one had a slit throat and the other was as pale as a ghost. He suddenly realised that they were the same people he had seen in the science lab with Rodney just a short while ago, although the significance of that realisation was lost on him at the moment.

He then reeled a little in shock when he saw a third figure lying face down and unconscious on the control panel. He saw the Canadian flag on the man's arm and braced himself for the worst.

He tapped his radio, "Lorne, I need your assistance."

A moment later, the Major stepped into the Jumper to join him. He whistled before he spoke when he too saw the carnage, "The worst of the fires are out Sir. I think we should be safe for the time being."

Sheppard walked over the female scientist and checked for a pulse or any signs of life; finding none he turned to Lorne and pointed down at the prone figure of the other scientist on the floor, "Help him, while I help Rodney."

Lorne nodded and crouched down while Sheppard walked over to Rodney. He noted in alarm that McKay was taped to the controls and to the chair and was bleeding heavily from numerous injuries.

Sheppard put his hand under Rodney's head and placed it close to the man's nose and mouth. There was blood smeared across his face and shining on his lips and chin. He felt a small breath as it blew across the back of his hand faintly. He quickly grabbed his knife and carefully cut through the bonds. McKay's arms fell down to hang limply by his sides, almost trailing on the floor, but he stayed in his chair with his face turned towards John.

Having no idea how badly Rodney had been hurt and knowing he was still breathing for the time being; Sheppard decided not to move him until Carson could take a look.

He strapped an oxygen mask over the scientist's face from the medical kit and then wrapped pressure bandages around the wounds he was able to see. He pressed one hand against McKay's side and the other to his leg and hoped that Carson would hurry up with his medical team.

He turned to see how Major Lorne was and as his eyes scanned around the cockpit, he noticed a bloody knife and a roll of duct tape on the floor which had been thrown across the cockpit as the craft pitched down. He frowned when he saw Major Lorne doing CPR on the male scientist.

Sheppard reached up with his red and sticky hands and tapped his radio before once again pressing it down against Rodney's side, "Sheppard to Dr Beckett."

"We're on our way Colonel. What's the situation?"

"There are three civilians. One has a slit throat, another, well Major Lorne is doing CPR I'm not sure of his condition or the extent of his injuries."

Sheppard turned back to look at the pale and blood streaked face of the man he was trying to save. He steeled himself and prepared for the report on the condition of his friend, "And Rodney. I saw a knife, I think he's been stabbed several times. He's badly bleeding from the chest, side and leg. I'm not sure how long he's been like this. Hurry."

There was a slight pause before Carson spoke, "We've just left the transporter and we can see the smoke from over here. ETA one minute."

Sheppard sighed and spoke quietly into McKay's ear, "Hang on Rodney, Carson will be here soon. Don't you die on me before he gets here."

Lorne was still counting out compressions in a whisper behind him and would stop every now and then to give the other scientist breaths.

Sheppard's hands ached from keeping up the pressure and Rodney's blood began to soak through the bandages and through his fingers. McKay's breath was now audible inside the mask in the form of a shallow wheeze.

As Rodney's breathing became quieter and more laboured, Carson rushed into the Jumper with a full medical team in tow.

He looked at the scene and muttered, "Oh my god," before pointing to another Doctor with him to help Major Lorne. He then leant over next to Sheppard to examine Rodney. He expertly inserted IV lines into Rodney's arms and then grabbed his stethoscope to listen to the back of McKay's chest. While he worked, another member of the medical team gently pushed Sheppard away and took his place. She put extra bandages over the ones already on Rodney's side and leg and kept up the pressure.

Sheppard was quite glad that he had been forced away and looked down in shock at his blood soaked hands. There was very little room in the cramped cockpit so he walked away and swept some debris off the bench in the rear compartment before sitting down. Major Lorne joined him a few seconds later and they shared a silent look of worry.

Carson called out behind him, "I need a backboard and a collar and I'm going to have to intubate."

The Doctor with the other scientist called out for a defibrillator.

Carson used his hands to check Rodney and muttered under his breath, "Spine is intact, no obvious limb fractures." As he checked McKay's chest close to the knife wound he stopped and frowned, "One, possibly two broken ribs."

The backboard was lowered down next to the chair and Carson, with help from his team, moved Rodney gently away from the controls and lay him down. Carson quickly and expertly slid a tube into the injured man's mouth and down into his lungs and then they carried him away.

Sheppard turned around to see the other scientists were also on stretchers. The woman had a blanket over her face, but as the man was placed on the waiting gurney outside, the medical staff continued in their efforts to bring him back with CPR even as he was pushed away.

Sheppard was dazed for a moment and Major Lorne spoke, "Come on Sir, let's head over to the infirmary and meet up with Dr Weir and the others."

John nodded and walked out of the wreckage with Major Lorne.

Dr Beckett came out of surgery looking tired and worried. He looked around at Sheppard, Teyla, Ronon and Dr Weir and said, "I've got Rodney stabilized and repaired as much of the damage as possible. But there was extensive internal bleeding from the knife wounds. Not to mention two broken ribs from where he was stabbed in the chest. There is always a risk we may have missed something and he is very weak."

Sheppard nodded grimly and Dr Weir asked, "What about the others, Dr Silvestro and Dr Evans?"

Carson looked at her sadly, "I'm sorry lass, neither of them made it."

Dr Weir pursed her lips and looked away.

Ronon asked to the gathering in general, "Do you know what happened to him in the Jumper?"

Dr Beckett shook his head, "We got Rodney's blood work back from earlier after the analysis was complete. There was nothing unusual about it." He sighed, "If you'll excuse me, while I'm quietly confident that Rodney's usual stubbornness will hold fast and pull him through, it could still go either way. I need to keep monitoring him just in case. He's too weak for you to see him at the moment, but I'll call you back later."

Elizabeth looked up and said, "Of course."

Sheppard said, "Rodney had been acting strangely ever since we went into the Ancient building on our mission this morning."

Teyla frowned, "That is true, but why would he not ask us for help if he were in trouble?"

Ronon grunted in agreement, "What about the video feeds?"

Sheppard nodded, "Maybe they can shed some light on exactly what's been going on over the last few hours to have culminated in this."

Sheppard tapped his radio and asked Zelenka to meet him in the Briefing Room in five minutes.

They all sat in the Briefing Room and watched Rodney's strange conversation with his staff. Sheppard winced when Rodney said he had been feeling 'heart attack inducing pain.' He wished McKay had told him something, anything about what was going on. Maybe then he would not be lying in the infirmary fighting for his life.

They continued to watch and Zelenka switched the feed to follow Rodney as he went to his quarters. He fast-forwarded and they saw the scientist leave his room and head back to the lab.

Sheppard noticed the gun now strapped to Rodney's leg and sighed. He had failed again in that respect. McKay had obviously known he was in danger and Sheppard had blithely and unknowingly stripped him of his only protection.

They watched him go into the lab and sit down. Zelenka again skipped the video on a few hours until Rodney started talking. They listened tensely as he spoke about Replicators and how they wanted to destroy Atlantis.

They all flinched and Ronon growled as Rodney was pushed down onto the ground and hit the table. Sheppard had to restrain himself from jumping out of his seat in fury as the two scientists assaulted Rodney as he stood defenceless and trapped with his arms behind his back.

Sheppard then grimaced when he saw his own conversation with Rodney, where it was now so obvious he was in pain and deep trouble. It made Sheppard feel a crushing weight of guilt over why he had not forced Rodney to come with him back to the infirmary straight away.

Weir looked over at Sheppard with a sad face and indicated for them to continue watching before anyone said anything.

Teyla gasped when she saw Rodney run into the fist in the corridor and collapse.

Sheppard reached up and tapped his radio, "Major Lorne, I want you to locate and escort Corporal Harvey to the brig."

They saw Rodney leave the transporter and get pushed onto the floor. They eventually lost him as he entered the Jumper. Most of the rest they would need to analyse the logs from the Jumper or wait for Rodney to wake up and tell them.

A stunned silence filled the Briefing Room when Zelenka shut down the video feed.

Radek looked down at his laptop blankly and muttered, "How is Rodney? I heard he had been hurt, but I had no idea."

Elizabeth turned to him, "He's in a bad way, but Carson's with him."

They were about to start discussing the video they had just seen, when Elizabeth's radio activated, "Beckett to Dr Weir."

She held up her hand to the others and replied, "Go ahead Carson."

"I've found something you'll want to see. Dr Zelenka too."

She looked up at Radek, "He's here with me now, we'll be right there."

She stood up and left with the others all following her.

Rodney's team, with Zelenka and Weir stood crowded around Dr Beckett in his lab.

He was studying some data on his screen and frowned as he looked up at the people gathered around him who were watching in expectation.

He said, "We managed to get a blood sample from Rodney, although it was difficult to find any of his original blood left in him after such injuries and so many transfusions. I also obtained blood samples from Dr Evans and Dr Silvestro."

Beckett pushed himself away from the desk and stood up before he said, "Dr Zelenka I think you need to see this."

Radek walked over and peered at the screen. He pushed his glasses up and sat down to analyse the three blood test results displayed on the screen. He typed and few keys and frowned.

"They are definitely Replicator nanites." He continued to type for a few more minutes and then spoke again, "They are completely inert. I believe they have run out of power, which is unusual for Replicator cells, unless they wanted to be completely separate from the host. That would explain it, as they would not be able to draw any energy from the surrounding tissue to stay operational for long."

Dr Weir frowned, "Are they still a danger to us?"

Zelenka looked up from the data, "I do not believe so, but I will need to analyse this data in more detail."

Dr Beckett said, "I will need to take blood samples from everyone on the base to make sure all the nanites are deactivated just in case they spread to anyone else. I will see if I can develop a method for removing them from the bloodstream as well."

Elizabeth nodded, "Good work and keep me apprised."

Ronon asked Beckett, "Can we see McKay yet?"

Carson replied, "Yes, I checked him. He's still very ill, so only for a few minutes please."

The team shuffled in quietly around Rodney's bed in the intensive care area of the infirmary. John thought McKay looked dead. If it were not for the steady and slow beep of the heart monitor and the sigh of the ventilator he would have thought his assumption was correct.

Rodney's whole chest, abdomen and upper leg were wrapped in white bandages which almost blended in with his pale complexion. There was dark purple bruising around both of his wrists.

Images of Rodney thrashing and struggling against the restraints trying desperately to free himself while he was being stabbed with the knife flashed through Sheppard's mind and made him wince.

Teyla reached down and gently grasped Rodney's left hand, careful not to disturb the IV line, she threaded her fingers through his and said quietly, "You are very brave Rodney and we are most grateful that you did not do as they wanted."

He paid for that bravery with his blood, Sheppard thought as he smiled at Teyla sadly. He found that he could not say anything in front of his team as he still felt guilty about letting this happen to Rodney at all.

John stayed for a little longer after the rest of his team left with Dr Weir. He leant forwards close to Rodney's deathly pale face and whispered, "I'm so sorry Rodney, but I'll make it up to you, I promise. But only if you keep fighting and live."

He was saddened when there was no response from the scientist, who just lay completely still with his eyes closed. He patted Rodney's shoulder gently and left to head down to the brig and speak with Corporal Harvey.

"I swear it, Sir. I don't remember anything," Corporal Harvey said to Sheppard as he stood to attention behind the forcefield in the brig.

John was still unable to believe what he was hearing, "You assaulted a civilian, Corporal and the head of the science department no less. There are serious repercussions for such an act."

Harvey glared back at him, "I do not remember hitting Dr McKay as you are accusing me Colonel, Sir."

Sheppard frowned as he remembered something about Ancient gene carriers from the video feed he watched earlier. He looked back up at the Corporal's face. He was still standing stiffly to attention and not daring to glance at Sheppard.

John knew the man did not have the gene and suddenly remembered that this meant he could have been controlled like the two scientists who kidnapped and tortured Rodney.

He snapped his eyes back up at Harvey, "At ease Corporal. Dr Beckett will be down soon to take a blood sample. I'm going to keep you in here until he's given us the all clear."

Harvey looked a little confused and only slightly relaxed his stance when Sheppard walked away.

Sheppard spent the rest of the day co-ordinating the blood tests for Dr Beckett. He figured the man had enough on his plate, what with Rodney not being fully out of the woods and having to analyse all the tests.

John then went and sat next to Rodney in the infirmary. He stayed for such a long time that he nodded off and nearly fell out of his seat. One of the nurses set him up with a bed so that he could stay there and be the first to hear any news about his friend.

Dr Beckett also stayed up most of the night working on the blood samples in his lab. He found that everyone on Atlantis had trace amounts of nanites in their blood streams and he was very glad that Zelenka was also helping him and kept reassuring him that every sample he had tested the nanites were out of power and no threat.

Zelenka also advised him that the nanites were beginning to break down when they studied another more recent sample taken from Rodney. He could not explain how or why the tiny machines were disappearing from his system. He suggested it may have been in an attempt to make their attack undetectable after it was over. "Perhaps they were going to try and make it look like Rodney had lost it completely and destroyed us using his own free will," Beckett had muttered darkly during one of their conversations.

Rodney rejected the ventilator the next day as he started breathing on his own. Carson told everyone that he was making excellent progress and should be fully awake in a day or two.

Sheppard sat with Rodney as much as he could and smiled as he saw some of the colour returning to his face.

His head was lolling to the side as he drifted off to sleep when he was woken up suddenly by a noise from the man lying on the bed in front of him.

Rodney was muttering in panic, "The Replicators! They're controlling everyone they're going to kill me unless I kill everyone else. Oh no no no! One of them has a knife and he says I can't even ask Sheppard for help…"

The rest diminished down into an incoherent whimper and Sheppard stood up and gripped McKay's shoulders as he rode through the nightmare.

He spoke gently, "You're safe Rodney. They've gone. I'm here."

McKay's eyes opened slowly and looked up at Sheppard. They were unfocused and soon closed again as Rodney fell asleep.

Sheppard sighed in frustration and sat back down in his chair.

Another whole day later, Rodney began to fully wake up. Carson kept checking on him, but he was too traumatised to say anything.

Sheppard still sat next to him as he gazed wide-eyed and fearfully up at the ceiling.

John could not stand it for very long and decided he needed to say something after they had sat like it for half an hour.

"Rodney, you should've said something to us. There were so many opportunities."

McKay tilted his face away from the ceiling towards John and closed his eyes, "I-I-I tried, but you didn't seem to realise. I couldn't say anything directly, but I thought even you would've been able to figure out something wasn't right." He opened his eyes and looked at John, "They threatened to kill you if I said anything."

"And they very nearly killed you instead."

"At least I knew what was going on and saw it coming. I couldn't let them do that to you."

Sheppard smiled at him, "Thanks Rodney, but I am able to defend myself and it's my job to protect you. I hope you never hide something like this from me again."

Rodney mistook his tone as berating and sighed sadly as he turned his gaze back up to stare at the ceiling once more.

Sheppard frowned and asked, "So what happened on the Jumper? We tried to reconstruct the logs, but Zelenka said they were too badly damaged."

Rodney sighed and winced as his broken ribs shifted slightly. He closed his eyes and mumbled, "I don't want to talk about it. Not yet."

Sheppard patted his friend's shoulder, "That's okay, we'd just like to know what happened to Dr Evans and Dr Silvestro."

A frown creased Rodney's forehead. He knew that both scientists were dead, but did not realise he was the only one who had been present and knew how they had died. He felt he owed it to them to tell someone exactly what had happened so that their deaths would not be meaningless.

He steeled his nerve and began to speak. He felt a weight lifting from his chest as he finally told someone else exactly what had happened to him in the fated Jumper. The craft now lay in pieces in the Jumper Bay, where Zelenka was trying to repair it.

Rodney slowly recounted everything that happened to him. He furrowed his brow and closed his eyes as he told Sheppard about how he was tied up and brutally stabbed whenever he did not do as the Replicators asked.

Sheppard felt proud at how much Rodney had been able to endure before he was finally broken and fired the drone towards the Control Room.

He was therefore quite shocked to find out that Rodney had not actually broken at all and he was going to send the drone off course at the last moment even if it meant he would be stabbed again and probably die.

Rodney said, "I only fired it to give you time to think of a way out of the situation. It's a shame your solution involved shooting my Jumper out of the sky."

Sheppard replied, "Well it was the only thing I could come up with in the time you gave me."

A long silence filled the air after Sheppard spoke and he thought Rodney had drifted off to sleep.

He was therefore surprised when Rodney spoke tiredly, still with his eyes closed, "You know what John? I do feel better now, I'm glad you made me tell you what happened. I don't think I would have been able to survive for much longer with something like that buried in my memories."

Sheppard smiled as he looked into McKay's pale face. He knew it would take time. Rodney had been returned to them damaged, but certainly not broken and he would eventually learn to deal with the memories and the scars.

The End

A/N – This was going to be a two part Puddle Jumper Mayhem story. Wasn't I surprised when it turned into this! Thanks for reading (and for the reviews) x Varda x