Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

The Phantom of Atlantis

As Elizabeth dumped her bag in a room that could best be described as an office, located a short distance from what appeared to be the main control room for the city, she was only slightly annoyed when her radio activated; as expedition leader, she should have known she wouldn't be allowed much opportunity to have some time to herself before people started calling her about what they'd found.

"Doctor Weir," an excited voice said on the other end of the radio, "you have to come and see this!"

As she pulled the radio off her belt once again, Elizabeth briefly allowed herself to wonder why she'd agreed to something as demanding as this, before she reminded herself that she'd wanted to learn more about the Ancients and this was the only way to do so; the sheer range of discoveries made so far just helped to reinforce why she'd come this far in the first place.

"I have a lot of things to see," she said, trying to make it clear that she was interested in whatever they'd found even as she walked back towards the control room to attend to more immediate matters. "Just be careful."

As she walked into the control room, she instantly turned her attention to McKay as he studied the console before him uncertainly, clearly puzzled at something that Elizabeth couldn't immediately make out.

"Something wrong, Doctor McKay?" she asked, walking over to stand beside the scientist as he curiously studied the control panel before him.

"I'm not… sure, really," McKay admitted as he turned back to look at her, confusion clear on his face. "I mean… well, look at this," he continued, indicating the console before them. Elizabeth noticed that there were several triangular buttons on the console that each featured what appeared to be constellations, much like those on the DHDs in the Milky Way galaxy, making it relatively easy to deduce what this console was for.

"I have to admit, I don't see the problem," she admitted apologetically as she turned to look at her head scientist. "I mean, it's different from the DHDs that we've seen back home-"

"It's not the appearance that's the issue; it's… well, feel it," McKay said, grabbing her wrist and placing it on the console. For a moment, Elizabeth didn't realise what the problem was, and then her eyes widened as the reason hit her.

"It's… warm?" she said, looking inquiringly at McKay for confirmation that she'd noticed what he wanted her to notice.

"Exactly," McKay confirmed, nodding at her. "From what I know of DHDs, they're generally just the temperature of whatever planet they're on unless they've been in recent use and the crystals have been energised; in other words, since this thing isn't meant to have been used for the last fewmillenia, itshould be as cool as everything else here. Since it's warm, that implies that it was used recently, and since just us dialling in wouldn't have required this DHD to do anything…"

"Someone recently used it at this end…" Elizabeth whispered, the implications of that fact instantly hitting her.

Somebody had recently used the DHD in Atlantis- used it so recently, in fact, that the naquadah generator that powered the DHD had yet to cool off.

Therefore, somebody had recently been in Atlantis very shortly before they'd arrived.

Therefore, somebody was still living in Atlantis, and may have recently left the city expecting to be able to return.

In other words, Elizabeth mused to herself as she reflected in more detail on what she'd just discovered, Atlantis may not be as uninhabited as we thought it was when we came here.


AN: I have no idea if the above information about the DHDs generating heat when used is even close to being the case, but since it doesn't actively contradict anything we've learned about DHDs in the show, and I need it for the first clues to be provided to the expedition members that there's more going on they know, just assume it is
Before she could ask McKay for any further ideas regarding the possible implications of the DHD being recently active, Elizabeth's radio activated once again, forcing her to focus on more immediate matters.

"Doctor Weir; Colonel Sumner," the voice at the other end of the radio said. "Can you come down and meet me, please? We're three levels down from you."

"On my way," Elizabeth said briefly, before she put the radio back on her belt and glanced over at McKay. "If you come up with anything about your discovery that could help us work out the why of it, let me know as soon as possible; until then, keep quiet about it to avoid panic."

For a moment McKay looked like he was about to protest, but he nevertheless nodded in quiet understanding.

So far, they had no real evidence that Atlantis might have other inhabitants beyond the fact that the DHD was warmer than the rest of the city; there could have been all kinds of alternative explanations for it being warm that hadn't occurred to either of them yet. If they told Sumner or anyone else about the DHD being active before they'd spent any time trying to find out whether there could be another explanation, they ran the risk of starting off a city-wide panic before they even fully knew the situation they were dealing with.

"See what else you can find out," she said, nodding briefly at her head scientist before she turned towards the stairs leading towards Sumner's current location.


A few minutes later, she had rendezvoused with Sumner a few levels down from the main control room, the man looking at her with a relatively neutral expression even as he continued to hold on to his gun.

"Only been able to secure a fraction of this place," he said, responding to Elizabeth's first question before she could even ask it, turning to walk away from her even as he beckoned her to follow him with a brief jerk of his head. "It's huge."

"So it might really be the city of Atlantis?" Elizabeth asked, looking curiously at the commander of her military division as she walked along after him, wondering what he wanted to show her.

"I'd say that's a good bet," Sumner replied, without elaborating. For a moment Elizabeth was going to ask him what he meant by that, but then she saw what lay immediately before her and all further questions were driven out of her mind.

"Oh my God…" she said, her eyes wide with awe as she walked towards the sight before her. It was a window that looked out from the tower they were currently in- and it had to be a tower; it was too tall to be anything else- to reveal a vast city structure laid out before them. Another tower was immediately visible in front of the window, apparently about as tall as the one they were currently standing it, and an assortment of other buildings were positioned around it, each one of varying height.

What really stood out about the view, however, was the ocean surface just visible far above the peak of even the tallest tower that Elizabeth could currently see, as well as all the water spread out before them.

"We're under water…" she breathed softly, almost unable to believe what she was looking at.

"I'd say we're under several hundred feet of ocean," Sumner confirmed, his tone sounding far more grim than Elizabeth's ashe looked up at where the sunlight was only just visible above their heads. "Can't dial out, this could be a problem…"

Before he could say anything more on that topic, the sound of running feet reached Elizabeth's ears, followed closely by the sound of Rodney McKay's voice.

"Colonel, Dr. Weir!" he began, as he hurried towards them. "You need to hear this; we're underwater, but there's some kind of a force field holding back the wa…"

His voice trailed off as he took in the window before him, his pace slowing as he walked over to stand beside them.

"Boy," he said finally, "that is impressive, isn't it?"

After a moment's silence as the three of them took in the sight before them, McKay spoke up once more.

"Uh…" he said, turning back to look at Elizabeth, gesturing back in the direction he'd just come as he spoke, "Doctor Beckett has, uh, found something you should see."

Taking one last opportunity to take in the sight before her, Elizabeth turned to follow McKay towards whatever Beckett had discovered, Sumner close behind him. After a brief walk through the corridors of the city, the three of them arrived in a large, circular room, with Beckett standing on a platform as he faced the glowing form of a woman, slightly transparent, who was currently talking to him.

"It's a hologram," Beckett said by way of explanation, glancing over at the three new arrivals as they entered the room with a slight smile on his face. "The recording loops; this is my second time through."

"What have we missed?" Sumner asked, raising an inquiring eyebrow as he studied the holographic woman in the centre of the room.

"Not much," Beckett replied briefly, before the group focused their attention back on the hologram before them, just as what appeared to be a vast 'map' of the galaxy appeared above them (Briefly, Elizabeth wondered how the figure could be speaking English when this system had been created thousands of years before the language had developed, but shrugged the thought off soon enough; it wasn't exactly impossible to assume that Ancient technology included some kind of translation program that automatically adapted this system to narrate information in a language that those watching it could understand).

"In time," the woman said, drawing Elizabeth's attention back to the image before her, "a thousand worlds bore the fruit of life in this form. Then one day our people stepped foot on a dark world where a terrible enemy slept. Never before had we encountered beings with powers that rivalled our own."

Elizabeth definitely didn't like the sound of that; the Ancients were generally seen as the most technologically advanced form of life in the known universe prior to their Ascension. If something existed here that could equal them, if not surpass them completely…

Elizabeth wouldn't like to face something that dangerous in a fight, that was for sure.

"In our over-confidence," the holographic woman continued, "we were unprepared and outnumbered. The enemy fed upon defenseless human worlds like a great Scourge until finally only Atlantis remained. This city's great shield was powerful enough to withstand their terrible weapons but here we were besieged for many years in an offer to save the last of our kind we submerged our great city into the ocean. The Atlantis Stargate was the one and only link back to Earth from this Galaxy, and those who remained used it to return to that world that was once home. There the last survivors of Atlantis lived out the remainder of their lives. This city was left to slumber, in the hope that our kind would one day return."

As Beckett stepped down from the platform, the hologram vanished, leaving the expedition members to look around at each other as they took in what they'd just learned.

"Huh," McKay said after a moment's pause. "So the story of Atlantis is true; a great city that sank in the ocean."

"It just didn't happen on Earth," Beckett added.

"Well," McKay said, nodding thoughtfully as he reflected on the implications of their new discovery, "the ancient Greeks must've heard it from one of the surviving ancients."

"I don't like to think they got their asses kicked," Sumner commented, as he glanced over at Elizabeth, this voicing of her thoughts briefly distracting her from the technician that had just hurried into the room to talk to McKay.

"Let's hear it again from the beginning," Beckett said, moving to stand on the platform once again, watching as the woman appeared before them once again…

"Stop!" McKay yelled, looking sharply up at the doctor. "Turn it off."

As Beckett stepped off the platform, Elizabeth and Sumner turned to look inquiringly at McKay.

"Is there a problem?" Elizabeth asked, looking inquiringly at McKay.

"Well… you could say that," McKay said, looking slightly uncertain as he looked at the other people in the room. "My team's been running scans of the city, and so far we've only detected a single Zero Point Module in working condition. It looks like it's got a decent amount of power left in it, from what we can tell, but since we can't detect any more…"

"We've got no way of knowing how long it could sustain us under these conditions, right?" Elizabeth asked, looking at McKay for clarification.

"Exactly," McKay confirmed, nodding briefly at the base's commander as he headed for the door of the room. "I'm heading back to the control room; I might spot something that the rest of the team missed…"


"So you're saying that the only other ZPMs here are depleted?" Sumner asked, looking critically at McKay after the scientist had revealed his findings to them a few minutes later. "We're almost certainly light-years away from anything else the Ancients built in this galaxy, and the only source of power we have is what's connected to the power drive right now?"

"Hey, I'm as confused about it as you are; maybe they didn't want to risk the city being damaged from the potential explosion if something went wrong with the spares, so they kept them somewhere off-world or something like that," McKay retorted, snapping briefly at the expedition's military leader before he sighed and leant against the wall, holding his head in one hand. "I just wish I knew what I was missing here; the numbers just don't work…"

Glancing over at Sumner, Elizabeth was relieved to see that she wasn't the only one who didn't know what McKay had meant by that last statement; he was clearly as confused as she was.

"'The numbers don't work'?" she repeated, looking inquiringly at McKay. "What numbers?"

"Well, look at the situation here," McKay explained as he turned to look at her. "The city is meant to be powered by three Zero Point Modules when operating at full capacity; based on what we learnt in the holographic chamber, it would seem that the Ancients left Atlantis just as it was at the time, with the ZPMs remaining 'plugged in'- for lack of a better term- in case they ever wanted to return. Obviously, they never actually did return, but the reason is still obvious nevertheless..."

"Obviously," Elizabeth said, waving a hand in a prompting manner as she looked inquiringly at McKay. "So… what?"

"So," McKay said, looking critically at Elizabeth as he spoke, "if nobody's been here since the Ancients left, how is it that our teams have found three depleted Zero Point Modules lying around, and one connected up to the main power supply that's still almost at twenty-five percent of its full potential power capacity?"

Elizabeth blinked.

She had to admit, the implications there definitely weren't promising…

"You think somebody's been here since the Ancients left the city?" Sumner asked, looking critically at McKay as he spoke.

"I'm sure of it," McKay confirmed, nodding resolutely at Elizabeth as he turned to look at her. "There's no sign that they're here now, of course, but if they return…"

Sumner sighed slightly as he turned to look at Elizabeth.

"Doctor Weir," he said, already looking slightly apologetic before he'd even said what he was about to say, "under these circumstances, I feel it would be best to send the majority of the expedition members back to Earth until we can better ascertain the current status of Atlantis. Doctor McKay-"

"Can't do that," McKay said bluntly.

After a moment's stunned silence, Sumner turned to glare pointedly at McKay.

"I believe I just gave you an order, Doctor-" he began.

"An order I would be glad to obey, were it not for the fact that we can't go back to Earth," McKay interjected.

"What?" Elizabeth said, staring at the scientist in ever-growing confusion. "We have a ZPM-"

"We already tried to dial Earth when we realised we had the power to do so," the technician from the hologram room- Elizabeth vaguely remembered that his name was Peter Grodin; she'd tried to memories the names of the expedition when she'd picked out the teams, but it was hard to recall everyone specifically given the sheer scale of people who'd been assigned to the task- said, dialling the gate as he spoke. "We managed to enter Earth's address into the Stargate easily enough, but when the wormhole actually connected…"

As soon as the eighth chevron had connected, the wormhole activated, only for the traditional 'Kawoosh' of energy to be contained by some kind of… the only term Elizabeth could come up with was 'force field'… over the Stargate, preventing the typical 'explosion' and rendering the 'gate virtually useless.

"It looks like the Iris on the Earth 'gate," Sumner commented, as he studied the Stargate before turning to look at Grodin. "Any ideas what's causing it to turn on?"

"As far as we've been able to determine, it's like… well, it's like someone programmed the DHD to activate that force field in the event of someone attempting to dial Earth or any other address in the Milky Way galaxy; when I tried to dial some of our allies, such as Langara and Hebridia, the shield still came up," Grodin replied, looking apologetically at the Colonel as though he was expecting the man to shoot the messenger. "We tried dialling a couple of the addresses from the Ancient database that are located in this galaxy, and the wormhole connected without the shield being activated, but it always activates when Earth's dialled. I tried shutting it down, but the system seems to be protected by a password of some kind, and, given my limited knowledge of the Ancient language, I thought it best not to try and crack it at the moment; I don't think they would have installed anything too damaging in the event of an incorrect password being entered, but I'm not going to risk it yet."

"Did you try sending a message through to the SGC to ask for some suggestions about shutting the shield down?" Elizabeth asked. As much a she'd tried to recruit the best for this expedition, she still regretted having been unable to recruit Doctor Jackson and Colonel Carter from SG-1; their knowledge of Ancient culture and science would have been a significant asset to have on-hand for a situation like this, but if they could just send a message through the Stargate...

Unfortunately, Grodin swiftly dispelled that hope with a shake of his head. "That was the first thing we thought of, but it didn't seem to work; the shield seems to serve to block our transmissions as well as us ourselves. Not only can we not travel back to Earth, we can't even send them a message to let them know what's going on here."

"Is that the way it's designed?" Sumner asked, looking anxiously at Grodin. Elizabeth couldn't blame him; if they couldn't receive signals through the shield when it was raised, they'd have no way of knowing if the wormhole was from one of their teams or somebody else, which would render them vulnerable to enemy infiltration.

"Fortunately, it just seems to be something else that happens when Earth's dialled," Grodin replied, prompting a slight sigh of relief "We sent a MALP through the Stargate to one of the first planets in the Ancient database and we could receive the signal fine with the shield up or down. It would appear that, as far as we can tell, somebody seemed to want to guarantee that Atlantis wouldn't be able to contact Earth in particular, whether it be as a result of physically going through the Stargate or transmitting a message; maybe they wanted to avoid someone sending a computer virus through or something like that."

"Not meaning to poke any holes in your theories," Doctor Beckett said, raising a hand slightly as he looked around the room at the others, "but if that's the case, how were we able to get here in the first place? I mean, if this wormhole activates whenever Earth's dialled…"

McKay shrugged.

"Best guess, whoever set this thing up had no problem with people coming here from Earth because they knew there'd be no danger in that direction; they just wanted to stop people from going from here to Earth to prevent… something," he said, raising his hands defensively as Sumner glared at him. "Hey, I'm a physicist, not a psychiatrist; how am I supposed to know why people would do something like this?"

"OK, so going back to Earth isn't an option; maybe we could try relocating the majority of the expedition to somewhere in this galaxy?" Elizabeth asked. "If there actually is someone living here, it might at least be worth while seeing if they'd be willing to permit some of us to remain to conduct research; maybe we can find a planet out there that would be willing to provide us with somewhere to stay until we make contact?"

For a moment Sumner simply stared silently at her as she stood before him, until he finally nodded in confirmation.

"Agreed," he said simply, before raising a hand to touch his radio. "Security teams one and two, rendezvous in the gateroom; we'll be going through in a few minutes."

Even as the colonel issued the orders, however, Elizabeth couldn't help but wonder if they were taking the right course of action.

Admittedly, their inability to contact Earth was frustrating to say the least, but the fact remained; whoever had done that had almost certainly had Earth's best interests at heart, if he was willing to go to that much effort to stop someone at this end from accessing it.

The question she most wanted to know the answer to right now was, if someone had rendered the Atlantis Stargate incapable of allowing the user to travel to Earth to try and keep Earth safe, what had they been trying to keep Earth safe from…?