NOTES:

Thank you to everyone who has read, left reviews, and/or faves on my other SGA stories. I'm thrilled you all are enjoying them.

This story takes place immediately following events in s02e03 Runner.

This one kind of got away from me and is twelve chapters, so get ready!

As always, this story was made better due to the efforts of my beta reader, Lyn.

John watched as Ronon stared at the screen showing the destruction of Sateda one last time then left the control room without saying another word. He nodded to the two Marines assigned as an escort and said, "See that he gets back to his room."

"Yes, sir," one of the Marines said, and led the way out of the control room.

"Chuck," Elizabeth whispered, "recall the MALP."

"Yes, ma'am."

The flickering images disappeared as the screen shut down, and John ducked his head. He couldn't imagine the type of pain Dex had to be in at the moment. How would he react if he saw images of Earth, or Atlantis, in ruins?

"John?" Elizabeth said on her way back to her office. "We need to talk."

"Yeah," John agreed with a sigh, and followed her into the glassed-in office.

'What do you want to do now?" she asked once she was seated behind her desk. "With his homeworld destroyed, there's nowhere for Mr Dex to go." She paused and looked down at her desk. "It may not have been the best idea to bring him back to Atlantis. We are trying to stay hidden."

John frowned. "He's not going to tell anyone we're still here."

"You don't know that," she replied. "He did kidnap you and Teyla."

"Only because he didn't know who we were," John insisted.

"He certainly knows now," Elizabeth replied, and John could hear the mix of concern and exasperation in her tone.

"He hates the Wraith just as much as we do." John stopped and thought about the images from the planet. "Probably more," he amended, and straightened his back. "He's not going to give us up."

Elizabeth studied him for a moment longer, then sat back in her chair. "What do you intend to do about Ford?" she asked.

John was a bit surprised at the change of topic. He'd honestly expected a bit more of a fight where Dex was concerned. "We found him once, we'll find him again."

Elizabeth looked down at her desk and picked up the stylus for her computer.

"What?"

"Are you sure that's such a good idea? Like you said, he ran into the Wraith culling beam."

"To escape the planet!"

Elizabeth sighed. "I understand that, John." She paused a moment. "However, he chose running into that beam over coming back to the city. Have you thought about that?"

John rubbed a hand over his eyes. He hadn't thought of much else since they'd returned. He thought about the promise he'd made to Ford's cousin, that he would find Aiden and bring him home.

"We didn't leave him. He ran away," he remembered Rodney saying while they were on Earth.

"We will need to tread carefully, or he will only continue to run away from us," Teyla had said after Ford left in the jumper.

John stared at the bowl on the corner of Weir's desk. Was he supposed to just give up? he wondered. Leave Ford to fend for himself? Both McKay and Teyla thought Ford was running away from them. Was he the only one who couldn't see the truth? Would Ford, or Teyla, or Rodney abandon him if their roles were reversed and he was the one affected by something that fundamentally changed him? John shook his head and looked down at his hands.

"Have you had a chance to talk to the rest of your team? What do they think?" Elizabeth asked after a few moments of silence.

"McKay and Teyla want to find him, too," John insisted.

Elizabeth studied him for a moment, and John looked away. "I'm sure they do," she finally said. "But did you hear what Rodney said before Caldwell left?"

John replayed the conversation a few hours ago with Caldwell in his head.

"Based on the quality time I spent with Ford, he was definitely not thinking straight," he remembered McKay saying. He hadn't thought anything of it at the time, just Rodney trying to help prove John's point.

Elizabeth leant forward in her chair. "Something happened between Rodney and Ford," she said. "There's something he's not telling us."

"He seemed fine in the meeting."

"Yes, that's what's worrying me. When have you ever known Rodney to be fine after something like what happened today?"

Elizabeth had a point, John realised.

Rodney had disappeared soon after their return to the city. At the time, John had assumed McKay had gone to get cleaned up and checked out by Carson. John had been busy dealing with Ronon and explaining to Elizabeth why they had brought him back with them; he simply hadn't been paying much attention to where Rodney was or what he was doing.

When he'd arrived for the debrief with Elizabeth and Caldwell, Rodney had already been in the room reading something on the computer in front of him. John had given him a quick once over, and he'd seemed fine. Now John wondered if his concern for Ford and the distraction of sorting out quarters for Dex had let him miss something with Rodney.

John scrubbed a hand through his hair and stood from his chair. He turned to the door. "I'll talk to him," he promised.

Elizabeth nodded. "As for Ronon Dex, you need to find out what he wants to do now that he knows what happened to his homeworld."

"And if he decides to leave?" John asked from the doorway.

Elizabeth twisted the stylus in her hand. "We'll cross that bridge if we have to."

John left the office and headed first to the mess hall for a couple of cups of coffee before heading down to Rodney's lab.

"Colonel Sheppard!" he heard a voice call when he entered the mess hall. He turned to see Teyla enter the room behind him.

"Teyla," John replied and stopped just inside the door. "Something I can do for you?"

She smiled and held out her hand. "With everything that has happened over the past few days, I have not had a chance to return this to you," she said as she dropped a silver coin in his palm.

John glanced at the coin and saw it was the challenge coin he'd given to her before the siege, in case he didn't survive. He ran his thumb over the stylised image of Afghanistan, the memory of sitting on a hill in California superimposed over the memory of sitting in the infirmary telling Teyla how he'd made the decision to come to the Pegasus galaxy.

"You never told him?" John asked as he flipped the coin over to see the eagle in flight on the opposite side.

Teyla shook her head. "You asked me to give Rodney the coin only if something happened to you."

John nodded. "Thanks," he said, and dropped the coin in his trouser pocket.

"You are welcome," she replied then hesitated.

"Was there something else?"

Teyla nodded at John's pocket. "You should tell him, John. If it was important enough for Rodney to know of your decision and what it meant to you after you died, it is just as important for him to know now that you survived."

John smiled slightly. "Maybe I will. Someday."

She studied him for a moment, then changed the subject. "Nothing has changed with the plan for tomorrow?"

John pursed his lips. "I still don't like this idea."

Teyla nodded. "I know. However, Halling and I have both been to Hyax many times. We can complete the trades without compromising the safety of Atlantis."

"I get that. I just don't like the idea of you being off-world without backup."

Teyla smiled. "I will have Halling with me, and as I said, the people there know us. There should be no danger."

"It's that 'should' part that concerns me," John told her, his tone serious.

"We will be fine."

Teyla followed as he turned toward the mess line and the coffee urns at the end of one of the counters.

"I have not seen Ronon since our return to Atlantis," she said. "Has he decided to stay in the city?"

"I don't think he knows what he wants to do yet. From what you told me about these runners, he's a free man for the first time in seven years. That's got to be a lot to take in."

"Perhaps I will see if he is interested in joining me for supper," Teyla suggested as John carefully picked up the two cups and headed for the exit. "The city can be intimidating if you are not used to it."

John chuckled. "Not sure Ronon Dex has ever been intimidated a day in his life."

Teyla frowned. "Do not let appearances fool you, Colonel. I suspect what we have seen of Ronon so far has been a defence mechanism, not unlike Rodney's acerbic attitude. It is meant to keep people at a distance."

John thought about what she'd said for a moment then nodded. "You may have a point," he admitted. "I'll keep that in mind."

He watched as Teyla left the mess hall then headed for the transporter that would take him down to the lab area. As he walked, he thought about Ford running away from him, again, Ronon standing in front of the screen as the MALP camera panned over the destruction of his world, and the cryptic statement from Rodney about his afternoon with Ford.

There wasn't anything he could do for Ford at the moment, he finally admitted. He would have to hope the Lieutenant would find a way to escape the Wraith or they would get information on where he was so they could mount a rescue. He didn't like the idea, but he'd have to accept Ford hadn't given him much choice.

Ronon was a different problem, and one John thought he had an answer for. He'd just need to get Dex, not to mention Rodney, Teyla, and Elizabeth, to agree. Ronon had proven he was more than capable of taking care of himself and was good in a fight. Being a Runner for the past seven years also meant he had intel on various planets, something they could use.

But would he want to stay? After seeing the destruction of Sateda, John wouldn't blame Ronon if he wanted to leave and seek vengeance on his own. John would have to find a way to convince him it would be better for both sides if Ronon chose to stay and help Atlantis fight the Wraith.

John tapped the control for the transporter as he balanced the two cups of coffee in one hand.

If he were honest with himself, John had to admit he hadn't given much thought to Rodney throughout the day. He'd had his hands full looking for Ford, getting kidnapped by Dex, convincing Dex not to shoot them, and then talking Elizabeth and Carson into removing the transmitter. Once Ford disappeared into the Wraith culling beam, John's only thought was to get his people off the planet in case more Wraith decided to show up.

Now he wondered if he hadn't made a mistake assuming Rodney was more or less okay after his encounter with Ford.

John exited the transporter and stopped short in surprise. The hallways around the lab areas were usually quiet. Unless there was some sort of immediate issue, most of Rodney's scientists stayed in their own labs or debated a problem in one of the conference rooms down the opposite corridor.

Now he found chaos as he tried to get down the hall and around the corner where Rodney's lab sat without splashing hot coffee either on himself or one of the milling scientists. He looked around and saw Zelenka standing on a chair at the junction of two hallways, a tablet computer in one hand, as he tried to make himself heard over the general hubbub and noise.

"Doctor Heller and the botany team is down the hall and through the double doors," Zelenka called over the sound of several conversations as he pointed to the hallway across from him.

John watched as three people, including the red-headed woman who had spent so much time with Rodney during the trip out in the Daedalus, head down the indicated hallway.

"Chemists, you are down another floor," Zelenka said, and pointed to a huddle of people standing behind John. "See Doctor Hooker for lab assignments."

The group of men and women turned back to the transporter and John heard the hum as the transporter engaged.

Zelenka looked up from his computer and gave John a half smile and a shrug as Sheppard walked past.

John nodded back and turned down the hall where Rodney's lab was, thankful to leave the gaggle of new scientists behind.

"No, no, no!" he heard Radek cry, and John looked back in Zelenka's direction. "The Geology labs are on other side of the section. Take equipment there!" He watched as two men groaned before they turned around and headed in a different direction hefting a large box between them.

John stopped in front of Rodney's lab, balanced the two coffee cups in one hand, and tapped the sensor to trigger the door.

He waited a few seconds and frowned. When the door didn't open, he tapped the sensor again.

"He has kept the door locked for the past two hours," Zelenka said from behind John. "He is not answering the radio, either."

"You sure he's even in there?" John asked with a glance at the door.

Zelenka nodded. "I saw him when he came down. I wanted to ask him about the new lab assignments. He told me to deal with it and then locked the door." Zelenka paused and looked down at the tablet computer. "I heard what happened with Lieutenant Ford," Zelenka added. "Rodney did not seem his usual self."

John grimaced. First Elizabeth and now Zelenka telling him something was wrong with McKay. Something he hadn't bothered to notice. He really needed to get his head back in the game.

"Thanks," John said with a tiny smile. "I'll see what I can do."

Zelenka nodded, and with a last look at the door, he went back to directing the new scientists to their work areas.

John waited until the hallway was clear, then tapped his earpiece. "Rodney, it's John." he waited a moment, and when he didn't get a response, tried again. "McKay, I'm outside the lab. Open the door. I brought coffee."

He was about to start pounding on the door when he heard the door whisper open.

"Go away," Rodney growled and turned back to the work table.

"Hey," John said, and stepped into the lab before Rodney could close the door again.

"I'm busy, Colonel," Rodney said shortly.

John pursed his lips at the use of his rank. Rodney calling him Major, or now Colonel, only happened when he was angry or upset.

The Ancient box Rodney had been working on for the past several months sat on the work table with assorted crystals lying around it. Another bad sign, John told himself. McKay usually only worked on the mystery box when he needed something to do with his hands while he thought through some other problem.

John followed him back to the work table and frowned when he noticed McKay was limping.

"What's wrong with your leg?" he asked as he set one of the cups on the worktable, pulled a stool around, and sat down across from Rodney. He hadn't noticed anything wrong during the debriefing, and he hadn't felt anything through the mental link, either.

Rodney looked up with a glare. "I don't know, Colonel, maybe it has something to do with getting caught in a trap and left hanging upside down while my supposed friend and team leader went haring off into the woods."

"Ford -"

John saw Rodney's hand clench around the screwdriver he held, and John stopped speaking. Elizabeth had been right, he realised. Something had happened when Rodney had found Ford. Or had Ford found Rodney? John wondered with a sinking feeling in his gut.

He had assumed the 'ray blast' that had hit Lorne was from Dex and Rodney had become lost trying to find help for the Major, eventually running into Ford instead.

Had it been Ford who'd shot Lorne? And then what? Kidnapped Rodney?

Based on the quality time I spent with Ford, he was definitely not thinking straight.

John suddenly remembered the bloody wound in Ford's shoulder and felt his stomach clench. At the time John had thought Ford's injury was something from his fight with Dex.

"I shot him, too," he remembered Rodney saying hesitantly in the debriefing. If Rodney had actually fired on Ford …

"You never did tell me what happened to you today," John said when Rodney went back to working on the box, pointedly ignoring him.

Rodney grunted and pulled another crystal out of the box, checked it and put it back in a new slot.

"Rodney," John drew out the name, "talk to me."

Rodney dropped the screwdriver and glared across the work table. "What do you want me to say, Colonel? That I spent part of the day with Major Lorne, who did little more than belittle my worth on a 'gate team? Or how about being kidnapped by a man I thought was a friend, who instead threatened to kill me, and almost succeeded. Twice! Then I get left with some hairy giant who thinks it's funny to threaten me with a knife, before he finally decides to cut the rope around my leg, letting me drop to the ground, nearly snapping my neck in the process."

John was a bit stunned by the sudden tirade, but Rodney wasn't done yet. He stood and paced back and forth between the table and his desk, limping with every step.

"And after all of that, my team leader, once he finally shows up, doesn't say anything except 'We need to get back to the jumper' and walks away without even bothering to find out if I can move." Rodney stumbled and braced his hand on the desk. "First Mason, and now Ford. How many more supposed friends or colleagues are going to try and shoot me?" he finished, and John heard the hurt underlying the anger.

John stood and placed himself in Rodney's path as he turned in his constant pacing.

"Sit down before you make that leg worse," John said gently.

He tried to tell himself he'd known Rodney wasn't hurt that badly thanks to the mental link. In reality, he had to admit he'd been angry at himself for Ford running away from him again, and other than checking to make sure both McKay and Dex were following him, he hadn't been paying much attention to either of them on the hike back to the ship.

Rodney scowled at him but sat back on his stool. "Now he notices," Rodney muttered under his breath, and John chose not to hear it.

Rodney picked up the coffee cup, stared at it for a moment as if wondering where it came from, then took a drink.

John scrubbed a hand over his face as he sat back down on the stool across from McKay. He remembered hearing the rapid fire from a P-90 just before he found the clearing where Ford and Dex were fighting. Had Ford actually tried to kill Rodney? What would he have found if Ronon had been just a little slower reaching them?

"He tried to throttle Carson, and he attacked Doctor Zelenka in the jumper bay. I don't think either of us can really say one way or the other what Ford will do at this point," Elizabeth had said to him when Ford first went missing.

The thought had never occurred to John how much danger Rodney might have been in if he found Ford. John had partnered Rodney with Lorne for a couple of reasons during the search. As his second in command, John needed Lorne to start working with McKay and hopefully build a relationship, and he needed Rodney to start trusting Lorne for the same reason.

More importantly, John had wanted someone Ford knew on each of the search teams. Lorne was there more to protect Rodney from any dangers on the planet. Like strange Runners, John thought wryly. Not from Ford himself. John had simply assumed Ford would listen once one of his teammates finally caught up with him.

When Ford had chosen to run into the Wraith beam instead of coming back with them, John had been shocked and more than a little hurt by Ford's actions. He'd spent the trip back to the jumper replaying everything that had happened trying to figure out where he could have done something different to convince Ford to come back to the city. Rodney had glared and mentioned something about his leg when they had left the clearing, but John hadn't paid attention, other than to check periodically to make sure he was keeping up on the way back to the jumper. He'd assumed McKay was mostly fine, just grousing to let Sheppard know he wasn't happy John had left him with Dex.

"What did Carson say?" John finally asked with a nod at Rodney's leg.

Rodney studied him for a moment, then shrugged. "No permanent damage," he finally said, his tone conciliatory. "Don't walk on it too much and ice it every hour."

"What about your neck?"

"Shoulder," Rodney corrected shortly. "It's a lovely shade of purple."

They sat in silence for a few minutes, Rodney working on the box, John finishing his coffee.

"What happened to Conan, anyway?" Rodney asked a few minutes later, his tone neutral, and John accepted the peace offering.

John snorted. "His name is Dex, Ronon Dex."

"We never got to the pleasantries while I sat under a tree wondering if you were going to come back, or if Ford had killed you, or if the Wraith had scooped you up in a beam of light and I'd never see you again."

John ducked his head for a moment. Okay, he thought to himself, not quite forgiven. "Elizabeth sent a MALP to his planet."

Rodney looked up from the Ancient box when John hesitated.

"It doesn't look like there's anything left," John finished.

McKay sat in silence for a few moments. "That's, umm … What's he going to do now?"

"Don't know. Not sure he knows."

"But you have an idea."

John smiled and stood. "Maybe." He picked up the empty cups and turned toward the door. "Zelenka is going a little crazy out there trying to wrangle all of your new scientists, you know."

"It's good for him. Besides, I'm not supposed to be walking around." Rodney looked up as John stopped at the door. "Leave it open. Radek can come get me if he needs something."