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 sat in her office the next day, going over the various reports of what had taken place during the quarantine period, she couldn't stop herself letting out a brief sigh of relief as she confirmed that nothing serious had happened after Dumais' death. All members of McKay's team had been analysed by Doctor Beckett after his team had reached them, with their blood showing no trace of the nanovirus

The only member of the expedition with any long-term 'damage' as a result of the virus was Peterson; although the detonation of the naquadah generator had destroyed the nanites before the virus could do any physical damage, he had been ordered to undergo psychiatric evaluation with Doctor Heightmeyer to help him through his reaction to the virus. Elizabeth was currently thinking of relocating Peterson to a calmer area of Atlantis- maybe one of the jumper survey teams or something like that- until a more permanent solution presented itself, but so far nothing had immediately come to mind…

"Doctor Weir?" a voice said at the door.

Glancing up, Elizabeth wasn't surprised to see Colonel Sumner standing at the entrance to her office, a stern expression on his face as he looked at her.

"Yes, Colonel?" she asked, putting the reports she was reading off to the side as she looked up at her military commander. "What can I do for you?"

"We need to talk," Sumner said, his expression grim as he walked into her office, standing in front of her desk despite the chair that was positioned close to the desk. Elizabeth didn't need to be a diplomat to recognise what Sumner was doing by rejecting the chair; he was attempting to establish his control of the situation by assuming the 'higher position' in their discussion.

"All right," Elizabeth asked, looking coolly back at Sumner as she raised her hands in front of her, making it clear to the man before her that she wasn't intimidated by his actions. "What seems to be the problem?"

"Your attitude towards me regarding my opinion of the Phantom's plan," Sumner replied, his expression betraying nothing about his own feelings as he looked at her. "Your attempts to countermand my orders to the security team doesn't exactly give the impression that we're effectively establishing a chain of command-"

"Are you saying I'm not allowed to have personal opinions about the way this city is run?" Elizabeth countered, stepping up from her chair to look directly back at Sumner.

"What I object to is you voicing those opinions during that kind of public communication," Sumner countered, his arms folded. "It undermines the chain of command that's required if we're going to successfully operate in Atlantis, to say nothing of encouraging the idea that the Phantom might not be a threat; until we have any conclusive evidence that he's no danger to us, he should be treated as a potential threat at least-"

"I understand your position on the Phantom, Colonel; what you need to understand is that I will not accept you trying, whether intentionally or otherwise, to make him out to be a greater threat than he actually is," Elizabeth interjected, staring coldly at the man standing opposite her; even if John didn't want her to say anything that could incriminate her as a potential ally of his, she was not going to allow him to become the Atlantis scrapegoat. "If you possess a legitimate reason for attempting to find him, then you are, of course, completely within your rights to do so; I've never intended to imply otherwise. However, if you start making up excuses to go after him- such as accusing him of releasing this virus despite the complete lack of information that he's done anything like that-, I will be forced to have you taken off active duty until I feel certain that you are not going to allow some… personal vendetta to affect your judgement."

"'Personal vendetta'?" Sumner repeated, glaring at her. "If you're-"

"I've already tried to make it clear that I understand your position on the Phantom; it's only when you start accusing him of committing crimes without evidence that I will actively attempt to oppose you," Elizabeth said, her tone cool as she continued to glare at Colonel Sumner. "As I told you yesterday, you are not going to turn this hunt for the Phantom into the Salem Witch Trials; I respect that his status as an independent operative in the city might put us at risk in a time of crisis, but I will not permit you to accuse him of doing something when you have no evidence. When you have genuine evidence that he has committed a crime, then you can feel free to present it to me; otherwise, the Phantom is innocent of any possible malicious intent until you can prove that he is guilty. Understood?"

Further conversation was cut off when Doctors McKay and Beckett walked into the office door, looking uncertainly between the two commanders as they glared at each other, Elizabeth silently daring Sumner to contradict her while Sumner looked back with an expression that made it clear he wanted to say something in defence of his earlier accusation despite a lack of inspiration for what that could be.

"You guys have a minute?" McKay asked, looking uncomfortably at Sumner and Elizabeth as the two of them turned to look at him and Beckett ; evidently the Canadian knew that he'd just walked into an argument but at the same time had no real idea what the conflict had been about. "We've been able to spend some, uh, quality time with the, uh, nanovirus samples."

"From what we can tell, they've all been incapacitated," Beckett added. "Looks like the Phantom was right about the wee buggers; the computers that ran them were shut down by the EMP pulse generated by the detonation of the naquadah generator, but the pulse was too far away to affect any of our technology while it was in its dormant state."

"Well, that's good to know," Elizabeth said, nodding at Beckett with a slight smile; at least she knew that the Phantom had told them the truth about that (Maybe it would help her convince Sumner to go easier on the Phantom in the future; he'd had the chance to potentially cripple their ability to run the city by shutting down their own technology while leaving his own ability to control the city unaffected, and yet he'd gone out of his way to let them know what he was planning so that wouldn't happen).

"Yes," McKay confirmed, nodding briefly at her before his face became more solemn. "Also, upon further investigation, I think we can rule out that they were created by the Wraith. Putting aside the fact that the Wraith wouldn't have any need for a WMD- they're killing us because they need us for food, not because they sadistically want us dead-, they're different than any Wraith technology we've come across thus far."

"If not the Wraith, then who made them?" Sumner asked, looking critically at the Canadian scientist.

"Well," McKay said, as he looked over at the colonel, "so far we haven't discovered anything to contradict the Phantom's claim that they were an Ancient weapon that didn't quite work out the way they'd planned; they certainly look like they could have elements of Ancient technology involved in their construction, but there's really no way to be sure unless we can find something else about where the Ancients acquired the virus in the Ancient database…"

"Work on it as soon as possible," Sumner said, looking pointedly at McKay before he turned back to look at Elizabeth. "I'll be issuing orders to increase the security patrol rate as soon as we're certain all strands of the virus have been eliminated from Atlantis."

Elizabeth opened her mouth to try and object- how often did she have to repeat herself before Sumner understood that she wouldn't accept him automatically treating the Phantom as though he'd already proved he had malicious intentions towards the city?-, but Sumner cut her off before she could even say the first word.

"This is not about the potential danger he could pose," he said, looking pointedly at her to make it clear that he'd taken what she'd said earlier into account. "This is in response to the fact that he clearly knows more about the city than we could have expected, after an experience like this, I think it proves that we could use his knowledge in getting a better idea about how this city operates."

"And what if he has his reasons for wantin' to stay independent?" Beckett asked, looking over at Sumner with a critical expression. "For all you know he might have valid reasons for not wantin' to let us know about what's in some parts of the city-?"

"If he has valid reasons for not telling up about himself, I'll accept them when I hear them; until then I have to proceed on the basis that he's a potential threat," Sumner replied, looking pointedly at the doctor before he turned back to face Elizabeth. "I'll send you reports on the new security team layout as soon as I have it arranged, Doctor Weir; in the meantime, make sure that your people know the situation."

With that, the colonel turned around and walked out of the office, leaving the three doctors alone as they looked at each other before McKay broke the silence.

" 'Your people'?" the Canadian repeated once Sumner was out of earshot, shooting a glare after Sumner that suggested he would have hit the commander if he'd been present. "What, does that include everyone who isn't part of his 'military chain of command' thing?"

"Well," Elizabeth said, trying to phrase her response in a manner that wouldn't reveal her true feelings about Sumner's orders to McKay and Beckett- as much as she trusted them, Sumner had made a valid point when he said that they needed to create the impression of a united front if they were going to cope in Atlantis; even giving these two the impression that there was dissent among the city's two leaders could cause problems-, "it's all a matter of prioritising, really. Since the military members of the expedition tend to view Colonel Sumner as their commander, I'm generally seen as the leader of the civilian population, so he probably considers it only sensible that I be the one to make sure you and your respective staff members know about his plans regarding the Phantom…"

"Yeah, talking of the Phantom, what is Colonel Sumner's problem with the guy?" McKay asked, looking over in frustration at Elizabeth. "I mean, I'm not saying that masked guy was right in not telling us that the Ancients had created a virus that would have killed almost a third of our population if it got out- and I'm still not entirely happy about him shooting me like he did-, but this whole 'we must eliminate the Phantom' thing the Colonel's got going on is just ridiculous!"

"I have to agree with Rodney, Elizabeth," Beckett added, looking over at her with a slightly grim expression. "The Phantom might not have told us much about himself, but everything he's done so far has definitely helped us out of situations that we might not have been able to handle ourselves; how can Sumner still say he's a threat when the man hasn't done anything more serious than stun us when he doesn't have the time to talk?"

"It's… just the colonel's nature; he doesn't like having an unknown element introduced into the city in a situation like this," Elizabeth said, constantly reminding herself that she wouldn't help John in the slightest by speaking out too vocally in favour of him and attracting attention to herself for her attempts to speak out in his defence. "He's a military man by nature; as far as he's concerned he needs to know everything about the situation we're in if he's going to properly defend us-"

"Yeah, defend us when he's barely even made a real effort to get to know us beyond our essential skills!" McKay groaned, staring briefly upwards in frustration. "Don't get me wrong, he's a good team leader when we're out in the field, but seriously, have you ever seen him even bother to spend time with us outside of missions?"

"He did arrange for you and Teyla to receive training-" Elizabeth began.

"Oh yeah, learning how to kill people; that's a really great bonding activity, isn't it?" McKay countered as he glared out of the door in the direction that Sumner had just walked. "I mean, at least Ford actually tries to socialise with me and Teyla now and again; every time I try and talk with Sumner when we're off-duty about something that isn't related to the next mission it's like trying to get blood from a stone! I get that we're in a military situation and we have to exercise 'professional detachment' in case our personal feelings cloud our judgement when we're in action, but come on, would it be asking that much for him to show more interest in us as something other than his job?"

"Colonel Sumner has his way of doing things; as long as he's the military commander, we need to accept that," Elizabeth said, wishing that she could tell McKay she agreed with his opinion without actually going against John's wishes (And why was his opinion so important to her?). "I assure you, I'm doing everything I can to prevent him from taking his… vendetta… against the Phantom too far, but otherwise there's really nothing I can do about his attitude towards his responsibilities on Atlantis. If he wants to maintain a professional detachment, that's completely his decision; I can hardly order him to spend personal time with the rest of you."

"Fine," McKay groaned, as he turned around and walked out of the room, shaking his head in frustration as Beckett and Elizabeth looked after him.

After a moment's silence, Beckett sighed as he walked over to sit down opposite Elizabeth.

"It's not exactly been easy, has it?" he said reflectively.

"Working with Colonel Sumner?" Elizabeth asked, looking over at the doctor with a slight smile. "I know he's not the… easiest person to get along with, and his methods can be a bit… harsh at times, but-"

"That's not what I meant, lass," Carson said- with only the two of them here now Elizabeth felt more comfortable thinking of him by his first name-, looking at her with a slight smile. "I meant having to let the colonel go after the Phantom."

Elizabeth blinked.

"W-why would that be… difficult?" she asked, wishing she didn't sound so surprised; it hardly helped the impression that she had no personal interest in John's safety. "I've told you, I see Colonel Sumner's reasoning-"

"Elizabeth, you and I spent a lot of time together down in Antarctica while we were sorting out who we wanted for this expedition, and I think I got to know well enough to know when there's something you're not telling people," Carson said, a slight smile on his face as he looked at her. "I saw you when you were talking about how you and the Phantom dealt with that shield issue we had during the storm; you spent a bit more time with him than you're telling us, aren't you?"

For a moment, Elizabeth could only stare back at Carson as the Scottish doctor smiled at her, before she finally sighed in resignation.

"Well… maybe a little," she said at last, trying to think of a way of phrase what she was about to say without actually giving away how much she'd learnt about John during that brief meeting. "It wasn't much; he just told me that he had a safe way of getting around the city that would allow him to avoid the lightning strikes, told me that he'd spent a great deal of time learning how to operate Ancient technology, things like that…"

"You mean you really did speak to-" Carson began, before Elizabeth held up a hand.

"Please… don't ask me anything else," she said, looking earnestly at Carson. "It's not that I don't trust you; it's… well, it's…"

"Complicated?" Carson asked, another slight smile on his face as he looked at her, only a faint trace of disappointment in his eyes. "I understand; you'd… rather some things stayed private, right?"

"It's not that they're embarrassing or anything like that," Elizabeth said as Carson moved to stand up, not wanting her friend to get the wrong idea about her motives. "It's just that…"

She sighed. "As Rodney said, the Phantom hasn't actually done any harm; I just… don't feel like there's any point in talking about it when it doesn't really have any bearing on anything."

For a moment Carson simply looked at her in a manner that suggested to Elizabeth that he knew she wasn't being totally honest with him- he'd always been able to read her rather well in that manner; she had never been sure if his ability to know how much people were telling him was part of his medical training or part of his own personality-, but he finally nodded in understanding and stood up.

"Fair enough," he said, as he smiled slightly at her. "Just remember, if you need someone to talk to about all this, my door's always open."

"Of course," Elizabeth replied, nodding back at Carson as he walked out, leaving her sitting alone in her office once again, the paperwork still spread out before her.

Well, she mused to herself, glancing around her office, that went as well as could be expected.

On the one hand, it was nice to know that she wasn't the only one who thought that Sumner's attitude towards the Phantom was exaggerated, but she still didn't really know how anyone would react to the idea of her actually… feeling something for him beyond simple curiosity.

Hell, she didn't even know how to feel about it; she wasn't even sure what she was feeling! She'd barely even spoken to the Phantom beyond what was necessary to convey the immediate information about whatever crisis they were currently up against, she knew nothing about him as a person beyond his first name and the fact that he'd been active in the Pegasus Galaxy for the last decade or more-

Elizabeth paused.

Hold on a minute… she thought, almost ashamed that she hadn't realised it before. 'John' isn't a name native to this galaxy… so how did he get it?

It was always possible that the Phantom had told her a false name, of course, but Elizabeth didn't entirely believe it; his hesitation might have suggested he was thinking up something aside from the truth, but even with the cloak concealing most of his body from view, Elizabeth knew enough about body language to feel confident that he'd told her the truth about his name.

If anything, that only added to the mystery that seemed to be growing about the Phantom. While the idea that he came from Earth would certainly account for him installing that program that prevented them from dialling Earth- he'd worked out Earth's address and hadn't wanted the Wraith to be able to access the planet if they found Atlantis-, it did nothing to account for how he was meant to have come to the city in the first place.

Even if he'd come here by means other than the Stargate, once he'd discovered Earth's address, why hadn't he simply used the Stargate to go back? After all, it was only the Stargate that dialled the wormhole that needed to have power; according to McKay, the receiving wormhole could take over if there wasn't enough power at the point of origin to maintain the wormhole long enough for someone to travel through it, but otherwise power was only required at the sending end. The Stargate Program may not have existed at that point, but the Stargate itself had already been transferred into the Cheyenne Mountain Complex for testing; it would have been a shock when it dialled, but the Phantom could surely have dialled Earth without any trouble…

Great… Elizabeth groaned, as she slumped back into her chair, one hand pressed against her forehead. Even the answers I get only leave me with more questions

She acknowledged that John- or whatever his full name was- must have his reasons for not telling her everything, and she'd respect them unless the time came where she felt that she was in a position where she had to learn the answers…

That didn't mean she couldn't feel frustrated at the mysteries his presence was presenting to her, did it?


Even as Elizabeth pondered the mysteries of the Phantom's existence, the subject of her thoughts was currently crouched above her office, silently watching her as she spoke to her senior staff, conflicted thoughts flying through his head.

On the one hand, he was grateful for this new evidence that Elizabeth wasn't alone in not regarding him as the threat that Sumner perceived him as; his brief conversations with Teyla and Doctor Beckett notwithstanding, talking to people when you were your only hope in a crisis situation didn't guarantee they'd accept you when the situation was calmer. As it was, however, their brief conversation just now had made it clear that McKay and Beckett at least sympathised with him and acknowledged that he might have his reasons for his actions, even if McKay clearly wasn't as big a 'fan' of his as the other two.

On the other hand… the casual way in which Elizabeth and Doctor Beckett had spoken to each other… the way that he'd called her 'lass' in that accent of his… the way the doctor had looked slightly disappointed that she wasn't telling him more about her meetings with him… his casual comment about how they'd spent a lot of time together back on Earth…

He'd sworn long ago that he'd never attack anyone unless they gave him a reason to do it, but right now he was strongly tempted to take his gun and see about rearranging Beckett's-

NO! he berated himself, cursing as he turned around and began to crawl along the maintenance tunnel to his current hiding location (It was about time for him to see about having a meal anyway; anything to distract him from his current line of thought).

As he'd reminded himself only a short time ago, nothing mattered but that Elizabeth was safe.

If it meant that she was safe to live her life with some doctor with a stupid Scottish accent who couldn't even be bothered to shave properly- it seemed like every time he saw the guy he had at least a day's worth of stubble; it made him look like he couldn't decide whether or not to grow it out-, he'd just have to deal with that.

Her safety was the only thing that mattered.

He had protected Atlantis so that she would have a chance to live a proper life in it; if that life was with him, he would have… liked it, of course… but if it wasn't, he would settle for what made her happy.

If only it didn't hurt so damn much…

God… he groaned, as he felt the faint trace of his tears begin to gather around the eyeholes of his mask. Just once… I'd like something to work out my way…

He knew it was selfish, but he couldn't help it; ever since he came to this city, she'd been the only good thing that had ever really happened to him…

Hell, she'd been the only good thing in his life, period; she had made him feel like he was worth something when his own family didn't seem to care what he wanted to do, making him feel like crap every time he objected to his father's-

STOP IT! he cursed himself. NO living in the past, remember?

His life now might not be perfect, but he was doing what he wanted; that was more than most people ever managed to have the chance to accomplish.

If only he could stop himself from wishing that he could have that one last thing for himself, everything would be fine…

God, I really hate Scottish accents.