A/N This is AU. What might have happened if Rodney hadn't take the large dose of Wraith enzyme in The Hive? The first two chapters are from Sheppard's POV, and gives his part of the story. Rodney's POV is in the following chapters.

!!Warnings!!: Though it's not graphically described, it is clearly stated that rape occurs in the story. Please don't read if you are uncomfortable or disturbed by this. There is also some violence.

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"Where the hell did they go?" John turned to Major Lorne. "Get to the gate and get me Zelenka. Now." He started to pace.

"John, might he not have gated somewhere on his own? The Alpha site, perhaps?" Teyla, of course, would try to reassure him. Unfortunately, he knew better.

"No. I had Lorne check. Look at this place." He pointed to the scattered remains of the camp. "They left, and it doesn't look like everyone went peacefully."

Ronon had been scouting around. "Nothing here. They left maybe two days ago."

"Let's hope Zelenka can get the gate address from the DHD." He waited, pacing and staring into the trees. When the little scientist finally arrived, he had to restrain the urge to lean over his shoulder. He couldn't help, however, asking how it was going... every ten minutes or so.

"Colonel Sheppard, Rodney may be able to work with you lurking like a large ape behind him, but I cannot. Please do not ask for progress reports every few minutes." He narrowed his eyes. "I will do everything I can do to retrieve the last fifty planets, but it will take some time."

"Fine. I'll go wait over here." He really didn't like to be idle. He leaned against a large tree and closed his eyes. If only he'd made them take Rodney along, or he'd insisted on Ford letting Rodney go. He should have made the Daedalus drop him at a Stargate and come back for him right away instead of going to Atlantis.

"Stop it." He opened his eyes to see Ronon standing in front of him.

"I should have made sure he could go back to Atlantis. Do you have any idea how hard it's going to be to find him if they want to stay hidden? Ford's men came from all over the galaxy. He could be anywhere." That was the big problem. Where was he? If Rodney hadn't gone willingly, and he was pretty sure he didn't, then they took him. If they took him, they weren't going to give him back. It would be up to them to find him. He just hoped they would. They had a whole galaxy to search.

"OK, I have them. Let us return to Atlantis so I can start going through this list." Radek stood and clutched his laptop to his chest. "I do not like leaving the labs."

Hours later, after post mission physicals and showers, they gathered for the briefing with Elizabeth. "Radek was able to narrow the list down to 32 planets. The other 18 have space gates." She gazed at him, and John met her stare, hoping his face was unreadable. It really wouldn't be good for everyone to see how close he was to exploding. His anger at himself was dangerously high.

"We will send teams to these planets, but it will take some time. In the meantime, I suggest you all get some rest."

John couldn't sleep, so he ran. He went to the mess and pushed some food around on his plate. He couldn't help but notice that it was one of the few meals that Rodney really enjoyed. He dropped his fork onto his plate with a clatter. A shadow fell over his table. Looking up, he tried to manage a smile. Teyla stood with a compassionate look on her face.

"John, why are you here alone?"

"Because I lost one of my best friends." Oops, didn't mean to let that just pop out. He sighed and backtracked. "I'm just a little tired."

"I do not believe he is dead. Neither should you."

"I didn't mean that he was... dead. I meant lost him as in it's my fault he is missing." He shrugged.

She tilted her head and gave him a small smile. "You did not misplace him, he was taken. We will find him, John." She laid a hand on his shoulder and squeezed. "We shall keep looking until we do."

He watched her walk away. Maybe someone would be in the gym. He could use a long sparring session.

Of course, Ronon would be there. Only two marines were training with him, but he easily downed them with only a few moves. As they joked good-naturedly, Ronon looked at him from lowered brows.

"Come to spar?"

"Yeah. Thought it might help me sleep." Sheppard stretched his muscles. They circled each other like two lions. He managed to dodge the fist that suddenly appeared in front of his face.

"Don't do this to yourself."

John twisted his lips and landed a blow to Ronon's back. "I'm not doing anything." That's right. He's safe on Atlantis while Rodney was God knew where. "I left him there, Ronon. I barely spared him a thought the whole time we were gone."

"We had other things to worry about."

"Yeah, being on a Wraith hive ship is something to worry about." He didn't quite manage to block the strike to his side, and his breath wooshed out. "But after that? I didn't even really think about him while we were on the Daedalus. It never occurred to me to wonder what he was doing."

"You were mourning your friend."

"No. I spent the time thinking that I messed up." John tried to land a hit, but Ronon was too fast. "I was worried about what I was going to tell Elizabeth, about telling Ford's family that he was dead. I wasn't worried about McKay."

"You let it eat at you, you won't be any good to anyone." Ronon's leg swept him off his feet. "Trust that we'll find him."

"Yeah?" John was angry. He stared at the outstretched hand. "That sounds like faith. You have any faith left, really? 'Cause I don't." Miracles happened here, when McKay did the impossible. They didn't happen just because.

"You don't leave your people behind, remember?"

He lashed out, rage suddenly draining away. "But I did, didn't I? I left him there, and now we have no idea where he is." Unspoken was the possibility that Rodney was dead. No, he would not believe that until he touched his corpse.

"We'll get him back." Ronon sounded absolutely certain. "If not, we'll at least find the men who took him." Ah, keep looking, if we find Rodney, and he's dead, the least we can do is kill the men who took him.

John knew he had it in him. He'd done it before, allowed men to die because they were a threat to people he cared about. He'd killed men for that. He would take life or give his own for Atlantis and her people, but a select few were different.

His team was probably the sum and total of those who really knew him- and loved him anyway. For them, he would suspend his own moral code. He would not lose any of them. If he did, this galaxy would find out just how dangerous he could be.

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It was almost six weeks before Elizabeth finally asked John for a private word. "You knew we couldn't keep up the search indefinitely. We'll offer some rewards, ask all the teams and any allies we have to keep their eyes and ears open for information about Rodney. But we have to go back to searching for new trade agreements and alliances."

"It hasn't even been long enough to follow up on half the leads, yet."

"We can't spare the man-power. The Daedalus helps, but you know we need to find enough food for everyone in Atlantis." Her look was understanding. "I miss him, too. We all do. We've done all we can, now we have to move forward."

"Well it sucks." Sheppard met her eyes. "

She looked at him and said, "I'm sorry, John."

He turned and walked away without a word. His sense of failure pressed in on him from all sides, but moved through it. He had too many responsibilities left to give in to his self-recrimination. He'd damned well do his duty more thoroughly from now on.

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It was two months after losing Rodney that Lorne sought him out. Apparently, he was making the marines nervous. They were worried about his stability. He was too angry, too unpredictable. He was pushing them too hard. He penalized them ruthlessly when he felt they allowed any civilian to be placed in danger. John made it a point to require all civilians to learn basic marksmanship and gun safety, as well as self-defense.

His constant watchfulness created a level of tension between Sheppard and the rest of the expedition that had never been there before. They worried that he was becoming too cautious, he worried they weren't careful enough. It had finally come to a head when several marines offered informal complaints to the 2IC. Lorne had tracked him down to explain and request that if Sheppard couldn't stop riding them so hard, could he take a few days off, at least.

Sheppard looked at Lorne. "I'm fine."

"Sir, part of my job is to give you back-up. If you need the help, I have to get you help." Lorne frowned at him.

"I'll be fine. I am fine." Sheppard twisted his lips. "But I'll take a few days off, if it will make you happy."

But he wasn't fine. He ran through the halls of Atlantis, running until he was exhausted. He couldn't shake the guilt, the sense of blame that he knew lay squarely on his own shoulders. He took a week off, then two. Teyla and Ronon spent time with him, thought they carefully avoided mentioning their missing team member. Seeing the worried and distrustful looks he was receiving from most everyone made him spend the day in his room, thinking. He made an appointment with Kate.

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It was three months later that John was finally convinced to choose a new scientist for his team. Radek adamantly refused, looking angry at the suggestion. SGA-1 tried out nearly a dozen other scientists, and either he found them lacking or they refused to go off-world with his team again. Amidst complaints from both Sheppard and the scientists, he'd felt both Elizabeth and his team giving him concerned looks. He retreated to his room to calm down and think.

After talking to Kate, he finally he allowed an engineer by the name of Rollins to take the position, though he made it understood that unless Rodney came back physically unable to go off-world (and he also made it clear that Rodney would be back) the position was only temporary.

Rollins wasn't incompetent, but he wasn't nearly a scientist of Rodney's caliber. Barely out of his twenties, he lacked the wonder and excitement the older man had. He was intimidated by John, Ronon and Teyla. There was no banter or friendly insults. He obeyed orders instantly, even if they were wrong. And he had no sense of humor. John missed his friend.

John knew that he had to lower his expectations. No one was going to be like Rodney. He'd give the man a chance. It wasn't like Rodney was coming back.