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

AN: Well, here's the "Hot Zone" chapter that I said I'd write, which will go on to mark the most significant shift in Elizabeth's 'relationship'- albeit a highly unconventional one- with the Phantom to date, as he finally begins to talk to her directly; hope you like it

AN 2: This chapter also marks the end of my use of "Phantom of the Opera"-inspired titles, as John begins to become 'John' rather than 'the Phantom' to Elizabeth (Just out of curiosity, I have two quick questions; 1: did anyone guess that was where I was getting my titles from, and 2: can anyone give me the original line on those cases where I 'tweaked' the line for the purposes of the plot?)

The Phantom of Atlantis

As she sat in her office going over the paperwork before her, Elizabeth couldn't help but allow herself a rare relaxed smile as she studied the latest reports from the various departments around the city.

So far, baring reports of flooding in the areas that had been hit by the waves before she and the Phantom-John; old habits really were hard to break- had managed to raise the shields, the news of the city's condition in the aftermath of the storm a couple of weeks was really surprisingly good. None of the rooms in the flooded part of the city appeared to have been significantly damaged by the waves that had struck them during the storm, and even the conduits themselves had come through more or less intact; the worst thing that any of the survey teams had discovered so far was a slight case of flooding in some of the more distant areas, and the water level barely came up to their ankles anyway.

At the moment McKay, Zelenka and Ford were walking through another flooded part of the city with an exploration team in an attempt to get a better idea of the damage that might have occurred- if any; so far nothing untoward had been detected in those parts of the city and a previous team had been through it and found no structural damage, but McKay had insisted on taking a second team in case there was anything of scientific value in that area -, leaving the rest of the staff to simply kill time according to their own preference. She vaguely recalled Sumner saying that he and Teyla were going to have a sparring session- after Teyla had taken out their one-time Wraith prisoner single-handedly Sumner had expressed an interest in learning how she'd accomplished such a feat, even if he was apparently still having some trouble mastering it-, while she had decided to take advantage of the temporary quite to study some of the reports she'd been receiving from the other departments; if anything, their access to a ZPM appeared to be creating far more work than she ever could have expected as ever more devices were activated by the expedition that apparently would have remained dormant without the module. Some of the science team were even hopeful that they'd stumbled across some information about creating- or at least 'refuelling'- ZPMs in one of their latest discoveries, but to date there had been nothing definite either way.

That was the problem with their research, really; the Ancient database was so vast, and their knowledge of the language so comparatively limited- once again she wished that the SGC had been able to spare Doctor Jackson for the expedition; his knowledge of Ancient was practically without equal-, that it made it hard to be sure if they had actually found something or if they were just getting over-excited by the few words they did know the meaning of in some files. Even the progress in finding the password for the shield that would stop it from preventing them from returning to Earth was still only making the bare minimum of progress; they'd managed to determine that the password was composed of anything between five or eight letters, but until they could actually find any clues to the specific word they were forced to resort to the process of entering every single possible Ancient word of that length that they could find until they'd identified the correct password.

If Elizabeth ever needed another reason to talk to the Phantom, there it was; the possibility that he'd be able to tell them the password to get back to Earth…

And why was it, even when she was fully aware that he had a brutal nature that left with little to no qualms about practically mutilating people to get what he wanted, she still wanted to talk to him; if any other person had demonstrated that kind of behaviour it would have horrified her…

"Doctor Weir?" one of the technicians said from her door, breaking into her train of thought as she glanced up from the file to look at him. "It's almost time for Doctor McKay's team to check in with the results of their survey; you wanted to be informed…"

"Thank you," Elizabeth replied, nodding briefly at the man as she stood up, picking up a pad with some of the forms on it as she walked out of the office; she just needed to confirm a few requisitions by some of the science departments for additional supplies.

"Doctor Weir?" McKay's voice said over the speaker just as she had walked up to stand beside the main control console; when he wanted to be the man could be surprisingly accurate at doing things on time, even if he sometimes complained about it. "You there?"

"Right here, Rodney; go ahead," Elizabeth replied; she had managed to get used to calling McKay 'Rodney' in public to encourage the informal attitude she wanted to establish in Atlantis, but Sumner's 'stick-to-the-rules-about-military-detachment' attitude meant that she found it easier to think of him as 'McKay' for when she was writing reports to prevent any 'slip-ups'. She trusted Sumner as a military commander, of course- his 'obsession' with getting rid of the Phantom aside, of course-, but given that they'd found themselves dealing with what was essentially a war situation, the less excuses she gave Sumner to question her ability to govern Atlantis under these conditions the better. "What's it like out there in the suburbs today?"

"Essentially," McKay replied casually, "with the exception of the upper level Storage Room- which the lovely and talented Dumais informs me is in no immediate danger-,"- Elizabeth couldn't help but smile slightly at that image; the idea of McKay flirting, even in that rather obvious manner that she'd just overheard, was somehow rather amusing-, "this pier's in relatively good shape."

"Even after all the flooding from the storm?" Elizabeth asked as she automatically signed her name on the forms before her.

"Well," McKay replied casually, "it's dark, it's damp and it smells terrible, but from an engineering standpoint we're good."

At that comment, Elizabeth allowed herself a slight smile of relief; after all the problems she was having to deal with the daily running of the city- to say nothing of her own internal issues on Phantom-related matters; if only she could finally work out what she felt for that man-, it was always a relief to have something simple to deal with.

"Head back," she said simply, as she finished signing the last form, passing it to the nearest technician to take to the necessary department heads.

"Heading back," McKay replied briefly before the radio cut out once again.

Shaking her head slightly at the latest report- it might have been uneventful, but the way things had been going recently a little peace and quiet was definitely not something to be sneezed at-, Elizabeth headed back towards her office; maybe now she could finally catch a few minutes' rest…


As Elizabeth walked back to her office, she was unaware of the silent observer watching her from the maintenance tunnels above the control room, ever determined to remain available in the event of a problem arising in Atlantis that might threaten its leader's safety.

In many ways, his recent 'visit' to Elizabeth's older self- he knew that, based on the story that Elizabeth had told him after he arrived, she was technically an alternate self of the Elizabeth he now knew rather than an older one, but it was simpler to think of her that way- had actually been rather cathartic; it had allowed him to get a lot of things off his chest that needed dealing with. The knowledge that he'd ruined his chance with Elizabeth due to the brutality of his actions during the invasion still hurt, of course, but at the same time the satisfaction he felt when he saw her still walking around Atlantis, knowing that he was the reason the city still had its leader, helped to make up for it.

When he'd originally made the promise to protect her, he'd done so out of respect and gratitude; the fact that things had… changed… for him since then didn't negate the fact that the original intentions behind him making the vow remained. He'd promised the older Elizabeth that he'd protect Atlantis for her younger self, and he'd done so; the fact that things were more… complicated… now didn't excuse him from his original vow.

Still, he was grateful that, for the moment at least, the city had nothing more to worry about than the usual problem of cracking the shield code that would allow them to dial Earth once again; after the chaos of the Genii's attempted invasion, it was really rather nice to have the opportunity to relax for a bit. With Sumner's teams currently checking out the more distant parts of the city in an attempt to find him- with him constantly changing his hiding-place and leaving little to no real sign of his presence in his 'abandoned' hide-outs, it was highly unlikely that they would ever manage to successfully track him down-, it was a rare moment when he felt comfortable enough simply relaxing in the main control room, allowing his attention to drift slightly as he looked out at the people who had brought life to this city where there had been nothing but himself and the ocean for the last twenty years…

"Beckett!" McKay's voice suddenly yelled over the radio, cutting into his train of thought; keeping his 'acquired'- not stolen; nobody had been using it- radio constantly tuned into a city-wide frequency might help him keep track of any important calls, but it was prone to be a bit startling on occasion. "I need a medical team down here, stat!"

That statement, almost more than the words themselves, instantly shook him out of his 'relaxation' mode and back into the 'Phantom' mindset.

Why would a medical team be needed for a group carrying out a structural survey in that part of the city? he thought to himself, slightly surprised at this latest turn of events. I've been over that area already, and McKay just confirmed that nothing was seriously wrong; why would he want a medical team over there?

Something didn't quite add up; McKay clearly wasn't in any pain himself, and that area was definitely structurally sound, so why was he asking for a medical team…?

"McKay," the familiar Scottish accent of Doctor Beckett suddenly said over the radio, his calm tone a welcome distraction from John's increasingly confused train of thought, "this is Doctor Beckett. What exactly is the nature of the emergency?"

"It's too late," McKay replied, his tone grim as he spoke. "They're gone."

John blinked in shock.

Someone- two someones, if hat McKay had just said was accurate- had actually died over there?

The situation had just become far worse than he'd originally expected; he'd been expecting someone to have been injured by a damaged wall at least…

"Who's gone?" Beckett asked; to his credit, his tone was brisk and direct, displaying no emotional reaction but instead sticking exclusively to the facts of the situation that was now before him. "How?"

"Wagner and Johnson," McKay said briefly by way of an explanation. "I need a containment team here."

"I'm sorry?" Beckett replied, clearly surprised at the request. For a moment John thought that he heard Lieutenant Ford's voice- most likely at McKay's end of the radio; he was fairly sure the lieutenant had joined McKay in carrying out the survey-, but then McKay began to speak again and his attention was called back to the scientist.

"People don't just see things and drop dead, Lieutenant," McKay was saying, evidently still slightly frustrated at whatever had just taken place down in that part of the city. "We spent the last hour surveying unexplored areas of this city; I think Wagner and Johnson were exposed to something."

For a moment John vaguely heard Lieutenant Ford's voice trying to say something, but then McKay interjected with a very pointed "And if they were infected, there's a very good chance that we were too."

"I recommend a Level Four quarantine until we know what we're dealing with," Zelenka's voice suddenly said, the Czech scientist's statement far clearer than Ford's previous comments; either he was closer to McKay than Ford was or he was making a more deliberate effort to ensure that his voice was heard over the radio.

"Agreed," McKay said by way of confirmation. "Carson, you hear all that?"

"Aye," the Scottish doctor replied. "We'll get to the hazmat gear and head down. Sit tight; I'll make sure Doctor Weir's briefed."

"Thank you very much," McKay replied one last time before the radio connection was terminated, leaving the Phantom sitting silently in the tunnel as he contemplated this latest turn of events.

A containment team needed in case they were… exposed to something? John thought to himself, a confused eyebrow raised behind his mask as he went over what he knew of the experiments that he'd found records of in the Atlantis databanks over the years. But the Ancients never experimented with biological warfare; after the mess they made with the Wraith they swore off ever trying something like that again, no matter how bad the situation got. The only thing that's evenclose to a biological weapon in the city is…

He froze.

Oh no… he groaned, as the implications of this latest turn of events hit home. Not that

He knew he should have moved that thing out of the city as soon as possible; why hadn't he learnt anything from that mess with Jinto after the young Athosian accidentally released that energy-sucking shadow? Just because there weren't any children on Atlantis any more after they'd all been relocated over to the mainland- Halling tended to alternate his time between his duties on Sergeant Bates' team and some time on the mainland with his son- didn't mean that some adults wouldn't accidentally trigger the systems!

Rationally, he knew that the current situation was far from being his fault; if nothing else, since the expedition had arrived in the city he'd had no opportunity to discard the nanites through the Stargate. Besides, he'd been too uncertain about how Sumner would have reacted to Elizabeth revealing that she was receiving information from the Phantom to risk letting them know that way; anything else he might have tried to fill them in on the problem was too subtle to be certain of success.

Besides, he'd never managed to determine a safe way of removing the containment devices from that room without releasing the nanites into the air at the same time, and even then he wasn't certain where he'd send them to once he actually reached the Stargate. Most of the things he'd discarded on abandoned planets during his time in Atlantis consisted mainly of the old plants that had been filling the corridors when he'd first arrived, along with some old Ancient experiments that either didn't work, had run out of power, or did nothing that he might be able to use against the Wraith (After all, he hardly wanted the Wraith to be able to use them against him if they'd discovered them). The risk that the Wraith would recover the nanites and find out a way to use them to make humans easier prey- maybe reconfigure them to simply render humans unconscious rather than trigger a stroke like they had originally- was just too great for him to risk it; at least when they were here he could make sure the nanites didn't cause any harm.

So much for that little theory… he groaned, as he glanced anxiously at his watch; he definitely needed to try and leave Elizabeth some kind of message about any other 'surprises' the city had to offer once he'd had the time to note down where everything was. Assuming he'd memorised the survey team's schedule correctly- and he accurately recalled the names of the deceased; 'Wagner' at least sounded unusual enough to stick in his memory-, he probably had just under an hour or so before someone else succumbed to the nanites that had been released.

That wasn't anywhere near enough time for McKay and his team to work out what they were dealing with. No matter how good they were at their jobs, they didn't know what they were dealing with and had no way of working out what it was based on their current minimal clues; somebody was going to die if they were left to work this out on their own.

If he wanted the expedition to have even a chance of getting through this latest mess without any casualties…

He swallowed, already anxious about what he was about to do.

He'd have to talk to Elizabeth directly, let her know what they were up against, and hope that she didn't just call Sumner and arrange for him to be sent into a trap for being a complete bastard with no regard for others…

God, if only he hadn't let his temper control him after Kolya had told him she was dead; he'd feel a hell of a lot more comfortable doing this if she didn't know what he was capable of at his worst…

"May I have everyone's attention please?" Elizabeth's voice suddenly said over the city-wide broadcast system, drawing his attention briefly off his own fears; maybe something had been discovered about the situation since he'd last heard a radio message. "We have run into a questionable medical situation, and at Doctor Beckett's suggestion, we have decided to put the city into a self-regulated quarantine. For at least the next couple of hours, I need everyone to stay where they are, and report anyone moving freely through the halls. I hope you'll understand. Thank you."

John knew that the statement should have reassured him; they were aware of the situation and were taking every possible step to contain it to one part of the city rather than risk it spreading any further.

It didn't.

If anything, the words used only reminded him of just how much trouble he could be facing right now. If he didn't act now to let Elizabeth know what he was planning, then there was a very real chance that the city would initiate a lockdown and he'd be left with no chance whatsoever to solve this problem; the city even locked down the maintenance tunnels when quarantine defences were activated, and he wasn't exactly keen on keeping his shield device on for the time it would take to collect what he'd need, even if he'd been certain that it would stop the nanites from 'infecting' him.

Admittedly, his current plan for dealing with that particular problem was rather… vague, to say the least- he had no real idea what he was but if he could just have the chance to talk with Elizabeth and have her put him in touch with the right people, he was certain that he could get a better idea of the possibility of it being successful.

"Here goes nothing…" he mused, as he waited for a few seconds- since there was no reason for her to remain in the control room Elizabeth would probably head back to her office after making that announcement, which increased the possibility of him being able to talk to her without anyone else hearing him- before he turned on his own radio.


"Doctor Weir?" a shockingly familiar voice said in Elizabeth's ear just as she was sitting down behind her desk. "Are you alone?"

If Elizabeth hadn't already been sitting down, she was certain she would have fallen to the floor- or at least leaned against a wall- in shock at the sound she had just heard.

The Phantom was talking to her?

After spending the last few months in the city and only receiving a short note from him- during the Genii invasion he'd mainly been occupied with talking to Kolya rather than her, so she didn't exactly count that as him talking to her-, he was now talking to her?

Elizabeth wasn't sure whether to be glad at him finally breaking his apparent 'vow of silence'- in terms of the information he might be able to give them about the city; she was not an obsessed fan who wanted the chance to talk to her 'hero'-, or concerned about the fact that their current situation was serious enough to make him want to break his vow in the first place.

"Hello?" the Phantom- John, she reminded herself, his name is John- whispered again; Elizabeth had been so shocked at the unexpectedness of hearing his voice that she'd almost forgotten he was still waiting for a reply. "Elizabeth, are you-?"

"I'm here," Elizabeth replied, keeping her voice low as she glanced at her door; Sergeant Bates was standing just a short distance away from her office, but so long as she kept her voice low while talking she was confident she could carry on the current conversation without attracting attention. "As… interesting… as it is to hear from you again, we do have a situation right now-"

"I am aware of that; I actually called to let you know what you're dealing with," John replied, his tone sounding remarkably casual as he spoke, as though he wasn't talking to the leader of the people who were under orders to bring him in for questioning at the first chance they had.

"What we're-" Elizabeth began, before his meaning struck her. "You know about the virus?"

"It's not a virus," John replied simply.

Elizabeth blinked in confusion.

"Excuse me?" she asked, puzzled at the latest turn of events. "But two people have died without suffering any injury-"

"I should rephrase that; it's not a biological virus," John continued. "It's artificial in origin; the deaths were caused by nanites that were part of the Ancients' last major weapon against the Wraith that were abandoned when the programming proved incomplete and the nanites were determined to be potentially dangerous to innocent parties."

"Right…" Elizabeth said, unable to keep the uncertainty out of her voice. "Uh… assuming that I don't know what nanites are…"

"They're microscopic robots that are used to complete specific tasks that their small size makes them ideal for," John explained (Elizabeth was grateful that he didn't sound amused when he spoke; for some reason the thought of John thinking less of her was… unpleasant, for lack of a better term). "No bigger than a conventional single-celled organism- less than a billionth of a millimetre, really-, the virus is programmed to terrorise its victims by tapping into their visual cortex and then rupturing an artery in their brain, causing its victims as much terror as possible before their demise. They were designed to be unleashed on the Wraith as a last-resort weapon, commonly inducing visions similar to those generated by the Wraith; I think the designers were the vindictive sort and wanted the Wraith to be on the receiving end of those 'visions' they're always using to terrify their victims for once. Unfortunately, the programming the Ancients used to create this particular group of nanites- I've read some comments in the database which suggest that they made more later but I haven't managed to find anything conclusive - was inefficient; rather than just being deadly to the Wraith, the nanites were lethal to everything that wasn't an Ancient- or, at the very least, doesn't possess the Ancient gene in some form or another."

Even with her admittedly limited knowledge of biology, Elizabeth shuddered.

That definitely didn't sound good…

Then she fully registered what John had just revealed to her.

"The Ancients made these things?" she yelled incredulously. "What were they thinking-?"

"As I said, they made a mistake in the programming; it was intended to be a weapon against the Wraith, but in their desperation they activated the nanites before the programming was complete and they turned against anything that wasn't an Ancient," John's voice replied. "By the time they realised their mistake, they found it easier to simply contain the nanites in a near-abandoned part of the city rather than try and rewrite the code so completely; personally, I think they wanted to keep them around in the event of a 'Doomsday Scenario' in case the Wraith ever gained access to Atlantis and they had no other option but these nanites. There were some references in the database to them trying to create a new bunch of nanites later, but the information is all general and that's not really important right now; as far as I can determine that experiment was abandoned as well."

"Right…" Elizabeth said, shaking her head slightly as she leaned back in her chair, trying to process everything that she'd just learned. "So… how does this help us deal with it?"

"Well," John replied, his tone solemn as he continued to speak, "I do have a plan, but if I'm going to be able to confirm that it will accomplish my intended goal, I need to talk to Doctor McKay."

Elizabeth blinked.

The Phantom was actually going to talk to someone else…?

And God, that sounded self-centred when she phrased it like that; she just meant that, after he'd spent so long only talking to her, it was strange to think of him being willing to talk to other people. It wasn't that she thought she was the only person he had a right to talk to, of course, but given that he'd only ever made contact with her- not counting his encounter with Teyla, Carson and Lieutenant Ford during the Genii invasion; on that occasion they had made contact with the Phantom rather than him going out of his way to find them- she felt somehow…

Elizabeth stopped herself right there; this was not the time to think about that!

"Why?" she asked, pushing any thoughts about her reaction to the Phantom's desire to speak to someone else aside; there would be time to give them a more in-depth analysis once this crisis was over.

"I need to confirm the blast radius of the nuclear explosion that would result if I detonated a naquadah generator in the upper atmosphere," John replied, his tone surprisingly matter-of-fact for such a statement.

Elizabeth's eyes widened at that last statement.

"You want to what?" she repeated, barely remembering to keep her voice down; the last thing she wanted was to attract the attention of Sergeant Bates during a conversation with Atlantis's 'Most Wanted'. "Are you even sure McKay won't… you know…?"

"Try to trick me into handing myself over to Colonel Sumner?" John replied, sounding almost amused by her concern. "Don't worry about it; I already have a… pretty good idea how he'll react to me, I just need to let you know what I'm planning so that I don't accidentally wipe your hard drives when I set off the blast."

"What 'blast' are you talking about?" Elizabeth asked, growing increasingly confused at the conversation she was having. "I mean, I may not have seen many nuclear explosions, but I wouldn't think that one in the upper atmosphere could have that much effect on us…"

"The blast itself won't; it's what else it causes that will solve the problem…" the Phantom explained, sounding almost like he was smiling as he continued to speak. "I can go over the fine details with McKay; I just need you to do exactly what I tell you and we should be able to get the expedition out of this alive without any more death."

Elizabeth knew very well that, if Colonel Sumner had been present, he would have insisted on knowing more about the Phantom's plan.

But she was not Colonel Sumner; she was the leader of expedition, talking to the man who had apparently lived in the city for the last several years of his life, who had informed her that he had a plan that could save them from this… nanovirus… without any more death.

She might not know everything he was planning, but she had seen enough of him in action to know that what she knew was simply what she needed to know.

"All right," she said, settling back down into her chair as she kept her voice low. "What do you need?"


AN 3: If anyone wonders what I meant by that comment John made about the Ancients swearing off biological warfare after 'the mess they made of the Wraith', my reasoning is thus; since all the evidence we have available so far suggests that the Ancients played at least some role in the evolution of the Wraith, until we learn otherwise I'm assuming that the Wraith came about as part of an Ancient experiment that went wrong- my personal favourite idea is that they created the Wraith to be soldiers against the Ori but they lost control of the experiment for some reason and didn't realise what had happened until it was too late-, thus leaving the Ancients reluctant to resort to biological means of waging war in case they accidentally created something worse than the Wraith next time.

A bit of a stretch, I know, but I think it makes sense; I just don't want to say anything explicit as I'm trying to keep this as close to the 'real' series as possible- meaning that I'm changing nothing that took place prior to the Phantom's arrival on Atlantis- and don't want to contradict anything we might learn about the Wraith's origins as the show goes on