A/N: Thank you so much for your positive comments. Now I'm a little bit worried that you will find the first couple of chapters to be slightly disjointed but if you bear with me things start to flow better. There's a fine line between giving enough detail and boring the reader rigid hopefully for the most part I've stayed on the right side of that line.

Chapter 1

Train Keeps A Rollin'

He couldn't see the face of the man talking; a bag was thrown over his head and his arms were bound behind him. Laying on his side against the cold stone, he felt light headed; the cloth of the bag was humid with his breath and sweat. The rasping voice of the priest had stopped and been replaced by the soft tones of another man, this man didn't shout or rant, his voice was almost soothing, genial; but what he said wasn't.

"You wish to know what became of your friends? Yes? Very well. We killed them." Sheppard felt his chest tightening; it made sense, that was why they hadn't come for him.

"Once they noticed you missing, the two warriors, Dex and the Athosian woman, split up to find you. From our vantage point higher up the gorge it was easy for our men to pick them off, their concern for you made them careless." He tried to force the emotion down, replace it with anger but found that the only anger he felt was directed at himself. He curled himself into a ball, wishing he could block the words out, but needing to hear them at the same time. "Once they were taken care of, we attacked the others. The Guennec are not military minded, they barely put up a fight. But McKay and Weir, they died valiantly, I will say that for your doctors, each begging for the other's life. You should be proud of them. In the end we killed the man first, it seemed only right that as your leader Doctor Weir should be the last to die. She never faltered, she remained defiant right up until we put the bullet in her head; an extraordinary woman." The voice paused, letting the words settle before continuing.

"Since then we have made several successful attacks. I won't lie to you we have suffered losses also, but none as devastating as those your people face. So you see by refusing to tell us what we want to know, you are just delaying the inevitable. And in doing so you will sentence more of your people to their deaths."

But Sheppard couldn't answer, in fact he barely heard the last words the man said; his mind was filled with the images of his friends dying, their blood spilled. Ronon's and Teyla's broken bodies, Elizabeth and Rodney trying to save one another, that's exactly what they would do, McKay braver than he knew, Elizabeth strong to the last. They were his responsibility, his greatest fear in life was that he would fail them, but that was exactly what had happened. His friends were gone and he hadn't been there for them, he'd been careless and stupid in letting these people take him so easily and the people he cared for most had paid the price.

ooOoo

It had been almost an hour before anyone had missed him. Remembering that fact was painful for Elizabeth; how could they have been so stupid? They had all been busy with their work, she hadn't even realised that so much time had passed. Rodney had forgotten all about his laptop and had commandeered hers. Ronon had returned to his flirting with the young archaeologist. It was Teyla who first voiced her concern and as soon as she had pointed out the Colonel's absence Elizabeth knew something was wrong and she knew by the tension in the rest of his team that they also sensed it. Ronon and Teyla took off almost immediately; they found the puddle jumper where they had left it, still cloaked and untouched. None of the inhabitants of the nearby settlement had seen him; no one had reported any Wraith activity and Teyla had not sensed their presence.

The Guennec chancellor Lewyn had offered up every assistance he could, many of the Guennec people had joined the search efforts themselves; Caldwell had taken the Daedalus and scanned the planet from orbit, but Colonel Sheppard was no longer there. McKay had come up with a possible gate destination but that had just led them on a wild goose chase. They had asked all friendly races to pass on any information they might hear and Teyla and Ronon had worked tirelessly, travelling to trading planets and talking to the ordinary citizens instead of governments and councils, hoping beyond hope that someone, somewhere knew what had become of their commander but, despite their best efforts, they had discovered nothing. It was as if John Sheppard had disappeared into thin air.

In the forest, Ronon had found the area where he believed Sheppard had been ambushed; there were drag marks in the soft forest floor heading back toward the gate. She told herself that the fact they had taken him with them was a sign that he was still alive, even though her rational mind told her that wasn't necessarily the case, and her previous life working for the UN had given her far too great an understanding of the horrors that awaited some hostages.

The return to Earth had been delayed so the Daedalus could help with the search, but in a few hours Elizabeth and Colonel Caldwell would begin the slow journey back to Earth. She would meet with the international committee and debrief them on the progress of the Atlantis expedition exactly as had been planned. Sheppard was to have stayed behind, so at least one of them would have been there should any crisis arise, but he had become the crisis, and now Rodney would take command of Atlantis in his stead.

Everyone knew that Rodney blamed himself but few realised how much guilt she carried. It was difficult knowing that, while she had been standing in the sunshine, running her hands across the cool, pale stone of the ruins, laughing and joking with her companions and feeling more relaxed, more free than she had in months, somewhere in the trees above the gorge John had been taken from them.

She wondered how it had happened. He hadn't fired his gun, so they must have taken him by surprise. Did he know what was happening to him? Had he tried to call out for them? Was he in pain? Was he dead? She'd heard people say about the missing that not knowing was the worst thing, now she knew that it was true. Of course, Sheppard and his team had gone missing before, as had Lorne's team, but never for so long, never leaving her feeling so powerless.

Elizabeth watched from the control room balcony as Ronon and Teyla returned through the gate; she didn't have to ask if their mission had been successful, she could tell by the tired expressions on their faces that they had drawn another blank. With each passing day that the teams returned with no news, the city felt a little emptier.

The Satedan glanced up at her, making eye contact enough to convey his frustration and regret at not being able to bring better news, and turned and headed across the gate room, leaving Teyla standing alone. Elizabeth smiled at the Athosian who wearily walked up the stairs to join her.

"I am sorry, we had hoped that the traders we saw today would know something, they travel to many worlds."

"It's okay. I think if we're gong to find anything out now it will be down to luck rather than anything else." She gestured in the direction Ronon had gone. "He's taking this hard, isn't he?"

"Yes." Teyla nodded. "Without Sheppard, I doubt he would have stayed here so long. There is a certain affinity between them." Elizabeth smiled at the comment; on the surface there was little resemblance between the hulking, brooding form of the runner and the lean frame and boyish exuberance of the Colonel but Teyla was right, the two of them had identified with each other from the start.

"Will he stay?" She'd been concerned that Ronon wouldn't stay on Atlantis now; he and Caldwell had a fragile respect for one another but, assuming that the Colonel was given command of the city, she was unsure if they would see eye to eye on things. Ronon was unpredictable and that wasn't a trait the military liked to encourage. John had understood Ronon but Caldwell was a by the book kind of soldier; Elizabeth suspected John had gotten bored of the book by chapter two and had gone off to do something fun instead.

"I believe he will for the time being, he has no where else to go." She sighed. "But in time, I can not say, he is…stubborn."

"I'd noticed. Try and talk to him; let him know he's needed around here."

"I will try." To Elizabeth's surprise, Teyla leant forward and hugged her. "I may not see you again before you leave, so I shall say goodbye now. May you have a safe and swift journey." She pulled back and smiled. "You shall be missed."

"Thank you, Teyla." Elizabeth watched her the Athosian leave; she was slowly coming to realise that the two of them were not so very different. Teyla knew the pressures of being a leader, of trying to balance heart and mind to do what's best for your people; she also understood that sometimes you found yourself torn between the two.

"Elizabeth?" Carson stepped up beside her. "Are you okay love?" She exhaled heavily.

"I'm fine." He looked at her with his patented doctor expression, one full of concern, and disbelief at anything his patients told him, especially if they said they were 'fine'. "I feel like I'm abandoning ship."

"Nobody thinks that. And you'll be back in a few weeks."

"I want to be here. If we find him, I want to be here, even if it's just to mourn him. Atlantis is a family and…"

"And Colonel Sheppard is the annoying older brother?" Carson offered. She looked at him with an affectionate smile and breathed out a laugh.

"Something like that. Annoying in an endearing kind of way though."

"Aye, you couldn't help but like the man, even if you could cheerfully throttle him half the time." Elizabeth gripped the railing tight, her voice tired.

"We're already talking about him like he's dead." Frustration and exhaustion filled her eyes. "We've given up on him."

"No one's giving up on him, we never will, but at the same time we can't put our lives on hold. We all have responsibilities Elizabeth, and right now yours are back on Earth." He reached out, putting his hand over hers and giving it a gentle squeeze. "If we hear anything we'll send a data stream right away, I promise."

"I know you will. Thank you, Carson." And, with one last glance at the gate, she turned and walked away, leaving a worried Carson behind her.

ooOoo

The priest roared with frustration and another blow landed against his kidneys. Sheppard felt his body convulse slightly at the strike but withdrew further in to himself, blocking it out, pushing his mind somewhere else.

"I hear the train a comin', it's rolling round the bend and I ain't seen the sunshine since I don't know when…" Filling his mind with the words, he blanked out everything else. The next kick hit him in the side of the head, causing him to roll over; lights danced behind his eyelids and he sang out louder. "I'm stuck in Folsom prison, and time keeps draggin' on, but that train keeps a rollin' on down to San Anton..."

"Careful Patriarch, you will damage his mind and then he will never be of any use to us." The calm voice of the soldier was faint beneath the roaring of the blood in his ears.

"I'm beginning to think his mind is already damaged." The priest breathed heavily, huffing and wheezing like a wild animal.

"When I was just a baby my mama told me. Son, always be a good boy, don't ever play with guns."

"Then let us try a different approach. We are in no hurry."

"Your methods have only succeeded in making him less responsive. What is he doing?"

"But I shot a man in Reno just to watch him die, now every time I hear that whistle I hang my head and cry…"

"I believe he is singing, sir." There was a hint of amusement in his voice. The priest practically growled but John suspected it was aimed as much at the guard as it was him.

"I bet there's rich…" Another brutal kick landed against his ribs, briefly knocking the wind out of him. "…folks eating in a fancy dining car." He was becoming breathless but still kept going. Hands grabbed his throat and pinned him to the floor. He could smell the priest's sweat as he fought to breathe, gasping in small pockets of air. The pressure increased and he could feel his lungs burning for oxygen.

"Patriarch, you're killing him. He will be of no use to us dead." Dead. The unseen guard was right, he would be of no use to them dead so he stopped struggling and let himself drift away.