Author's Note: Phew! That was a marathon effort! For those who don't know, I reply (or at least try to) to every review sent my way, and you are all being nice enough to send me these awesome reviews that it takes ages to reply! It's fantabulous! So, thank you all sooooo much! If you didn't get the idea from my replies...

Sorry, this chapter might be a bit slow, but it's got the explanations in it (thus the title) and the action soon picks up again after it!

Chapter 11: Explanations

Sheppard watched him with a curious glance as the Wraith shut the cell again, and left the two of them alone. Still speechless, McKay walked up to him, because John Sheppard was supposed to be dead, and yet this was the second time he had seen him. He was sure he was hallucinating. Just to make extra sure, he moved to poke the apparition.

The apparition swatted the hand away before McKay could touch him, and moved away, obviously worried about his cell mate's sanity.

Finally remembering to breath, McKay's jaw dropped, and he gave a relieved laugh, that threatened to become hysterics.

"I don't believe it," he said, unable to stop the grin, despite his current situation. Granted, his current situation had just gotten a whole lot better.

Sheppard, on the other hand, seemed to be still worried. Looking around, and realizing there was no one else in the room, he leaned forward.

"Do I know you?"

And McKay's hopes, and relief, and every good feeling that had come to him in the past thirty seconds crashed against the pointed rocks that lay at the bottom of his stomach.

"Know me?" he asked, his voice embarrassingly high. "Sheppard, it's me, McKay!"

Sheppard's jaw dropped, and he suddenly looked hopeful. Stepping forward a few feet, he took a deep breath. "Do you know me?" he asked, slowly, deliberately. McKay's heart skipped a few beats.

"You don't… you don't remember me, do you?"

The man scowled. "Remember you? I don't even remember me!"

"Oh."

It was all Rodney could say. Shocked, never expecting this, not in his wildest dreams, he had to sit down. This was just… too much. It was evil, that was what it was.

"Wow."

Sheppard squatted down in front of him, looking like all his wildest dreams had been answered. This was just unfair. "You do know me, don't you," he said, grinning. "I don't believe it."

McKay gave a laugh. "Trust me, I'm having a hard time believing it too." He shook his head. "You're supposed to be dead!"

Well that made the man spiral. Losing his relief, he stood up, backing away, suddenly suspicious. "We're not friends?" he half-asked. McKay's heart lurched, and he stood up immediately.

"No, God no, we are. It's just… you crashed, and your ship was going so fast, and the Daedalus couldn't detect any life signs on the planet…" He frowned, pausing. "Which is obviously not true. But we searched for you, but found no trace… I mean, the Daedalus couldn't pick up any life signs, and neither could the HUD on the jumper Lorne was flying, and… Oh my God."

Sheppard shifted uncomfortably, moving away slightly. "Yeah, apparently this place has some kind of device that their Ancestors left behind… Makes them undetectable from space."

McKay made the link immediately. "That miniature planet in the junk room!"

Sheppard must have taken it as some kind of question, because he shrugged. "I have no clue, it's just what they keep telling me."

McKay shook his head, getting that relief back, because damn it was good to see John again. "I can't believe you're actually alive. I told Sam you had more luck than God!" He lost his smile. "And we never would have found you if… Oh my God, we weren't even looking! We didn't think anyone could have survived that crash."

Sheppard shrugged. "I almost didn't," he answered. "The Latirans got me from the Dart before it exploded. Brought me here where one of the priests healed me as much as he could."

McKay gave a weak grin. "Well, I'm glad about that."

The colonel nodded, then seemed to grow unsure. It wasn't an expression Rodney was used to seeing on him. "So, uh, if you know who I am…" He gestured with his hands, and McKay got the picture.

"Sorry, right. Uh," McKay shook his head again. God, wasn't Atlantis going to get a shock. "You're name's John Sheppard. You're a Lieutenant Colonel in the United States Air Force. One of the best pilots in two galaxies."

"John Sheppard," he muttered, smiling. "I like it. So, I am a pilot. The Latirans figured I was."

"Well, they're right. Sort of. You're not so much a pilot now, as the officer in charge of the military in Atlantis."

"Atlantis…" That looked like it tweaked a memory. "I think I remember Atlantis. Water comes to mind."

McKay grinned. "Yeah, it floats. And flies. In fact, you've flown it before. It's the City of the Ancients."

"The Ancients?" he asked, suddenly uncomfortable. "So I really am one?"

"What?" McKay asked, wondering why the hell he thought that. "No. Why would you think that?"

The man shrugged, a bit put off by the sudden snappy tone. "Well, when I turned the Stargate on, the Latirans kept on calling me one of their Ancestors. You would not believe how hard it was trying to get them to stop."

But McKay wasn't listening. "You brought the Stargate online?"

Sheppard shrugged. "Only by accident. I mean, the Temple came on when I stepped inside, I found it, and then there was this crystal…"

McKay rolled his eyes. "Let me guess? You touched it." Sheppard shrugged. "Didn't you learn your lesson when you touched the glowing crystal that made… Oh, right. No memory." He gave a quick grin. "Well, here's lesson number one. Don't touch anything."

"So if I'm not one of these Ancients, how'd I do it?" he asked.

"Oh, you have their genetic… never mind, it's too complicated." He waved his hand, and sat back down. "Just rest assured you're not actually an Ancient."

Sheppard was looking at him like there was something wrong. "Are you always like this?"

"Um. Yeah," McKay nodded. "Pretty much. You'll get used to it. Again."

Sheppard nodded slowly. "And what's your name again?"

"Rodney McKay. I'm on your team, with Ronon and Teyla. Ringing any bells?"

The man snapped his fingers. "Rodney, dial the damn gate!"

Well that wasn't what he had been hoping for, but it was a start. Struggling to smile, he nodded. "That would be me. Resident gate dialler. Resident physicist. Resident expert on Ancient technology. I'm the one people usually turn to when something has to be solved by science."

Sheppard looked like he had no clue what he was talking about. Looking around for another seat, and finding none, he sat down on the floor. "I've been having… flashes, I guess you could call it." He licked his lips and went kind of solemn. "Just bursts of memory, mostly in dreams."

"What about?" McKay asked. Sheppard frowned at him.

"That's the problem. I don't know how real they are, or how recent, what order they go in, or anything like that. Reckon you can help?"

McKay shrugged. "I guess. Let's try it anyway."

Sheppard shifted on the floor. "I think the first one I had, I was in a Dart, and I think it was just before my crash."

To his surprise, McKay flinched. "Yeah. The crash. You know we heard it? Of course, that doesn't mean much to you, I guess. You have no idea how much it hurt everyone back in Atlantis. Hell, I heard Sam had tears."

"Sam is my…" He snapped his fingers. "Colonel Samantha Carter."

McKay smiled. "Yeah. Your boss. Well, our boss. At least we know your memory is going to come back."

Sheppard didn't look so sure. "I remember getting a Dart. I had to get off this huge ship, so I wouldn't get captured. Was that just before?"

McKay shrugged. "I don't know," he admitted. "I was unconscious when you crashed."

The other man seemed to hear something in that, and he leaned forward, that familiar, suspicious frown in place. "Why? Why were you unconscious? And why did I need a Dart in the first place? Why was I on that ship?"

McKay licked his lips. "You were rescuing me. Well, me, Teyla and Ronon. The Wraith had taken us a few days before, while we were on duty with some environmentalists on P3X-079. We had been staying at this village, it got attacked. The four of us managed to get away, but you, being all heroic, said we'd get the stolen villagers back."

"I do that a lot, don't I?" he asked, grimacing. It was what had gotten him in here in the first place. He could have gone and hidden with Samuel, but he had just had to fight the Wraith.

Rodney laughed softly. "Every time you can. Only this time, it didn't exactly go to plan. Well, truthfully it almost never does, but this time was even worse. We got the villagers out, and then we decided to blow the Hive ship up. Then you got stuck on the wrong side of a door."

He nodded. "I remember that. I told you to leave me. You and Ronon."

"And Teyla," McKay added, leaning over his knees. "You ordered us to leave, and Ronon, being Ronon, obeyed. Only they were waiting when we got out. Ambushed us, stunned us. Next thing I remember is waking up on the Hive ship, and we were in space. After that it gets a little hazy."

He shuddered, as if at some memory, and Sheppard looked away for a moment. Then he looked back. "Do you know what happened with me? I mean, I think I saw you getting caught. I remember seeing three people unconscious on the ground, and Wraith, with worshippers. Then I snapped a stick, something hit me… the rest I can't remember."

"That thing that hit you would be a bullet," McKay supplied. "Sam filled me in on the rest. The worshippers tried to hunt you down, keep you away from the Stargate." He grinned. "It took you a day, but you finally got through. Though you were exhausted and nearly dead from blood loss."

He frowned. "I think I remember that too."

"You would," Rodney told him, standing up. "Anyway, Sam said as soon as you were conscious again, you got together your best men, and came after us. You managed to rescue us, even in space, but an alarm got tripped as soon as we got near the hidden puddle jumper. You laid down cover fire as the rest of your men dragged us to the jumper. Only when you tried to get in, the route was blocked. You told Lorne to take off, grabbed a Dart, and blew the place to hell as you flew out. Only the controls were jammed, and you… went down."

Sheppard nodded, seeming to come to an understanding. "How did I find you if you were in space?" he asked quietly.

"One of your smarter moves. The enviro's who were with us, they had tracking devices they wanted to use to track any migration of some kind of cow thing on the planet we were on. You had one on you, being you, and you planted it on the Hive ship before it took off. These things were similar to ones used in this… uh, game we used to play, before it turned out to not be such a game. A couple of technicians tweaked them, so we could track the migration on this planet…" He could see Sheppard zoning out. "Never mind."

Nodding, the man stood as well, and began to pace. "So, if you thought I was dead, why are you here?"

"Looking for you, of a sorts," McKay told him with a shrug. "We saw the Stargate come online. It came on during your memorial service actually."

The man gave him a trademark John Sheppard glare, one of those 'so did not need to know that' glares, and Rodney just gave him another shrug. "What, we thought you were dead. Anyway, we assumed it was an Ancient who turned it on, and as you would… or should know, if you didn't have… you know, we would really like to meet an Ancient."

"But you got me instead," Sheppard said, looking away.

McKay stared at him. "Personally? I prefer to have found you." He gave a cough, trying to stop the red seeping up his neck. "Anyway, uh, now that explanations are taken care of… know any way out of here?"

Sheppard's eyebrows rose. "Me? How would I know?"

"Well, you have been here before."

"So?" Sheppard argued back. "I was here for all of ten minutes. I decided to leave before they all started bowing."

"So I take it that's a-."

McKay was cut short by the door opening. They both turned to face the front of the cell, greeting the three Wraith that entered as the life-sucking creatures opened the cell. And the scientist found himself waiting… And waiting.

Turning to Sheppard with a frown, McKay was finally struck with just how truthful the man was being about his memory loss. The man standing beside him was almost nothing like John Sheppard. The John Sheppard he knew would have been cracking jokes, naming the Wraith with mundane Earth names, and just generally trying to ease the nerves in the room by pretending cockiness and surety. Whereas this John Sheppard looked as nervous as McKay felt, not at all like a man desperately trying to think up an escape plan.

Swallowing, McKay couldn't help but return to the screwed way of thinking.

"Come," the lead Wraith ordered, and the two men obeyed, before the leader snapped its attention to Rodney. "Not you. Just him."

Sheppard gave him another look, and continued walking, flinching slightly as the two other Wraith grabbed his arms. The leader continued looking at McKay even as it shut the cell again, the shield going up. Anxious now, the scientist walked forward until he stood at the bars, watching as his friend disappeared around the corner in the company of the Wraith.

And there was nothing he could do about it.

His mind wouldn't shut off, though to be honest if he listened to it, he could ignore the growing fear in his stomach. But of all the places to find someone who actually knew who he was, a prison cell was the strangest.

But he had a name now. A name! And a home, and friends, and people who knew him, who could answer all those things he couldn't remember.

That was, if he lived through this.

He tried to steady his head, concentrating instead on where he was going. What was going on around him. Trying to see any way out of this.

It wasn't looking good. He knew there were plenty of Wraith around, and no doubt more kept on showing up through the Stargate. And soon a Hive ship would appear. It was inevitable.

Which just meant he had to get away before the Hive ship turned up. Yeah, sure, because that was going to be a walk in the park.

He suddenly recognised where they were, and he frowned, wondering what they wanted with him that had something to do with the Stargate. He was still trying to figure it out as the four of them entered the room.

The Gate was off, for now. With the Wraith escorting him, the number in the room reached eight, and with only one of him, those weren't good odds. This really wasn't looking good.

The Wraith holding Sheppard shoved him to a spot just before the device in front of the Stargate, and he barely kept his feet. He turned to look at them, trying to be confident.

The Wraith in charge walked forward until he was only a few feet from Sheppard, a triumphant smile on his face.

"You are the one who turned on the Portal."

Sheppard looked around, but found nothing that could help. He looked back to the Wraith. "Is there a question in there somewhere?"

That smile became more of a glare. "Did you turn on the Portal?"

Probably not much use in lying. "I… guess you could call it that."

The Wraith nodded. "Good. Now. You will show us how."