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

"The Wraith are after Earth?" Sumner said, his expression grim as he looked at Elizabeth where he sat opposite her in the conference room the next morning; McKay and his small team had already left via puddle jumper for the satellite, but Elizabeth had gathered the remaining department heads to fill them in on her latest 'revelation'.

"They're after access to Earth, at any rate; if they can get access to our Stargate and its control crystal, dialling Earth from there would hardly be that difficult," Elizabeth explained, looking around at the rest of the people in the room while trying to give off an appearance of at least slight uncertainty; she had to look like she wasn't certain about what she was telling them in case they started to think she had been told this by someone rather than coming up with it on her own. "We already know that the Wraith have at least some psychic abilities; with that in mind, it seems likely that they acquired at least some information about Earth's location when they were interrogating Captain Gemmel."

"Couldn't the Wraith just be after Atlantis for the technology?" Lieutenant Ford put in, looking uncertainly at Elizabeth. "I mean, no offence meant, Doctor Weir- your theory's an interesting idea-, but there is some pretty impressive stuff here…"

"Most of which the Wraith are incapable of using due to their lack of the Ancient gene," Zelenka added, looking critically over at the young lieutenant. "Much of the technology that the Wraith might find useful is specifically encoded to render them incapable of so much as turning it on, and what is left is- from what we have been able to establish about their technological capabilities- nothing the Wraith would want or need. Doctor Weir's theory seems to be correct; the only real reason the Wraith have for coming here is to gain access to Earth."

"And from Earth, the rest of the Milky Way galaxy wouldn't be far behind…" Elizabeth said, her voice grim as she looked around at her staff. "We have to make sure the self-destruct is prepared if we have to resort to the worst-case-scenario; no matter what else happens, the Wraith cannot be allowed to gain access to that control crystal or the Milky Way addresses we've dialled so far."

"I'll see what I can do about adding the ZPM's explosive potential to the city's self-destruct sequence; even with what power we have left it should be enough to do a sufficient amount of damage to the tower to damage, if not outright destroy, the control crystal," Zelenka said, before his expression fell. "Unfortunately, that only covers what Atlantis can physically offer the Wraith; that still leaves the Ancient database."

"Is that not kept within the central spire as well?" Teyla asked, looking inquiringly at Zelenka.

"Not completely; the main databank is, but that is not the extent of the storage facilities used by the Ancients," Zelenka corrected, shaking his head as he glanced over at the Athosian before continuing. "The problem is that these systems are incredibly redundant; there are back-up systems located all over the city. Even with the most powerful explosive force we can offer, I cannot guarantee that we could destroy all of the database terminals to such an extent as to render the information inaccessible."

"All right…" Elizabeth said, taking a deep breath as she looked directly at her second-best scientist. "What's the alternative?"

"Delete the database," Zelenka said, his expression grim. "I cannot guarantee that such a thing would be possible in the amount of time- particularly since I would also be attempting to back up any information we can before leaving- but I will do what I can."

"Get to it as soon as possible," Elizabeth said, not bothering to hide the slight trace of regret on her face as she gave the order; it might be necessary to make this decision in order to prevent the Wraith gaining access to the information in question, but the idea of erasing all of the knowledge in the Ancient database was a decision Elizabeth was certain she'd regret having to make if they made it through this….

"Doctor Weir?" a voice said from outside the main door, prompting Elizabeth to glance up to see Chuck standing there, looking anxiously at her. "We just got a call from the gateship; Miller says they're nearly at the satellite and Doctor McKay's preparing to disembark and investigate."

Elizabeth couldn't help but smile slightly at this latest news.

Finally, something seemed to be going their way…


A couple of hours later, with no further news from the gateship beyond that they'd made contact with the satellite and McKay was working at restoring the power, Elizabeth was only partly surprised to look up while going over some papers to see Halling standing at the door, looking slightly uncertainly at her; even after all his time on Bates's offworld team, he still sometimes felt uncomfortable when the situation called for him to speak to her on his own.

"Halling?" Elizabeth asked, looking curiously at him.

"May we speak?" Halling responded, nodding slightly at her.

"Please, have a seat," Elizabeth replied, indicating the chair on the other side of her desk, Halling swiftly sitting down in it. "How is the evacuation on the mainland progressing?"

"My people will be ready," Halling said simply.

"Good," Elizabeth said, briefly noting and wondering about Halling's turn of phrase- should she be concerned that the Athosians who'd remained officially on offworld teams, such as Teyla and Halling, generally seemed to be coming to identify themselves with the expedition more than with their people- before he continued to speak.

"Doctor Weir," he said, his unease growing as he spoke- evidently he was uncomfortable with saying this but clearly felt that he should-, "word is there is a plan in place to destroy Atlantis."

"There are concerns that the Wraith will be able to make it to Earth if the city is left intact," Elizabeth admitted, not bothering to ask where Halling had learned that information- right now information relating to the approaching Wraith cruisers was the only thing anybody in Atlantis was even remotely interested in talking about-, "but I assure you that plan will only be executed in a worst-case scenario."

"Such as three hive-ships flying towards Atlantis?" Halling asked (Elizabeth had to admire the man before her, really; even when discussing something so deeply part of who he was- his belief in the Ancients' protection was fairly well-documented-, he continued to maintain his control).

"We do believe we'll be able to destroy them before they arrive," Elizabeth replied, taking care to avoid giving voice to her own feelings on this matter; she was just as strongly against destroying Atlantis as Halling was, but she was partly ashamed to admit that her reasons had almost as much to do with the fact that John would almost certainly be lost to her if that happened as they had to do with the knowledge of all the history and information that would be sacrificed if the city was destroyed…

"I understand you fearing for the well-being of your people," Halling continued, his tone continuing to be uncertain even as his voice remained clear and resolved, "but it is not reason to destroy the city of the ancestors. Atlantis is a sacred place, and to even consider destroying it merely for self-preservation-"

"'Merely for self-preservation'?" Elizabeth repeated, almost hurt that Halling believed they could be so selfish; they were trying to protect everyone back in their original galaxy from the Wraith, this wasn't just about keeping themselves safe!

"This place is all that remains of the greatest race ever to inhabit the stars-" Halling began.

"And you would prefer that it fell into the hands of the Wraith?" Elizabeth countered; she had been trying to maintain a respectful attitude towards Halling's beliefs, but his last comment had practically demanded a response on her part as far as she was concerned.

"I would have faith that the Ancestors- and the Phantom, of course- would not allow that to happen," Halling replied. "They have been able to preserve Atlantis for ten thousand years-"

"The Phantom told me himself that he would rather this city be destroyed than allow it to fall into the Wraiths' hands, Halling," Elizabeth interjected; as much as she'd promised John that she would keep his contact with her secret, right now she felt that it was more important to reassure Halling that she wasn't completely disregarding the Athosians' opinions simply because she felt she knew 'better'.

Halling stared silently at her for a moment clearly contemplating what she had just said, before he spoke again.

"You claim to have spoken with the Phantom?" he asked, his eyes narrowed slightly as he looked at her.

Elizabeth didn't need diplomatic expertise to know what Halling's reaction meant; he thought that she was lying to him to try and convince him to accept her plan.

"I have seen him, Halling," she said, her mind latching onto the one thing she could think of that might convince him of her sincerity; the masks the Athosian children wore when playing as the Phantom covered the whole face, but that could just be because nobody could precisely copy the real thing… "The lower left side of his face is not covered by his mask, and the skin underneath it is pale."

For a moment, Halling simply stared silently at her, and then his eyes widened as he leaned in closer to her, his expression clearly stunned at this latest revelation.

"You have spoken to the Phantom?" he said, staring incredulously at her. "The secret of his mask is known only to the leaders of the people he trusts; all others only know that he wears a silver mask without knowing what it truly covers…"

"I have spoken to him, I promise you," Elizabeth replied, nodding back at the Athosian. "He has assured me that we shall have his protection as we fight the Wraith, but, if the situation becomes impossible, he assures me that the city can be sacrificed; no matter what else happens, he will continue to protect the Pegasus Galaxy, and I can assure you that we'll do everything we can to help him."

For a moment, Halling sat in silence, looking contemplatively at Elizabeth, before he finally spoke.

"You have the approval of the Phantom," he said, his tone solemn as he looked at her, his gaze no less intent than it had been when he'd entered despite the shift the conversation had taken. "It is… comforting… to know that you have not made this decision without consultation."

"I'm glad you feel that way," Elizabeth replied, nodding gratefully back at him, understanding what he meant; since the Phantom had fought against the Wraith for the people of the Pegasus galaxy for the last twenty years, Halling evidently felt that the Phantom would not have agreed with Elizabeth's planned course of action unless he was certain that it was the only choice left to anyone. "But I can assure you, Halling, we will not abandon Atlantis to its destruction until we are certain there is no other choice; Jo- the Phantom has made it clear to me that he will only allow us to destroy the city if he is certain that every other alternative has been exhausted."

She was putting words into John's mouth, of course, but she felt that it was appropriate enough in this instance; he might have never voiced his opinion on whether or note Atlantis survive, but Elizabeth was certain that John would only allow Atlantis to fall if he was certain no other option was left to ensure that the Wraith failed.

"That is… reassuring, Doctor Weir," Halling said, smiling slightly at her before his expression became more solemn once again. "If only I could believe that such an action- should it be required to prevent the Wraith from claiming this city- would not almost certainly leave this galaxy without its greatest defence, I would support it completely."

Elizabeth could only stare silently after the Athosian as he stood up and walked out of her office.

She had to admit, it was hard to find a response to that one. Even if she was able to convince the SGC to continue sending ships and teams out to explore this part of the universe after the city was destroyed, the loss of the Ancient technology in Atlantis- to say nothing of the security they enjoyed in the city itself- would be a significant handicap to any attempts to establish an effective opposition to the Wraith, to say nothing of limiting their ability to fight back; they had enough trouble trying to find an Alpha Site in this galaxy, how were they meant to establish a permanent headquarters on another planet?

There were some days where Elizabeth really wished she'd gone with her initial feelings and told Vice-President Kinsey where he could go when she'd met him; even before she learned about his long-time vendetta with the SGC, she hadn't liked that man…


"Doctor Weir?" a voice said, knocking at her door. Glancing up, Elizabeth was relieved to see Zelenka standing there; at least this conversation was liable to leave her feeling less like she'd be condemning innocents to save herself.

"Yes, doctor?" she asked, looking back at him. "What progress have you made?"

"Well, the results so far are mixed," Zelenka replied, shaking his head apologetically at her. "The solution's simple enough- corrupt the Ancient database to make it unusable- but it's the execution of it that is proving to be difficult."

"You're creating a virus?" Elizabeth asked, looking inquiringly at him to make sure she understood what he was suggesting.

"Essentially, yes," Zelenka confirmed. "A plain old computer virus, once introduced into the system, wipes the database clean. It could be downloaded as part of the self destruct countdown; might even affect the Wraiths' systems if they try to access it."

Elizabeth had to confess, that last would be a nice bonus, but having a means of erasing the database didn't answer the most important question she wanted to know the answer to right now.

"How much of it could we save?" she asked, looking at the Czech scientist.

"I'm sorry?" Zelenka asked, looking curiously at her.

"Of the database," Elizabeth clarified. "Could we transfer the data through the Stargate back to Earth, maybe-?"

Zelenka instantly shook his head.

"It won't work," he said apologetically. "Putting aside the fact that the sheer size of the database would require more than ten times the amount of hard drives we brought with us, Ancient systems are too complex for us to download information of this scale directly into our own systems over wireless transmissions; we need time to write a program that can effectively translate the Ancient data into something that we can use, and even then it shall take some time before the process is complete."

Elizabeth didn't need to ask how long it would take for them to download all the available data even if they had enough hard drives available; Zelenka's expression made it clear that it would take longer than they had available to them right now.

Although she had never been the type to let her emotions rule her actions, Elizabeth couldn't help but swear at this latest turn of events.

If they had to leave Atlantis, they really would lose everything…

"You have to be able to save more than that!" she insisted, looking desperately at Zelenka; they couldn't have come this far only to come away with so little. "How can I be expected to choose between Zero Point Module research and their work on ascension? Between weapons schematics and their notes on space travel? No matter what we choose here, invaluable information will be lost, and that's just what we've deciphered; we all know we've barely even begun to scratch the surface. What if we destroy… the cure for all disease, or even some piece of information that could lead to the downfall of the Wraith?"

Zelenka could only shake his head apologetically.

"I don't know what I can tell you," he said regretfully. "I will try to improve on McKay's compression ratios, but we are at war, Elizabeth. In war, there are casualties."

Elizabeth knew that well enough; her long experience with drawing up treaties had made her more aware than any non-soldier had a right to be of the losses that could be suffered in war.

She just wished there was something more she could do right now…


A few hours later, Elizabeth could only stare in frustration at the paperwork before her, wishing she could concentrate enough to figure out what she could do to provide some kind of positive contribution to the mess Atlantis was currently facing. After Sumner's teams efforts to scout out a planet as a possible Alpha Site location had resulted in them being chased off by a life-form that- according to Ford- looked remarkably like a dinosaur, their list of possible Alpha Sites if the SGC reinforcements couldn't get here in time was diminishing rapidly, and they still didn't really have a clear plan for defending against the hive-ships with access to only one depleted ZPM…

"Doctor Weir?" Chuck's voice said from outside her office door, prompting her to glance up from her paperwork. "We just detected the hive-ships arriving in this solar system; they'll be at the satellite within the next few minutes. We're about to try and make contact with the gateship to determine what progress they've made; we thought you should be there when we reach them."

Simultaneously excited and afraid at this latest news- there was no way of knowing how McKay's small team had progressed in their attempts to activate the satellite, but if it had worked out they might have found a way to stop the hive-ships from even reaching Atlantis in the first place-, Elizabeth stood up and headed for the control room, nodding briefly at Chuck as he activated the communication system.

"Gateship, this is Doctor Weir," she said, taking care to keep her voice calm; no matter how worried she was about how things were turning out, she would not show fear. "How are things progressing?"

"Doctor Weir, this is Gateship One," Miller's voice replied, sounding as calm as could be expected under the circumstances. "Doctor McKay has just finished routing the power to the satellite's weapon systems, and Doctor Gaul is inside the satellite; the satellite is currently powered down and we're waiting for the hive-ships to come into range before reactivating it."

"Good call," Elizabeth said, trying to restrain the sigh of relief she felt at the news that the satellite was active; at least they had a chance to strike the first blow now. "Let us know when you're ready to fire."

"Confirmed," Miller replied briefly, the radio subsequently falling silent.

After a few moments with no further sound from the gateship, more and more people gathering within the control room as the news about this latest turn of events spread throughout the city, McKay's voice finally spoke again.

"Doctor Weir," he said, his voice grim as he spoke, "it's McKay. Satellite is armed and ready. It should fire within the next minute or so. Keep your fingers crossed."

"Fingers crossed," Elizabeth replied, nodding in response to his statement as she glanced around the room at the rest of her staff; she could even see Sumner, Teyla and Ford off to one side of the room, clearly waiting for news of their teammate's fate. "Good luck."

Once again the radio fell silent, the tension increasing as the group waited anxiously for news from the small ship that now served as their only hope to deliver damage before their enemies reached the city, before McKay's voice finally spoke once again, glee evident in his tone alone.

"We have a kill!" he yelled, prompting cheers and applause thoughout the control room, Elizabeth smiling in delight as she saw a couple of technicians enthusiastically hugging each other; even Sumner seemed to have developed a slight smile.

"We copy that, Rodney," she said at last, as the cheering stopped.

"One down, two to go!" McKay said, a broad grin somehow apparent even across the vast distances between them as the radio fell silent once again.

For a few moments, the atmosphere in the room was charged and energised, each member of the expedition eagerly awaiting the now-seemingly-inevitable news that the satellite had destroyed another hive-ship, that they wouldn't even need the reinforcements from Earth for this first wave, that they'd saved the city by themselves…

Then McKay's voice broke the silence, his tone alone once again saying everything that needed to be said even before he spoke. "Atlantis, this is McKay. We have lost the satellite."

The sudden shift in mood in the control room was almost painful for Elizabeth to witness.

"Did you manage to take out any more ships?" she asked finally, deciding to address the central issue before any further questions were asked.

"Negative," McKay replied. "Two of the hive ships are intact." There was another brief pause, as though what he was about to say was especially painful for him, before he spoke again. "Elizabeth… Brendan Gaul was aboard the satellite."

The first casualty of the siege of Atlantis… Elizabeth replied, saddened at the news of that bright young doctor's future cut short so rapidly by forces so powerful that they would probably never even acknowledge his existence as a person.

"Understood," she said, bringing her attention back to the present; they would mourn Gaul once they had time. "What's thes tatus of the other two?"

"They're not coming any closer," McKay replied, the news providing so little encouragement that nobody so much as smiled at it. "Looks like they're rethinking their plans. At the very least, he's bought us some time."

"You can't do any more out there, Rodney," Elizabeth told him, fighting to stop herself breaking down at this newest turn of events.

She hadn't realised how much she'd been counting on that satellite until it had failed them…

"Return to Atlantis," she finished,

"On our way," McKay replied, terminating the radio and leaving the control room in silence.

This is it… Elizabeth mused as she looked at the people around her, nodding slightly in recognition of the resolve she saw on their faces. Our first line of defence has fallen… reinforcements might not be here in time… and our only hope to hold the line on our own lies in a power source that only has access to just over a tenth of its full power available to it and a man whose origins are a complete mystery even to me

She paused at that last thought.

Hold on… she thought. Why do I feel like I should know more about him? He's only spoken to me because he knows I won't hand him over to Sumner; why should I feel as though he should have told me more than he already has…?

She shook the thought off impatiently; it wasn't going to help her deal with the current situation to start thinking about what the Phantom should or shouldn't tell her… not to mention wondering why he felt as though he should have told her more than he had so far.

"Doctor Zelenka," she said, turning to look grimly at the Czech scientist, "make sure that virus is ready to be uploaded if we need it."

With that said, she turned to address the rest of the people in the control room, raising her voice to make sure that everyone in the room could hear what she was about to say.

"All right then, everyone," she said, her expression grim as she looked at the group now gathered before her, representing many of the expedition's senior members and division leaders, "we have only hours left for certain before those hive-ships reach here; everyone return to your respective groups and inform them to prepare for possible invasion. I want the control chair ready for use as soon as possible and all possible defensive systems ready to fire the moment those hive ships reach us; we might only have a few dozen drones, but we are going to make sure that those shots count."

She paused for a moment, making sure that she had everyone's attention before she spoke her final words.

"We came to this city to learn from the most advanced race ever to exist," she said simply, her arms folded as she looked at the people around her. "We are not going to let a race of alien vampires take it away from us without a fight."

With one last nod of acknowledgement at her people, Elizabeth couldn't help but allow herself a slight smile as everyone turned to begin their appointed tasks.

Here goes nothing


Up in the maintenance tunnels above the control room, crouched low on the ground as he studied the sight before him, John allowed himself a slight smile as he looked at Elizabeth issuing instructions to the people around her.

She was right about one thing; the Wraith would not take Atlantis without a fight.

All he had to do now was to make sure he did everything he could to make the fight more even in their favour, rather than favouring the Wraith.

Which means, John mused to himself, a grim expression underneath his mask, that I'll soon have to make contact with Sumner

The trick here was going to be to make contact at the right moment…