When things go South

Warnings: This story has a lot of violence and several chapters will have torture.

Author's notes: Thank you for your wonderful reviews!

So this chapter…this (and the next one) are the chapters that I had in mind since I was writing Things Could be Worse, the first fanfic of this 'Verse. I'm so glad I can finally publish it. I hope you'll like. Let me know your thoughts, it would mean the world to me.

Happy holidays and enjoy!

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The Enemy Within

When they exited the underground facility, Sheppard requested an update from the members of his team that were wreaking havoc on the surface. Ronon and Cadman were literally blowing up a forest, ambushing Genii soldiers, and being chased by them. Lieutenant Kemp and Beckett were flying the jumper above the Stargate. However, despite Kemp's efforts to keep them away, the enemy had managed to dial another planet and several soldiers were escaping through it.

Sheppard told all of them to move to the rendezvous point and to be on the lookout for Dean. He wasn't in the facility, and the Genii were probably shipping him off-world. McKay told them what had happened to him.

"Last time I saw Winchester… he was cuckoo."

Teyla raised an eyebrow. "What do you mean, Rodney?"

"Cuckoo, loony, insane, mad, crazy… pick a word. One minute he talked to me, the next he mistook me for his brother. He was shaking badly and kept looking around like he was hearing voices!"

"Was he feverish? His wounds could be infected…" She murmured in worry.

"I'll let Doctor Beckett know that he might be injured." Lorne added, activating his comm-link.

Sheppard only half listened their conversation. He kept surveying the woods ahead, trying to spot any sign of enemy activity. Kolya and his men must have dragged Dean into the forest to have better cover before moving to the Stargate; maybe they wanted to use him as hostage in order to escape the planet. Teyla was on his side observing the ground for a trail, and Lorne was defending the rear.

The glint of sunlight on metal revealed the muzzle of a gun in the foliage ahead. "Look out!" Sheppard barked and the team dove for cover.

A series of gunshots separated him from the rest of the group. His eyes caught a small glimpse of the Genii commander before he ran away.

"Kolya!" His shout reverberated in the forest, but his quarry was already gone.

None of his friends were injured. Sheppard ordered Teyla and Lorne to take Rodney and move out. He informed Ronon and the other two lieutenants he was in pursuit, then he followed the sneaky bastard.

"You're gonna pay for what you did! Do you hear me? I'm gonna catch you!"

They stopped, each hiding behind a tree, but Kolya had the higher ground. "I think you're mistaken, Colonel. I'm not the one being chased." Kolya fired at him, forcing Sheppard to retreat further behind cover as chips of wood sprayed into his face. He leaned out to return fire, but the Genii's position gave him the advantage.

Sheppard cursed to himself. It was another of his traps to lure him in that spot. The bastard and his never-ending schemes! He took evasive maneuvers, but it was a difficult situation and he didn't know the terrain like his enemy. Sheppard found another huge tree and used it for cover.

"You decided to hide, hmm? It suits you–back in Atlantis, you ran all the time," Kolya taunted him.

"Well, I'm the one who won back then, shall we try again? This time I won't aim for your shoulder!"

They kept shooting until the Genii ran out of bullets and, once again, began to flee.

"Not this time!" Sheppard ran after him. The enemy had stopped for a moment near a rock to take cover, before running again. Sheppard was too distant to see what he was up to; however, it gave Sheppard time to almost catch the man.

Kolya briefly smirked at him, then dove into a shaft in the brushes. It was probably another way to enter the underground facility. Sheppard was about to follow him when someone grabbed him from behind, and pushed him to the ground. From what he could see–and it wasn't much–it was another Genii soldier trying to suffocate him. Sheppard's gun had slipped during the fall along with his comm-link, but he tried to use all his training to get away from the enemy.

The ground shook under them, and a loud series of explosions could be heard from the shaft nearby. Sheppard had forgotten about the bombs in the tunnels; apparently, Kolya had, too. Due to the earthquake the guy behind him lost his grip, and Sheppard took the chance to elbow him and free himself. When he turned around he couldn't believe his own eyes.

"D…Dean?" he asked in shock.

Winchester was in front of him, more or less in good shape, and he was wearing a Genii uniform. The next thing he saw were the punches that Winchester was throwing at him. Sheppard defended himself, but his mind was unable to process what was happening. "Dean, stop! What are you doing!?"

Maybe Winchester had been able to escape by himself and he had grabbed a uniform to blend in, but that didn't' explain his actions. Sheppard couldn't fathom why he was being attacked, but with a punch and a kick in the stomach, he was able to put some distance between them. Quickly he regained a defensive stance.

Winchester took out a knife from his boot, unfazed by the hits. "My job, Sheppard. I'm gonna kill you!" And once again he attacked.

Of course he has a knife, why I am not surprised? Sheppard took out his knife as well, tried to evade his attacks and put some distance between them.

Sheppard shook the thought aside, and just watched the man in front of him. No jokes, no cocky smile. He didn't leave many openings and each of his moves were calculated. His eyes were hard and he seemed more mission–driven that he had ever been. Not even the first time they'd met had he felt such hostility from him. Winchester looked like he was seriously trying to kill him.

That couldn't be Dean.

For a brief moment Sheppard entertained the idea that the man in front of him was a clone and not the real deal, but the Genii didn't have that kind of technology–not even Kolya, with all his special resources, could pull this off. The man in front of him also used some of the moves Teyla taught them. The next wound he received confirmed his assessment. Sheppard cursed loudly.

Then what's wrong with him? He thought about what Rodney had said–maybe the kid was hallucinating again.

Winchester tried to aim for his neck, and Sheppard deflected the attack with his knife. "Come on, kid. Snap out of it! I'm not the enemy!"

With an elaborate move Sheppard pushed the knife away, sending it flying into the woods. However, in the commotion his own knife had slipped, too.

They were both unarmed, but that didn't stop the kid at all. "I'm Captain Winchester of the Genii Army. You're gonna pay for what you did, Sheppard!"

Sheppard was flabbergasted by those words. If Winchester thought he was a Genii, then the situation was way worse than Sheppard had imagined. A fake kick from the right, a punch on the left and then a series of moves that would make Ronon proud: the kid was kicking his ass and rapidly wearing him down.

Finally, Sheppard delivered a well-assessed punch that made Winchester stumble and retreat for a moment. They were both tired, and bruises covered their faces. Sheppard had a bleeding arm and a bruised rib, while the kid had a gash on his forehead and was limping. Sheppard saw him trying to wipe the blood from his eyes.

If Sheppard couldn't talk him out of this fight, he had to incapacitate the kid before taking him back home. Winchester, however, hadn't given him a break to come up with a strategy to do that.

"So…Captain, hmm? Did you finally decide to take my offer to join the Air Force?" Sheppard tried to joke, recalling a couple of times he had asked the same question while they were flying a jumper. He had mercilessly teased Winchester about his status in Atlantis as a paperwork nightmare.

"Pfft, please. Like I would join a bunch of flyboys…"

They both halted at his witty response. Sheppard hadn't really meant anything by saying that, but the slip was an obvious sign that the kid was very confused. He could see the turmoil those few words had triggered.

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Dean frowned at his own words. They had come out of his mouth without thinking. He didn't know why he had said that, and his head was hurting more than usual. Since the beginning of the fight with the enemy, the infamous Colonel Sheppard, his headache had been getting worse.

He had been on duty all night, and had skipped his daily medicine due to the enemy's attack on their base. The sounds of the forest around him, the small details that didn't match his memories, and the flippant tone of his enemy were confusing him. The hit on his head hadn't helped his situation.

"Dean…"

"Shut up!" He shook his head. The noise was hard to dismiss, but he attacked again. Dean knew his orders: Sheppard was the enemy. He had to kill him. Kill them all.

"Rodney told me what you did for him down there…"

It was frustrating: the familiarity the enemy seemed to have with him, how easily he was falling into rhythm with Sheppard during the fight like they had sparred several times before, and the overall feeling of wrongness that was assaulting him. It must have been because he'd infiltrated Atlantis that he felt like this. With each word that came out of Sheppard's mouth, small fragments of conversations began to play in the back of his mind, like ghosts hunting him.

It was just so damn difficult to keep going.

It seemed, however, that Sheppard didn't want to kill him: all his attacks had been non-lethal, like he was trying to capture him alive. It was ridiculous. He was a Genii, like he would allow himself to be captured alive. Dean knew what he had to do if he thought his mission was compromised.

Dean had just to kill Sheppard and the pain would stop, he was sure of it.

"Come on, kid–"

"I'm not a kid!" he snapped.

A flash of a memory hit him, and Dean backed away from the fight once again, his hands on his head. A corridor, a couple of marines and Sheppard aiming their guns at him. The two of them fighting a couple of Wraith together. A poker game in a lab, a planet full of strange plants, the laughter of children, a leisurely walk in a field with a bunch of people. Everything felt hazy and distant. Dean felt his whole body shaking from the pain, his mind on the brink of exploding.

He had to stop it. No more, he couldn't take it anymore.

While he was trying to regain his self-control, Sheppard slowly approached with his arms opened wide in a non-threatening manner, as if Dean was a wild, wounded, animal.

That, however, wasn't a smart move from his enemy.

Out of reflex, Dean kicked his right knee and Sheppard fell to the ground. Dean dashed to take one of the guns in the weeds and quickly stood up, aiming the gun at the man in front of him. His enemy. The reason he was in pain. At that distance he couldn't miss, even if his hand wasn't steady.

"I know you, Dean. Stop, you're not a killer."

Dean was barely standing, but Sheppard's assertion was ridiculous. His hands were drenched in blood–that was almost the only thing he could remember clearly from his past.

He glared at his enemy on the ground. "You're wrong."

But before he could pull the trigger, a red light struck him, numb paralysis seizing his limbs and making his legs give out beneath him. For a brief second, before he crashed to the ground, a thought hit Dean: that this, too, felt like an awful déjà vu.

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When Ronon heard on the comm-link that Sheppard was chasing the enemy leader, he decided to go and help his friend. However, he had to neutralize a couple of enemies before he was able to pick up Sheppard's trail. Moving through the woods in silence, he was able to sneak up close to where Sheppard was fighting a Genii. To his surprise, though, he saw it wasn't a Genii, but Dean.

Ronon drew his gun when he saw Dean aiming his own weapon at Sheppard.

"You're wrong," Dean said coldly.

Ronon knew that look: he was going to kill Sheppard. He switched his gun to stun, and fired without hesitation. Whatever was going on, he would find out as soon as he talked to Sheppard.

His friend let out a sigh before turning toward him. "Nice timing, Ronon. Thanks."

Ronon silently advanced from his position. He stood between them as Sheppard got up and massaged his sore knee. Despite his calmness, Ronon was waiting for an explanation.

Sheppard sighed again, he seemed unable to explain what had happened. "Come on, we need to carry him to the Jumper. Dean… He isn't himself… I think they messed with his brain."

Ronon nodded and handed over his comm-link. He didn't know much about the Genii, but he knew torture could mess people's minds. He gripped his gun tightly, hoping to encounter another bunch of Genii to give them what they deserved.

Sheppard retrieved his gun from Dean's hand and informed the others of their situation. Teyla and the others were already on board; Carson was attending McKay's injuries. Lieutenant Kemp flew the jumper to a closer location.

Ronon carried Dean, while Sheppard remained on the lookout. Without other encounters, they reached the rendezvous point. When they flew back to the Stargate, the remaining Genii soldiers had already disappeared into the wormhole. They watched as the 'Gate closed after them and the field became silent.

Ronon heard McKay babbling some curse under his breath. Without wasting any more time with the Genii, they dialed Atlantis and went home.

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"GET THESE THINGS OFF ME! I'll kill you SHEPPARD! I swear I'll KILL you! And YOU! And you!"

Winchester was yelling and struggling against the ties that held him to the bed. It was like watching a caged beast going rabid: his eyes had a murderous glare and he was thrashing around in order to free himself.

"Calm down, Dean. We just want to help you." Teyla tried to reason with him while keeping her distance.

"She is right," Sheppard added.

"Kill me now, Sheppard. Or you're gonna regret it. When I break free I'll put a bullet in each one of you!"

"You're not well, lad. We are not the enemy," Carson tried to sooth him.

When Winchester saw the syringe in the doctor's hand, he went ballistic. It took two marines to keep him still enough for the shot. When the drug kicked in, all the people in the room took a deep breath of relief.

It had been almost a day since they had returned to Atlantis.

The first thing they had done when they arrived was to rush the whole team in the medical ward. Carson had checked all his patients but, since Sheppard, Rodney, and Ronon weren't in critical condition, he left them to other members of his staff and he focused his concerns on the kid.

Sheppard had instructed him to restrain Winchester until it was deemed safe. At the time, Carson had shot him a painful look, but he did as he was told. Restraining the kid had seemed a cruelty, but Sheppard had seen him in action, and he couldn't take any risk. And after that outburst, even Carson seemed relieved they had restrained him. To be on the safe side, Sheppard had ordered two marines to stay in the med bay with their stunners ready, while the doctors did their tests.

For the time being, there was nothing else he or his team could do. Just wait.

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Doctor Weir had been glad to see both men alive, but from what she gathered from the team's reports, it was clear that the crisis wasn't over. She sent Major Lorne and Zelenka with a team of marines to check the planet, hoping they could find any information on what had happened there that might help Dean's recovery.

She went to talk with John while visiting the men in the infirmary.

"I don't know what to say, Elizabeth. They brainwashed him. I'm telling you, I fought with Dean and he seemed like another person. He didn't have the slightest hesitation: he wanted to kill me."

Elizabeth frowned. "Do you think that was Kolya's plan all along?"

"Yes...No…Maybe…but I'm sure he enjoyed the idea of turning one of my men against me," Sheppard ranted. "Rodney mentioned this guy, a Genii doctor…I think his name is Alastair. He was the one to torture Dean. He did something to him."

"Do you think Kolya is still alive? From what you said… he went in those tunnels right before the explosion."

"I don't know, Elizabeth. He should be dead, the entire underground facility collapsed when the bombs exploded."

Elizabeth nodded. Carson took that moment to bring some news. Rodney, Ronon and Teyla came closer once they spotted the doctor.

"Colonel, Doctor Weir. I have the results from the tests."

Elizabeth turned all her attention to him. "What's the diagnosis, Carson?"

"I found high levels of several different drugs in his system. Some of the components are similar to scopolamine and other hallucinogenic drugs, but others are completely unknown." Carson's expression was serious. "He has several wounds on his body, ligature marks and other signs of torture. Half of them are already healed so they must be a week or two older. I don't know what kind of drugs were used but the MRI, the EEG and the other tests show there are severe effects on the brain."

"They drugged him with…what? A roofie? Pegasus's version of LSD?" Rodney spluttered.

Carson rolled his eyes. "No, Rodney. It's different. These drugs are more powerful than what we have on Earth, and they are affecting certain areas regarding the memories."

"What are you saying, Carson?" Sheppard asked.

The doctor turned around. "From what we saw he firmly believes he is an enemy and I think… those drugs, and God knows what other forms of torture they put him through, made him compliant to do whatever they told him. This Genii's persona could be a way his mind coped with the stressful situation, or it could be what they tried to create all along."

Carson took a deep breath, like he was trying to steel himself. "There are documented cases in which waterboarding, electroshock and other torture techniques, along with the use of certain drugs, can make the prisoners so weak and pliable that they believe and do whatever they are told. In some cases, the victims themselves dissociated from their situation by creating another identity so they could bear the pain. Both hypotheses could be valid in his case. The human brain can take a lot, but everyone has a breaking point."

Elizabeth clenched her hands. She had approved Dean involvement in off-world's operations because he had proven himself capable, but, like every member of the expedition, he was under her responsibility and she had failed him.

"They suppressed who he was and manipulated him…Like we did with Michael." Carson added guiltily.

Sheppard stiffened at that statement. "That's not the same thing. We were trying to find a cure."

"Aye… but what we did was none the less cruel, Colonel."

Before they could get into that argument again, Teyla interrupted them. "Will he regain his memories?"

"I dinna ken for sure. I want to consult with Doctor Heightmeyer. Maybe we can try something, but for now we need to monitor his vitals."

A series of loud, warning signals came from the machines hooked to Dean. Carson ran to his patient who was shaking violently on the bed, still unconscious but jerking involuntarily against his restraints.

"What's happening?!" Sheppard shouted.

"Grand mal seizure," Carson replied tersely as he worked. "Without more of those drugs, he's going into rapid withdrawal. Stand back, please."

Elizabeth, Sheppard and the team gave space to the medical team, but they watched apprehensively the situation unfolded. The medical team moved promptly at Carson's orders, their main concern to stabilize the patient.

Finally, a nurse decided it was time for them to go, and drove Elizabeth and the rest of them out of the room.

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Several hours later, Carson returned. It was clear from his face that the situation wasn't good. Doctor Heightmeyer was with him.

"What happened, Carson?" Elizabeth asked.

"Doctor Weir, I'm afraid there isn't good news. As it is now, Dean is in an induced coma."

"What? Why?" Rodney squealed from Sheppard's side.

"Rodney…he had been constantly injected with drugs. The lack of those chemical compounds is affecting his body. We had to put him in an induced coma or we would have lost him in one of his seizures."

"So…we just have to wait until the drugs wear off his system to wake him up, right?" Sheppard tried to ask the obvious question they all had in mind.

"No, Colonel, it's not that simple," Doctor Heightmeyer replied while reading some test results on her data-pad. "The scans shows signs of intense brain activity. Doctor Beckett filled me in on the case. Given the circumstances just waiting is not the safest option. While his body is in a controlled pharmacological coma, his brain is in some sort of REM sleep. At the moment the stress he is in can put his life at risk."

Elizabeth tried to remember what little medical knowledge she had. "Is he dreaming?"

"Yes and no, Doctor Weir. We saw signs of intense activity from several areas of the brain, including the one where the autobiographical memory resides. During a normal REM sleep that area isn't very active, but Dean is in a coma… his brain activity shouldn't be so high. And some of those drugs affected his limbic system and prefrontal lobe. From what Doctor Beckett told me, it's safe to assume that right now some chemical compounds are breaking apart in his brain. Some information is overlapping on different neural patterns, causing the overload of data and the stress on his nervous system."

"Doc…" Sheppard scratched his head. "Pretend we don't have a medical degree."

A small smile escaped her lips. "I apologize. The autobiographical memory is crucial to defining ourselves. What I'm trying to say is that he is suffering because he is experiencing conflicting memories and this is putting too much stress on his brain. He isn't just dreaming, he is probably reliving memories too, but they are overlapping on each other. Maybe he knows some are real and others are fake, but he can't tell them apart. In this state, his dreams and memories are blurring together. The hyperactivity in his brain can lead to ruptures and internal bleeding, or a complete shutdown." Heightmeyer looked at each one of them in turn. "We still don't know much about the brain. When the drugs will completely leave his system, he could wake up and have some problems with his memories, or he might not wake up at all."

Sheppard looked first to Carson, then to Heightmeyer, hoping they could find a way to fix him. "What…What are our options? How can we help him?"

The silence filled the air.

"The induced coma is reducing the other side effects of the drugs, but it's not a complete solution," Doctor Beckett explained once again. "An operation isn't an option. He isn't stable enough to go through surgery and we could do more harm than good. We could use other drugs to slow his brain activity, but I'm worried about the reactions with the drugs he has already in his system."

"Studies on patients in a coma show that external voices can be heard and can help the patient in his recovery," Doctor Heightmeyer added.

"Talking to him while he is asleep. Right. You know, I don't think we can convince him of what is real and what not without talking directly with him." Sheppard frowned at the two doctors.

"Right now it seems like the only option, Colonel," Carson replied, tiredly.

"That's not entirely true, Doctor Beckett."

The eyes of the people in the room focused on Teyla. "What?"

"There is a story of a root with mystical proprieties…"

Rodney rolled his eyes as he heard the word "mystical". "Are we really that desperate, to talk about some voodoo stuff?"

Ronon, instead, gave her a long look. "Are you talking about the Xhosa?"

"Yes." Since the others in the room went silent, Teyla kept talking. "It is told that the Sindula root, or Xhosa in some other cultures, is a rare root used to communicate with one's ancestors by making a particular tea with it…it's a legend, but I heard stories of shamans that were able to talk to injured people in their dreams by adding a drop of blood, from their patients, in the tea."

"That's nonsense. What could a drop of blood do to let someone enter another's dream?" Rodney blurted, unable to help himself.

"It creates a connection between the wounded and the shaman."

"Teyla, I know that your people believe in this kind of things…but while a root is likely to give you some vivid dreams, it can't have the power to do what you say." Elizabeth tried to reason with her.

Sheppard was skeptical as well. Something like a magical root seemed a bit of a stretch–he understood both Rodney and Elizabeth's line of thought. If something could help Dean, it was science, not folktales. But he trusted Teyla. She wouldn't have told them about this root if she wasn't sure it could help.

Ronon moved from the wall and placed himself near Teyla. "I know those stories too. A woman on Sateda used to help those in need of a last farewell with the Xhosa."

"My fellow Athosian, Charrin… She knows the root, maybe she has some on the mainland. We could easily make the trip."

Beckett and Heightmeyer didn't say anything, but their faces told Sheppard how skeptical they were. He closed his eyes for a brief second, thinking. "All right… Let me get this straight. We need to help Dean, but we don't have many options…except talking at him on his bedside and drink an alien herbal tea?"

Since no one replied, Sheppard sighed. "Well then, why don't we do both?"

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Kolya had instructed Dalca to wait a day after the second team of Atlanteans left the planet before moving to the rendezvous point. It was a hidden bunker deep in the forest; only few people knew of that secret location.

Dalca arrived right on time. "They left. I think they fell for the trick."

Kolya appeared behind him, gun in hand, and surveyed the forest around them in order to ascertain he hadn't been followed. "Any chance Winchester did his job?"

"No, Commander. The Atlantean wasn't able to kill Colonel Sheppard…" Dalca stood still under his glare. "He was stopped before he could finish the job. However, I saw signs of instability while they fought."

They began to move toward the Stargate. With a little nod Dalca continued his report on the status of the men that were able to flee to another planet, the ones dead in the forest, and all the data they had lost.

"Another failure then. Useless scientists. Any trace of Alastair?"

"No, sir. He probably died in the explosion."

Kolya didn't reply, but he wasn't convinced. The vicious doctor was too cunning to die like that. If he was alive, Kolya was sure he didn't want to be found. Otherwise, he would have met them in the secret bunker as per orders.

Although, it didn't really matter. Alastair had failed. Like the other scientists, he hadn't produced any result worthy of his attention. This was another proof that he needed to rely only on his forces and his men to succeed. Loyalty to a cause couldn't be faked.

They left the planet. Kolya ordered Dalca to take a few men and transport the Wraith prisoner they still held in custody to the main hideout. It was time to extract other information from him. After that, they would lay low and make their enemies lower their guards. His opportunity to take his rightful place as leader of the Genii would come. He just needed a different plan.