Fandom: Doctor Who/Stargate: Atlantis

Rating: PG-13

Warnings: some violence

Spoilers: early season 4 SGA, season 3 New Who

Written For: Tali (aworldinside) for the Multiverse 5000

Betad by: lilbakht

Summary: The Doctor doesn't know why he's here, but he knows it's not an ordinary stop.

"This is all just a misunderstanding," the Doctor protested as rather large guards herded him into a cell. How was he supposed to have known that crawling under the ceremonial altar to take a look at the device built into its base was taboo? It was an Alteran device, and while they'd been almost as stuffy as Time Lords (rather more so, actually, in a few areas), they hadn't had any silly superstitions about things like poking around in perfectly ordinary devices. No reason to expect that their descendants (or children, or experiments, depending on how you looked at it) would be all uptight about what was really a rather ordinary experiment in alternative methods of generating zero point energy. "I didn't know you consider it a sacred relic—although, I'm not sure the Ancients would really appreciate being turned into gods, they try and stay out of mortal affairs these days—but now I know, I'll be properly considerate."

The device probably wasn't why he'd landed here, of all places; he'd been heading for the 209th Annual Poethon on Granathia II and landed here instead, and the TARDIS had felt—odd somehow. Expectant. He'd have checked the place out anyway, of course, but this wasn't just an ordinary stop.

"Meant no disrespect to the sacred chalice of … what was it again? Well, I didn't know I shouldn't touch it. I'll be more careful in the future. And the past, whenever I end up here again." Well. Martha might have been able to figure that one out, if she hadn't left him for a boring life on Earth with her family. Or Rose, Rose was good at that sort of thing. Come to think of it, most of his companions could have given him a nudge. Not Leela, though, in most situations, or … but then again, this inability to tell when he was being rude was really a trait of his current regeneration; he hadn't had this much trouble in the past, as far as he could remember. (Actually, he could tell when he was being rude more of the time than he let on. He just usually didn't bother about it.)

While he was musing this over in his mind, he was also trying to explain the misunderstanding to the guards (who were ignoring him) and cataloguing the cell they put him in. (He wondered what it was like to be human, a poor ape who could only follow one train of thought at a time. He'd done it for a while after the thing with the Chameleon Arch, but most of that experience felt rather … blurred, and he wasn't sure if that was how human thought felt or was the result of most of his consciousness being stored in a pocket watch instead of his head.)

"Hello," he said brightly to his fellow prisoners as the guards left. "I'm the Doctor." He bounced on his toes a few times, hands in his pockets. There was nothing quite so invigorating as a quick escape on foot (when the fate of the universe wasn't at stake, by preference) and it looked like a good bit of running for their lives was imminent. The cell was not bad, as cells went; relatively clean, no smells, and a nice padlock his sonic screwdriver could unlock in a jiffy whenever he decided it was time to leave. And neighbors to talk with, how lovely. If they were in for something as silly as he was, he'd have to take them along when he escaped. At least as far as the Stargate—this being a planet with Alteran technology, there was bound to be one somewhere.

"Doctor of what?" The human in the cell opposite his scowled. He was in early middle age, decently fit, and his eyes and mouth were edged with the beginnings of lines that didn't come from smiling. He spoke a North American dialect of English—Canadian?—translated by psychic implantation from the Stargate pattern buffer. And wore a uniform that looked suspiciously like it had been nicked from the set of a late-20th Century television science fiction set. He was eyeing the doctor suspiciously, crouched down among some gear—also suspiciously Earth-looking. Was that a laptop under that pack?

"Oh, this and that," the Doctor replied, bemused. Had he gotten his arrival time wrong, he wondered? Didn't think Earth-type humans were supposed to be out in other galaxies just yet. He reviewed the TARDIS' arrival for discrepancies while observing his surroundings, calculating the odds of a good thunderstorm or tornado from the changes in ambient temperature and air pressure since his arrival, and trying to get "London Bridge" unstuck from his head (what was it about human nursery rhymes?).

"'This and that?'" the human spluttered. "That's not possible. Doctorates are a very prestigious degree, given out after years of work in a particular field. You can't just decide you're smart and add it to your name—"

"Rodney," said one of his companions, an elegant Human woman dressed in the same uniform. She gave the Doctor a smile that managed to be apologetic and sincere while at the same time not dissociating herself from her companion. Really, it was a masterful bit of diplomacy. She probably needed to practice it often. "I am Teyla Emmagan, daughter of Tegan," she said. She used a Pegasus dialect with a typical matrilineal naming system and translation via Stargate thingamajigs; putting a non-Terran woman in their uniform was surprisingly open-minded for 20th Century Earth-humans. "This is Doctor Rodney McKay," she said, indicating the mouthy one, "and Ronon Dex."

The Human behind her—Ronon—gave a brief nod without saying anything. He was dressed more typically for a low-tech society, lots of leather, with thick dreads hanging down almost in front of his face. Must kill his neck—the doctor had never understood such fashion choices, but it wasn't as if humans were the only people with uncomfortable style.

"So, what brings you to the wonderful jails of KkThorymach?" the Doctor asked, making sure to hit the glottal stop at the end just right, hands in his pockets. He really ought to be springing them out of here soon, and it wouldn't do to spring them if they were, oh, axe-murderers or whatnot.

"We have come seeking Ancient technology," Teyla replied. "We had heard that the people of this world possessed a device which might provide power for a city or recharge other Ancient devices."

"Yes, they do have one," the Doctor said. "Right there in the temple, underneath the altar." Power was good; power sources (particularly ones used by advanced races like the Ancients) could be used for weapons, of course, but then so could most things if you were creative enough, and there were a lot of benign uses for power sources.

"We know," said the Earth-native sourly. "They let us get a good look at it before they threw us in here."

"The Thorymians believe that it was given to them by the Ancients for safe-keeping," Teyla said. "It is an object of much reverence to them, and they do not wish to see it fall into the wrong hands."

"They think any offworlder who touches it will 'desecrate' it by not kowtowing to it properly," McKay said scornfully.

"Can't imagine why they think that, McKay," Ronon said darkly.

"Oh, please, it's a piece of Ancient technology, not a holy relic."

"It is a holy relic to them, Rodney," Teyla said.

The Doctor sat back and watched them bicker among themselves. Entertainment, even—this jail had it all. Might not bother breaking out, just yet; it was rare that he got locked up when the fate of the world wasn't at stake, this was a lovely break, just what he needed. Wouldn't want to stick around too long, probably get bored, but nice for now.

Boots tramped in the hall outside; his companions in the cell across the way stopped bickering.

"Hello," the Doctor said to the guards as they came in. "Lovely jail you have here. Brilliant. Um, I don't suppose you've realized this was all just a misunderstanding and we're all free to go?" Probably wouldn't work, but you never knew.

"You will come with us," said the guard in front, pointing his spear at the Doctor through the bars of the cage while one of his friends sidled around and unlocked the padlock.

"Where are we going? Are you taking me to your leader?" The Doctor waved goodbye to his fellow prisoners as he was led out of the cell. They were probably safe enough for now, and he might be able to talk their way out of this.

John shifted uncomfortably, feeling the point of a spear at his back, and the baleful stare of the guard holding it. The guy was bigger and burlier than Ronon, and while John was fairly sure Ronon could take him in a fair fight, this guy could probably still cream him easily even without the spear.

John eyed the room he was in. It wasn't bad, as interrogation rooms went; clean, no instruments of torture laid out, no manacles or anything. Of course, they probably figured that with his friend Bubba with the spear behind him, they didn't need to tie him up. They were probably right.

He wondered what was taking them so long. Things had started out—well, not good, but at least they hadn't had him at spear-point. He would apologize for McKay, ask politely for permission to study the device, and the nice high priestess would counter with "sacrilege" and "offworlder" and the occasional "unbeliever," just for effect, and the whole thing would start over again. He was all about the wearing them down—if he didn't at least try, McKay would try to wear him down about it, and that just wouldn't be good.

Then one of the spear carriers rushed in and whispered something in the High Priestesses' ear, and her eyes had narrowed and John just knew something had happened (he just prayed it wasn't something his team had done). Bubba had come in and the priestess had left and here he was, wondering what was going on and wishing he dared use his radio to contact his team. They hadn't confiscated anything when they seized them, oddly enough, even the device McKay had been using to scan the Ancient thing in the temple, something about contamination and ritual purity. He hadn't been able to take any of it except the radio still in his hear with him from the cell they'd been tossed into, the guards had been pretty insistent about that.

The door opened and the Priestess swept in. "Here is the proof of your treachery, Colonel," she spat, stepping aside for the guards behind her to push a man inside.

John blinked. A suit and tie? Brown pinstripes? Converse? In Pegasus? That was a new one.

"Hello," the man said. "I'm the Doctor. What treachery?"

"Colonel John Sheppard," John replied automatically. "Doctor who?"

"Sheppard?" The man brightened. "Oh, right, that's what Earth-humans are doing in Pegasus. The Atlantis expedition! Nice to meet you. How is the old girl these days?"

"Do not pretend you don't know him," the priestess said sharply as John's eyes widened. "He is your compatriot, who tried to steal the Gift of the Ancestors to complete your desecration."

"Steal it? I wasn't trying to steal it, I was just looking!" the Doctor said.

"I've never seen him before in my life," John said. Though someone who could identify someone from Earth just by looking at them, and knew about the Atlantis Expedition—he really needed to find out what else this guy knew.

"Your lies will not save you," the priestess said. "The Ring of the Ancestors has not been used since your arrival. He came with you. You will all die for your treachery." She nodded to the guards and turned towards the door.

"I came by ship," the Doctor said. "Not Stargate."

"We weren't trying to steal or desecrate anything," John said, focusing on the immediate threat. "And if you just let us go, we'll never bother you again!"

Too late; the guards had followed her out and shut the door behind them. John could hear the lock snicking into place. The Doctor, still fairly near the door, examined it. He reached into his pocket and pulled out a small cylindrical device, metal, with a blue knob on one end. He waved it at the lock and the blue knob lit up.

John toggled his radio. "Okay, the nice high priestess has decided to kill us. Time to break out."

"We need to come get you out?" Ronon asked.

John lifted an eyebrow at the Doctor. "That thing open doors?"

"Piece of cake," the other man said. He jerked his head at the door. "There's a guard on the other side."

"Nah," John said to Ronon, "just meet us at the Stargate."

"We will see you there, John," Teyla said.

The channel closed, and John joined the Doctor at the door. "I'm ready when you are."

The Doctor pointed the device at the lock again; the end lit up blue and it started humming. Three seconds later, there was a quiet click. Once they got to safety, he'd have to see if they could negotiate for that little doohickey. The Doctor swung it open, and John stepped through, grabbing the guard and throwing him head-first into the wall. His head hit at an odd angle John hadn't anticipated, and there was a sickening crack of bones breaking. John leaned down and grabbed a knife out of its sheathe; he didn't know how to use a spear, so it was better not to burden himself with it.

"Did you have to do that?" the Doctor demanded, gesturing at the guard. "Couldn't just tie him up or something?"

"No time for that," John said shortly, starting off down the hall. The guy was only doing his job and John would have preferred not to have to do that, but at least this way the guy wasn't coming after them or spreading the alarm. "And they were going to kill us, remember? Better him than us or my team."

The Doctor fell in beside him, still complaining about his fighting. John mostly tuned him out, focusing on the escape and only listening something of importance in all the babble. It was a skill honed by years of working with McKay.

They'd made their way out of the building they'd been held in and were trying to find a way out of the Temple precinct other than the main (heavily guarded) gates, when the alarm went up. John heard running feet and ducked behind a stack of hay bales. The bales were conveniently stacked next to a building, providing cover on three sides—and the fourth was an alley little used, judging by the buildup of junk. The Doctor joined him, crouching down just barely in time. The space between the bales and the wall was big enough for the two of them, but not by much. Feet pounded past on the other side of the hay; John risked a glance around the edge just in time to see two guards disappear down the avenue leading to the main gate. He jerked back into cover as another pair of guards came into view, heading for the building across the square from them. "Looks like we're not getting out through the main gate," he said softly, hearing more feet run by on the other side of the hay, accompanied by general sounds of alarm.

"Probably right," the Doctor said cheerfully. What was with the guy? He seemed almost euphoric about being pursued by people who wanted to kill them. At least he was being quiet about it. "And the two guards posted across the street might be a small problem, too."

"Any suggestions?" John asked, not expecting any. His team had been held on the other side of a compound close to a small gate that probably hadn't even been guarded and had their weapons and equipment with them, so it was a pretty safe bet that they'd made it out. If they had, he'd tell them to get to the Stargate and call for a Puddlejumper filled with Marines. He doubted it was possible to escape the compound without help or weapons. The wall around the Temple grounds was fourteen feet tall, a smooth stone that wouldn't give them any handholds to climb and was too tall for them to stand on each others' shoulders. The main gate was too heavily guarded, and there wasn't enough cover to go skulking about looking for another way out, not with the alarm out.

"Actually, yes," the Doctor said. "As it happens, we should be able to get to my ship from here, once it's a bit darker. It's not far. If your friends can get out to the Stargate on their own, I can take you home that way."

"Sounds like a plan," John said. Better than sending in the Marines. Marines with P-90's outclassed guards with spears by a hell of a margin, but even guys with spears got lucky sometimes. And the fewer Thorymians who got hurt, the likelier it was Atlantis would be able to smooth things over later—the last thing they needed was more enemies. And if this guy did have a ship, he might become an ally against the Wraith, if they played this right, maybe have technology to share. At the very least, John might find out what he knew. At least that way they'd get something out of this mission. He turned on his radio. "Teyla, location," he said.

"We are outside the temple wall, and are making our way through the town," Teyla said. "So far, we have not encountered any serious difficulties. It will take us at least an hour to reach the Stargate."

John nodded, even though she couldn't see him. "Look, I'm still inside the walls, and they know we're gone; there are guards everywhere. But I'm with a guy calling himself a doctor who says he's got a ship we can get to once it gets darker. Get to the Stargate; call me when you're there."

"You sure?" Ronon said. "We could come back and get you—we've got the C4. Could blow a hole in the wall."

"Nah," John said, listening to all the activity in the courtyard. "Get back to Atlantis, let them know what's going on. Put the Marines—"

There were voices coming from the other side of the hay, probably less than ten feet away. John hoped they hadn't heard him; he'd been talking quietly and with all the ambient noise they were probably good.

"Sheppard!" Rodney yelled over the radio. John slapped a hand over his ear to trap the sound. "Sheppard, are you there? What's going on?"

John gritted his teeth, waiting, as Rodney worked himself into a panic. It took only a few minutes for them to move on, but a few minutes of listening to Rodney panic with no way to answer back felt like an eternity. At last he heard them moving off; he waited a few more minutes to be certain. "Sorry about that," he said as quietly as he could. "People within hearing distance. Can't talk. Go to Atlantis, I'll see you there."

"What? Wait, Sheppard, that's not—"

"We will check in with you every half hour," Teyla broke in. "One click on your radio for all is well, two for backup."

John clicked once.

"Say the word and we'll be back," Ronon said. "Good luck, Sheppard."

"Yeah, good luck," Rodney said.

John clicked once, and sat back to wait until it was dark enough to move.

The Doctor crouched in the cramped little space, listening to the ebb and flow of activity in the compound and watching his companion covertly. He knew all about the city of Atlantis, of course, had been there several times, both in its original incarnation as an Alteran city and as the Crown Jewel of Pegasus, centuries after that galaxy was freed from the Wraith. He'd sort of skipped the ten thousand years it'd spent on the bottom of an ocean (too boring), and he'd never popped in during the Atlantis Expedition's fight against the Wraith because they generally had things under control (and why Earth humans were better at protecting a foreign galaxy from alien threats than their own home planet he had no clue, but there you were). Might be interesting to drop by, say hello, see what the City was up to. She wasn't as smart or as aware as the TARDIS, of course, but that wasn't her fault poor thing. And ten thousand years on the bottom of an ocean with no other cities or ships to talk to couldn't have helped. Maybe that's what the TARDIS wanted, though if that were the case he didn't know why she hadn't just dropped them in Atlantis; the Earth team certainly hadn't needed his help to escape.

He stifled a sigh. Waiting was so tedious. Still, the chances of them making the TARDIS would be much better in about forty-five minutes. Time Lords couldn't see the future, of course (and wouldn't that be boring), but they could see possibilities and probabilities. Shapes, patterns, percentages: it was much easier to be in the right place at the right time if you knew what the right time was, even if you didn't know why it was the right time. He'd never tried explaining it to a human; he wasn't a prophet or a god or omniscient or precognitive or any of the categories humans came up with to explain the unexplainable. He was a Time Lord. Right now that meant staying here long enough for the excitement to die down a little but not long enough for someone to decide to search the compound. The Doctor would know what the right time was. He always did.

Didn't make the waiting any more fun, though.

Colonel Sheppard looked just as bored as the Doctor. Crouching in this cramped little space, staring at nothing, idly tracing circles in the dust.

Except … those weren't just circles. To a human, they would look so, but humans generally didn't have the spacial or geometric awareness to even read Gallifreyan script, much less write it out free-hand as the Colonel was doing. "Family," he wrote, and "safe" and "home," all in the tense that meant both "future probability" and "hope." He didn't even seem to be aware he was doing it.

Could Sheppard be another survivor of the Time War, hiding as a human until the temporal shockwaves resulting from the destruction of Gallifrey and all its people dissipated and it was safe? Was the Doctor not alone, after all, even with the Master's final death? Highly improbable, but discovering the Master had been astronomically unlikely, so why couldn't lightning strike twice? His hearts began to pound—one even skipped a beat before falling back into synch with the other. He reached out with his mind—Time Lords weren't telepathic, not in the sense humans normally meant, but he could feel the workings of a Time Lord mind, and yes, now that he knew what to look for the Doctor could see traces, the remnants left behind by a chameleon arch. Young, very young, not someone he knew, but Gallifreyan none the less. Possibilities spun out before the Doctor's eyes, not all good but still more than he'd had since Gallifrey burned, more even than when he'd realized Doctor Yana must be the Master, because he knew the Master of old and knew how very much evil the Master could do if he chose, knew he could never truly trust him.

The Doctor opened his mouth to speak, to turn probabilities into reality, but heard the tramping of feet again in the courtyard. Now was not the time.

It was going to be a very long three-quarters of an hour.

Finally, finally, the time passed and it was as safe to go as it would ever be. The Doctor turned to Sheppard and opened his mouth.

"'Bout time to go," Sheppard said. "Where's your ship?"

The Doctor closed his mouth. Right. Even as a human, some remnant of a Time Lord's perception remained; his time as John Smith had taught him that. "It's parked behind the north temple annex, looks like a blue box."

"And nobody's noticed it in all the running around?" Sheppard asked, raising an eyebrow.

"It's got a perception filter. Makes people not notice it, usually, unless they're looking for it," the Doctor said.

"Really," Sheppard said, sounding impressed. "Sounds handy. McKay would love that." He gestured to the narrow exit from their hiding spot. "After you."

The Doctor nodded and took a peek around the corner; there was no one within sight, so he stepped out and began walking briskly across the square. He could hear Sheppard following him.

As the neared the right street, the Doctor slowed, allowing Sheppard to take the lead so he could watch him. It would take them several minutes to cross the compound, more if they tried to avoid areas people were likely to be, and he wanted to watch Sheppard, hungry for the sight of one of his own kind.

It was a beautiful thing to watch—Sheppard walked surely between buildings and across streets, always stopping or speeding up just in time to keep them out of sight of guards, priests, priestesses, servants, anyone wandering around. Some of it was training; the military stamp was plain to see in his movements. But there was something more, as well: the awareness of a Time Lord, there for anyone to see. Maybe that was why the Atlantis Expedition had survived for so long, led by one who could see the flapping of butterfly wings.

John kept up a steady pace as he and the Doctor made their way across the compound. Not too fast, not too slow, just enough purpose that people would assume they had some business somewhere and dismiss them if they caught a glimpse in the dim light. John would stand out, but the Doctor's brown coat might pass for a priest's robe.

They were getting close; John was about to ask the Doctor where his blue box was, when he felt a prickling at the back of his neck. He broke into a run, knowing they were out of time. An alley crossed the street up ahead; John ducked down the right without having to ask. A shout went up behind them as he turned the corner, the Doctor at his heels, and if he'd had the breath he'd have sworn. The alley dead-ended in a small open area between buildings; the shout had drawn attention, and people were spilling out of one of them as they came out of the alley. There was the blue box, up ahead, and John really hoped it had some kick-ass engines or weapons, because it barely looked big enough for one person much less two, and it certainly didn't look like a spaceship.

The Doctor sprinted ahead of him, and John followed, dodging Thorymians—thankfully, none were armed, and none seemed to really know what to do. The Doctor got the box's door open and darted inside. John ducked as he entered; a rock flew over his head, barely missing him. He heard the door slam behind him, and stopped, taking a good look around.

It was bigger than it had looked from the outside. Given the dimensions of the small courtyard, it probably was bigger on the inside than it was outside. And it looked suitably alien, and vastly different from any technology John was familiar with, Human, Ancient, or Wraith, and it didn't look anything like the descriptions of Goa'uld or Asgard or Ori ships in the reports Stargate Command periodically sent.

Two thoughts warred for attention. The first was that they may have just stumbled upon the most useful ally in this galaxy. The second was how cool this ship was--McKay was going to love it. John couldn't wait to show him.

"It's bigger on the inside," the Doctor said, bouncing on his toes.

"I noticed," John said dryly.

The Doctor frowned. "Well? Don't you have any questions about how it works?"

"Not really." John shrugged. "I'm sure McKay will, when we get back to Atlantis. Speaking of which. …" He waved at the only thing resembling controls in the room, a console standing in the middle of the room, covered in knobs and dials and buttons.

"Oh! Right," the Doctor said, darting over and working a few controls. "There! We're not on KkThorymach any more."

"That's great, Doc," Sheppard said. "Now you can drop me off on the nearest planet with a Stargate, and I can call home from there. Maybe we can get McKay out, show him your ship—he'll have all the questions you want. More questions than you want, probably. And I'm sure Teyla and Ronon would love to thank you for rescuing me." Not that they'd needed the help, but it was a good pretext for keeping lines of communication open.

The Doctor waved a hand. "Oh, I'll drop you off on Atlantis when we're done talking if that's what you want, don't worry about that."

Sheppard tensed, hoping the Doctor just didn't know Atlantis wasn't on Lantia anymore. Otherwise, they had a bigger security breach than he'd thought. "What do you want to talk about?" he asked warily.

"Tell me about yourself, your life. What's the first thing you remember?"

"Why?" Sheppard asked.

"Humor me. It's important." The Doctor's face had lost its normal humor, but he didn't seem dangerous.

John couldn't think of anything it might hurt. "My dad gave me a pony for my fourth birthday. He and mom argued over whether I was old enough for my own pony."

"Parents—do you mean adopted parents?" the Doctor asked.

"No," John said. "My real parents, Patrick and Lisa Sheppard."

The Doctor frowned. "No chance you were adopted? Found wandering alone, perhaps, and taken in?"

"No," John said. "I have my Mom's eyes and my Dad's laugh, and there are pictures of Mom holding me in the delivery room. Why do you ask?"

The Doctor hesitated. "I'm not Human. I'm a Time Lord—I have two hearts, a respiratory bypass system, other assorted physiological differences from Humans or Alterans, the ones you call Ancients. I'm over nine hundred years old. I'm from a planet called Gallifrey."

"That's nice," John said, wishing Teyla was there. First contact always went so much more smoothly when she was present, and from the looks of this ship this was a contact they wanted to go well. "What does it have to do with me not being adopted?"

The Doctor looked away, staring off into space. "There was a war, a Time War. Gallifrey burned—there's nothing and no one left, I'm the only survivor." He paused. His face was set, and hard, and it was difficult to remember the man who'd been cheerful even in a holding cell just a few hours earlier. "Gallifrey wasn't just destroyed. It was wiped out of history. It never existed, and neither did any Gallifreyan, other than me." He took two steps closer to John, looked him straight in the eye. "But we could make ourselves not-Gallifreyan. We had a device, a Chameleon Arch, that could take the Time Lord essence out of us, mind and body both, and turn us Human while our essence was safely stored away."

John could hardly remember to breathe, the Doctor's stare was so intense.

"If someone was human when Gallifrey was destroyed, they could survive. The natural paradox would protect them."

"And you think that happened to me?" John said skeptically.

"I know it did." The Doctor held up a hand to silence him when he opened his mouth to protest further. "Can you feel planets move under your feet, as they spin through space? Can you see lines of probability stretching into the future, even if you don't know what they mean or what's going to happen?"

John's jaw clenched. How could he know? John had been twelve before he realized most people couldn't see the likelihood of all the potential futures of each second, and fifteen before he realized that most people couldn't feel the Earth's rotation. "Look, Doc, I'm sorry for your loss, but surely someone would have noticed by now—I've had just about every type of medical exam known to Earth and quite a few that aren't. Believe me, someone would have caught it by now. And like I said, I grew up on Earth with human parents." He would have known if he wasn't human. Even if only in dreams, he would have known. He would have.

"The Chameleon Arch is very good at its job," the Doctor said stubbornly.

"I already have one type of alien DNA in me," John protested. "Now you're trying to tell me I have two?"

"Alien DNA?" The Doctor frowned.

"I have the Ancient gene," John explained, "the one that activates and controls their technology. I have a very strong instance of it—that's why I was assigned to the Atlantis Expedition in the first place."

"Oh, right," the Doctor said. "I'd almost forgotten about that. The Alterans admired the Time Lords—we were older, more powerful, greater science and knowledge, had senses they lacked." He started pacing around the room, hands waving. "They were trying to influence their own evolution, doing some genetic tinkering—bit of a fad at the time, the Asgard and the Nox were doing it too—and they asked for permission to splice a little bit of Time Lord DNA in as part of the general upgrade." He stopped and lowered his voice confidentially. "Caused a lot of debate when the President authored it, Gallifrey was nothing if not insular and isolationist. But since there are some humans who have it through their descent from the Alterans, the Chameleon Arch wouldn't have taken it out."

"But there are humans who have it," John countered. "Why are you so sure I'm a Time Lord in hiding? Sounds like wishful thinking to me." Actually, it sounded a little insane to him, but he'd seen and heard weirder things in the Pegasus Galaxy (if not many), and the man did have a really cool alien space ship to back him up.

"When we were hiding, you were writing in the dirt," the Doctor said. "Not even aware you were doing it. You were using Gallifreyan script."

"I was not," Sheppard protested. "I would have known if I was. And I'd know if I was an alien, too."

"No, you wouldn't," the Doctor said. "The whole idea of the Chameleon Arch is to make you blend in, and that's easiest if you don't realize that you're different. It takes the bits of your personality and memories most like the time and place you're trying to fit in," he made a gesture that was either really obscene or a pantomime of trying to put a square peg into a round hole, "and shoves the rest down in your subconscious and the device holding your Time Lordiness."

"See, there you go," John said, stubbornly. Finally! Some way to prove it couldn't be true. "I don't have an alien device like that." He smiled cheerfully, hoping the Doctor would take his defeat good-naturedly.

"They're camouflaged, too," the Doctor said.

He darted away for a few seconds, and Sheppard was relieved. It was getting harder to make himself believe the Doctor couldn't possibly be right. Too much of this was striking a chord.

"Here," the Doctor said triumphantly, coming back. "D'you have a watch like this? Or, really, anything like this?" He held a pocket watch in his outstretched hand, warm metal with concentric circles etched in a familiar pattern.

John's mouth went dry. Surely he was seeing things. He took the watch from the Doctor's outstretched hand, turned it over, rubbed his fingers over the design. "I have a locket," he said. "It looks just like that. That same etching on the cover. Mom … Mom gave it to me, before she died. Told me to keep it safe, keep it near me, because it was an important family heirloom."

"There you have it," the Doctor said, bouncing on his toes again. "Where is it?" He bounded over to the control console, turned to stare at John over the top of his glasses.

"A safe deposit box," John said numbly. "I wasn't about to take it into a war zone."

"Let's go pick it up, shall we? Where's the deposit box?"

"What? No!" John shook his head. "I have to get back to Atlantis before they miss me."

"I did mention I'm a Time Lord, right?" the Doctor said impatiently. "This isn't just a spaceship. It travels in time too, you know. I can have you back on Atlantis before your friends, even if we took six months to explore the galaxy in between. Or longer."

"I still want to go back to Atlantis," John said stubbornly. Even if the Doctor was right, he wanted Doctor Keller to take a look at everything first. And he wasn't doing anything with a locket of potentially alien (non-human) technology without McKay checking it out. If he believed the Doctor's story. He tried to tell himself he didn't.

"Don't you want to be whole again?" the Doctor asked incredulously. "All of yourself in one body again? Don't you want to know what happened, how you came to be on Earth?"

"What would happen to me?" John asked. "Would I be changed?"

"Well, obviously," the Doctor said. "You'd be a different species. A Time Lord." He bounced on his toes a little, as if being a Time Lord were the coolest thing in the world.

If there was one thing Pegasus had taught John, it was that things were never that simple. "What about my personality? Would that change?"

"Yes," the Doctor said. "All the things that were stripped out to make a 20th Century Earth Human would be added back in. And any little flourishes that had been put in to make you blend in would be stripped out—but probably not completely, you've lived with them for so long."

"I wouldn't be the same person, then," John said. "Why would I want to do that?"

"But you'd be whole again," the Doctor protested. "Why wouldn't you?"

"I'm whole now," John said. He folded his arms. "I don't want to change. I have a job I love, friends, a place I belong—something I didn't even know I was missing until I came to Atlantis. If I became something else, I'd have to give that up. And it sounds like you can't offer me a place to belong as a Time Lord, even if I wanted to."

The Doctor's face fell. He looked old, and sad, and very tired. "You'd live longer, as a Time Lord. You'd be smarter, have senses you don't have now. I could take you across the universe, through time and space, show you things you've never dreamed of."

"If I've never dreamed of them, I won't miss them," John said as gently as he could. "And what's the use of living a thousand years if you outlive all your friends, everyone you know?"

The Doctor flinched and turned away. "There's nothing I can say to convince you?"

"No," John said.

"All right." The Doctor stood for a few seconds, head bowed, before inhaling sharply. "Well! Lots of things to do, and I know you want to get back to Atlantis and make sure your friends got back all right. Off we go." He began moving around the console with a brittle kind of grace, as if he would shatter once he stopped moving. It only took a few minutes. "Here we are, Atlantis, the Lost City, currently home to an expedition from Earth."

He hadn't looked at John the whole time. It was a relief. John walked to the door. "You know," he said slowly, feeling he had to offer the Doctor something, "just because I'm not coming with you doesn't mean you can't stay. At least for a while. I mean, I'm sure Sam and McKay would love to hear more about Gallifrey, and you could be a lot of help fighting the Wraith."

"I've done enough fighting for a dozen lifetimes," the Doctor said, voice low. He began fiddling with the controls in front of him. "And I have places to go, people to see. You'll do all right with the Wraith, though," he said, raising his head and flashing a big smile. "Don't need my help with that."

John opened his mouth to ask how, but the Doctor cut him off. "Time Lord," he said. "In a time-traveling ship. I've seen Atlantis, after the Wraith are gone. Beautiful city." He ducked his head back down.

"She is at that," John said. He waited a bit, but the Doctor didn't seem to be paying attention to him any longer. He put his hand on the door.

"Sheppard?"

John turned around. "Yeah?"

The Doctor still wasn't looking at him. "That locket—if you ever change your mind, just open it and look into it. It'll do the rest. And I'll know."

"Okay," John said. He waited for a few seconds, but the Doctor said nothing more and never looked up. John walked out the door, and found himself standing in a corridor in Atlantis. A mechanical wheezing sound filled the air, and he turned around to watch the blue box disappear.

"John?" Sam said from behind him. "What's going on?"

"Sam," he said, facing her. "I just got back from KkThorymach. Has my team made it back yet?"

"John, you haven't left yet," Sam said, frowning. "And what was that thing that just disappeared?"

"That was the time ship of the guy who gave me a lift," John said. "Things didn't go so well, and I got separated from my team. The guy I was escaping with offered to give me a lift home in his time ship, said I'd be home before they were. Guess he over-shot it a little." He shrugged.

"I see," Sam said. "Well. That's one mission debriefing I'll be interested to hear." She paused. "How bad was the mission?"

"All things considered, not that bad," John said.

Sam nodded. "Then I'll just … go down to the control room to see your team off to KkThorymach on schedule, to avoid a paradox. You go down to see Doctor Keller, have her check you out, okay? Make sure you don't meet yourself on the way."

"Right." John nodded, and headed off towards the Infirmary.

The Doctor stood by the control console, head bowed, listening to the silence of the TARDIS. He loved the old girl. It was nice, just the two of them together, exploring.

Granathia II. Poethon. He reached out to start the TARDIS moving.

John leaned back on the couch. "No, Rodney, I don't know how it worked, he didn't exactly give me a tour or anything. The controls looked kind of jerry-rigged, though, from what little I saw."

"Well, if his civilization was wiped from history, it's not like he can go home for spare parts, I suppose," Rodney said.

"He must be very lonely," Teyla said. "But I am glad you have chosen to remain yourself. There will be plenty of time later if you wish to change your mind, if his species is as long lived as he says.

"Think he'll be back?" Ronon asked.

John hesitated. "I don't know. Wouldn't mind if he did, wouldn't be disappointed if he didn't."

He took a drink from his glass, enjoying the discussion as his team started debating the likelihood of the Doctor's return. No, he wouldn't give up his team for anything.

He frowned, listening intently. Was that the wheezing of the Doctor's ship he heard?

He shook his head. Nah. Couldn't be.