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: This takes place a couple of weeks or so after the last chapter, at the same time as "Before I Sleep" occurred in canon; while the main events of that episode won't be happening here- John keeps the body of Elizabeth's future self somewhere a bit less easy to find than it was 'stored' in the show-, that's not to say there won't be some… interesting personal moments (On that topic, I hope the pot scene works out OK; I had a little trouble getting an idea for how John could give Elizabeth something when he's 'stuck' in Atlantis, but I think what I came up with works)

The Phantom of Atlantis

A couple of weeks later, with all offworld team members currently working on their own projects- Colonel Sumner, Lieutenant Ford and Teyla were carrying out surveys of some of the outer areas of the city while Doctor McKay led the science department in trying to crack the password that prevented them from re-dialling Earth-, Elizabeth stood reflectively on the balcony that had been unofficially designated as 'her' balcony- the balcony where she went whenever she wanted to think about recent events without anybody else bothering her-, her mind once again drawn to the central issues that had been plaguing her thoughts since Chaya's departure.

To this date, none of them had any clear idea about why she decided to depart like she had without providing them with any kind of explanation. It wasn't that Elizabeth felt they were entitled to the information, of course- she fully respected Chaya's right to not tell them things that she might want to keep private for some reason or another, particularly since she didn't seem to have any hostile intentions towards Atlantis-, but after leaving them so abruptly, she would have expected Chaya to at least explain her reasons out of politeness if nothing else. They'd attempted to dial Proculus again after Chaya had left, but their subsequent attempts to establish a wormhole had met with nothing but failure, the seventh chevron simply failing to engage; either the Stargate at the other end had been destroyed or Chaya had somehow prevented them from gaining access.

Although she hadn't voiced her opinion on that particular topic, Elizabeth was generally inclining towards the second opinion. She somehow doubted that Chaya would destroy the Stargate now after leaving it alone for all these centuries simply because they knew she was there, but preventing them from accessing the Stargate certainly fit what she knew of Chaya's personality; she wouldn't be surprised to know that the Ascended woman knew that Sumner wanted to question her for any further information she might have about the Phantom and had decided to avoid any possible confrontation in the easiest possible manner. Elizabeth freely acknowledged that Sumner couldn't actually do anything to make Chaya answer his questions, but that didn't mean that Chaya would want to have to put up with his questions anyway; preventing them from dialling the Stargate had probably seemed like the simplest option to avoid an uncomfortable situation.

She just…

Elizabeth sighed.

As much as the question of Chaya's motives and purpose remained a central issue, the one thing that Elizabeth really wished that she knew the answer to was what Chaya had meant by that last… comment she'd 'made' before she departed.

She had her theories, of course- given who Chaya had come to Atlantis to meet, coupled with the fact that she hadn't met many of the expedition during her stay in the city, there weren't that many people she could be referring to-, but with barely any actual evidence to base those theories on she was reluctant to actually voice them.

Besides, even if she was right- and she had her doubts that she was; why would… he… be interested in a diplomat in a city full of soldiers?-, why should it concern her? She barely knew the man, what she did know demonstrated that he was clearly a violent individual, he had displayed little real interest in getting to know her personally, he'd barely spoken to her beyond what was necessary for him to say in order to fill her in on the current crisis…

And yet, at the same time, he'd given her an Ancient shield device when he didn't have to, he'd told her his name (And it was his real name; she was sure of that if nothing else) when he didn't have to, he'd spoken to her for permission when attempting something as potentially dangerous as detonating a naquadah generator…

Even at his most brutal, when he'd killed the Genii soldiers who'd invaded Atlantis, the fact remained that he had killed them; if he'd genuinely been interested in violence simply for the sake of violence, wouldn't he have left them alive to 'prolong their suffering'…?

Why was it so important to her that the Phantom should turn out to be a good person?

As much as his actions had helped them to survive so far, she knew that Sumner had a valid point when he said that the Phantom's fundamental motives were still a mystery to them; there was always the possibility that he had some underlying motive for remaining hidden that none of them could guess at…

Elizabeth knew that there was a chance Sumner's suspicions were valid.

She was a trained diplomat; she knew that it was foolish to go into any situation and form an opinion of the people involved without first becoming aware of everything about the current crisis.

So why, even when she knew so little about the Phantom's own motives or background- given his surprisingly Earth-like name, even the galaxy he was born in was currently a mystery to her; 'John' didn't sound like a name from the Pegasus Galaxy but she had no idea how someone could have made it to Atlantis from Earth without using the Stargate-, did she spend her free time trying to figure out how his motives could be for the best without even considering the idea that he might have malicious intentions for longer than a few minutes? She might pride herself on being a good judge of character, but she'd only met the man once in person, and even then the meeting had only lasted for a few minutes at most; what made her so certain that-?

"Penny for your thoughts?" a voice said from behind her.

Elizabeth nearly jumped in shock at the sound of the voice.

"John?" she said, turning around to look at the masked man standing before her in surprise, his long black cloak draped around him as he stared nonchalantly at her. "How did you-?"

"Get here without being seen by the colonel's security teams?" John finished for her, a slight smile visible on the left side of his face, the right still hidden under the mask that now gleamed in the sunlight. "I know my way around the city fairly well; working out a path here that allows me to avoid being seen by them isn't as hard as you might think."

"Ah," Elizabeth said, nodding slightly at that before she decided to ask another, hopefully neutral question.

"And… you're sure you're safe being here?" she asked, looking pointedly at him. She knew that it could be taken as a threat on her part- implying that she might contact Colonel Sumner to let him know where the Phantom was currently located-, but given how he'd interacted with her so far she had hopes that he would simply interpret it the way she'd meant it; a simple question hoping for an answer that would explain why he trusted her as much as he seemed to.

"Well, if you'd wanted to let Sumner and his men catch me, I somehow doubt I'd be standing here right now; you haven't exactly gone out of your way to make it easy for them to find me so far," John pointed out, a slightly teasing tone in his voice that would have angered Elizabeth if anyone else had used it but somehow seemed… different… when it came from John. "Besides, the door's locked and the glass is currently opaque; nobody can come here or see who is here without your consent-"

"Hold on; the glass is opaque?" Elizabeth repeated, turning to look in surprise at the glass that she could have sworn had been transparent- albeit coloured- earlier, only to see that John was right.

It was opaque now…

But Elizabeth could have sworn-

"Just a little privacy feature the Ancients included; it wasn't like they wanted people to be able to see them if some of them decided they wanted to try something… different… out here, so those with the Ancient gene can change the glass to be a bit harder to see through if they wanted to be left alone," John said, smiling slightly at the incredulous expression on Elizabeth's face as he broke into her train of thought. "Advanced civilisation or not, they were still people when they lived here, you know; the fact that they ascended to a point where they don't actually have bodies any more doesn't mean they didn't have… urges…"

"Yes, I'm aware of that; someone back on Earth once had an… encounter… with an Ascended being that made that fact perfectly clear," Elizabeth said, cutting John off before he could go any further- there were some things that she did not want to think too much about, even with several thousand years between the events John was… hinting at… and the present- before she looked directly at him once again; evidently he wasn't going to clarify why he trusted that she wouldn't betray him any time soon. "Anyway, enough about the Ancients'… private lives; why are you here, anyway?"

"Oh, that's simple enough," John said, as he reached into his cloak with one hand before pulling it back out. "Happy birthday."

Elizabeth could only blink in surprise at the gesture, uncertain whether to feel touched or uncomfortable at the fact that John had risked being captured by Sumner's team just to give her a birthday present.

Then she realised just what he had given her, and her confusion only increased.

"A pot?" she said, looking back at John inquiringly.

She appreciated the gesture, but after the Ancient shield device he'd given her barely a week or so after she'd arrived in the city, a pot seemed like a pretty significant… change between types of gift.

"Given that it's hard to top an Ancient shield device in terms of something practical, I decided to just go for something nice visually and hope for the best," John said, shrugging nonchalantly as he looked at her. "I picked up a few things over my time in this galaxy- some little trinkets here and there to serve as mementos of the worlds I'd saved, that kind of thing-, and I found a few places around the city to keep them safe; I heard someone mention that your birthday was coming up, and I figured that…"

He shrugged. "Well, I thought you might like it; it's just a little thing, I know, but-"

"It's fine," Elizabeth said, raising a hand to cut John off before he could say any more, smiling slightly at the pot she now held in her hands before she looked back up at him. "It was… well, I appreciate the thought, John; thank you."

For a moment, John simply stood there, apparently uncertain about what he should do next, only for him to finally smile as he looked at her, the warm grin only partly visible but no less touching underneath his mask.

If Elizabeth had needed further evidence to assure her that John meant the expedition no harm, the look on his face right now was it; nobody that touched at somebody's appreciation of a simple pot as a gift could have plans against people they'd been trying to protect for the last few months…

And why was proving him trustworthy still so important to her?

"You're… welcome," John said at last, his tone suggesting that he was unfamiliar with that word passing his lips. Elizabeth couldn't help but wonder what could have happened to him in his past to make him uncomfortable with accepting praise- was he simply unused to staying around after he'd saved people from the Wraith in the past or was it something deeper than that?-, but shook that thought off; it wouldn't do her any good to think of questions that she couldn't learn the answer to at this point.

"Any chance I can return the favour at some point?" she asked, smiling slightly at him as she tried to change the conversation's direction to a more casual topic, only for the smile to fade as she saw John looking uncomfortably at her all over again.

"Uh… that's… really not practical; I… well, I lost track of dates a long time ago," John replied, looking apologetically at her, his discomfort at this topic easily visible even with his mask concealing most of his face. "I mean, I know how old I am in terms of years- mid to late thirties, really-, but I don't know the precise date or anything; I only even know it's your birthday because I heard someone mention that it was your birthday in a couple of days in a corridor a while back-"

"You 'overheard' someone in a corridor?" Elizabeth repeated, looking at John with what she knew was a slight trace of scepticism. As much as she might trust that he wouldn't betray Atlantis- after all the effort he'd gone to in order to protect the city for them when he could have just as easily driven them out, she was more than slightly convinced that he wasn't an enemy-, at the same time she couldn't help but be concerned about his ability to find out little things like that just by listening in on conversations.

If he could learn things like that about them just by listening in. what if someone- or something- else managed to gain access to the city and do the same…?

"Don't worry; I'm the only person who knows where to go to hear that kind of stuff, I assure you," John said, raising a hand to cut off the question before she could even ask it. "In any case, it took me ages to find some of my old routes, and that was when I had the city to myself and nothing but time on my hands while I was training; the odds of anyone finding the routes in an occupied city like this with no idea where to start looking and security teams all over the place are pretty slim, I assure you."

"You're… sure about that?" Elizabeth asked, looking uncertainly at the cloaked figure before her.

"Look, trust me on this; these access routes are not easy to find even if you know what you're looking for, and the only reason I even started looking for them in the first place was because I had a hunch there might be something there," John said, smiling reassuringly at her. "There's no way that the passages I use can be found by just anybody, I assure you; you'd need to actually know where to look if you were going to find anything that could do you some good, and even then the odds of you actually figuring out where to go once you were in there without any prior knowledge of how they're laid out are slim to none-"

"Passages?" Elizabeth said, raising a hand to look inquiringly at the man before her. "What 'passages' are you talking about?"

For a moment John simply stared back at her, an expression in his eyes that gave the impression he was suddenly trying to come to a decision on the spur of the moment, before he finally seemed to come to a decision.

"It's… connected to the way I… get around Atlantis," he said at last, looking uncomfortably at her. "A few passages here and there that aren't covered by the city's sensors; how I found them is a bit of a complicated story and I'd rather not get into it right now…"

For a moment Elizabeth thought about asking for more information- as the leader of Atlantis, she had a right to know about anything that might affect the city's security-, but she stopped herself before she actually said anything.

After all the time she'd spent telling Sumner that there might be a valid reason for the Phantom not telling them everything he knew about the city straight away, it would be almost hypocritical of her to insist that John tell her something if he didn't want to talk about it simply because she thought he should tell her. John had already assured her that nobody else knew of or could use the tunnels apart from him, and given how long he'd been here, she had little reason to assume that he was lying.

Besides, when you got down to it, Atlantis was John's city more than it was theirs; as he'd implied during his initial conversation with Kolya, if John didn't want them in the city, they'd probably have been driven out long ago. If he hadn't attempted anything by now- to say nothing of how much effort he'd gone to stop the nanite virus from spreading a few weeks ago; if he'd wanted to get rid of the expedition why would he have gone to so much trouble to protect them from something that could have lowered their population to a level that he could have defeated more easily?- he probably wasn't going to do so; John having access to some secret passages didn't change that fact that much.

If anything, the fact that he knew about Atlantis's secret passages and hadn't yet used them against the expedition only confirmed for Elizabeth that she wasn't wrong in trusting him; if nobody else knew about these routes, he could have easily faked an 'accident' for Sumner or some of the military personnel who'd been causing him difficulty so far, and yet he'd done nothing of the sort.

"Don't worry about it," she said at last, looking reassuringly at John as he stared uncomfortably at her; clearly he hadn't know how she was going to react to his statement. "I… well, as crazy as Sumner might see it as, I trust you."

It was hard to be sure with the shadows caused by the mask, but Elizabeth could have sworn that John's eyes widened at that last comment.

"Really?" he said, looking at her with a tone of barely-disguised surprise. "You don't… well, you don't want to know about the passages? I mean, Sumner'd probably be really eager to block some of the entrances up to limit my access to the city…"

"Well, the way I see it, if you'd been going to use your knowledge of the city against us you would have done it already," Elizabeth said, smiling reassuringly at him to take any potential sting out of her words. "Given the lengths you've gone to in order to protect the rest of my expedition so far, the fact that you know something else about this city that we don't doesn't change the fact that you've been nothing but helpful for us to date; if you don't want to tell me something about the city…"

She shrugged. "You've been here since before any of us; if you think it's not time to tell us about something, I'm hardly in a position to demand answers.

For a moment, Elizabeth and John simply exchanged silent smiles- Elizabeth couldn't help but wonder if John felt that same… stirring… in her chest as she did when she saw the half-smile under his mask-, only for the moment to be broken when Elizabeth's radio activated.

"Doctor Weir?" Doctor Grodin's voice said over her radio. "Doctor McKay just called; he wants to talk with you and Colonel Sumner about something he found in the Ancient database."

"On my way," Elizabeth confirmed, tapping her earpiece briefly to respond before she turned back to look at John. "Sorry, John; duty-"

"Calls, right?" John replied, nodding in understanding. "Don't worry; just make sure you get that pot somewhere safe. I'll… well, I'll be around for when you next need me, huh?"

"I wouldn't have it any other way," Elizabeth replied, a slight smile on her face as she nodded back at John as she placed the pot in her right hand and lowered her right arm down to the side; so long as she was careful and went directly to her office- she could easily claim that she wanted to check something out before she met with McKay-, she should manage to find a secure place to store the pot in her office while she attended her next meeting without anybody seeing the pot itself.

It might be paranoid, but she had a feeling that Sumner would even regard a pot from the Phantom as a potential trap…

It was only when she took in the glass window before her that Elizabeth realised that it had suddenly turned clear again; a quick glance behind her swiftly confirmed that John had vanished while she was moving the pot to her right hand, leaving no trace that he had ever been present.

Even knowing that she could trust him, Elizabeth couldn't stop herself from shivering slightly.

The speed that John must have to be able to vanish from view on an open balcony that rapidly, to say nothing of the depth of his knowledge of the city if he was able to arrive and leave what seemed like any location he wanted that rapidly…

The more she learnt about the man known to the Pegasus Galaxy as the Phantom of the Ancestors, the more grateful Elizabeth Weir became that what she learned also leant increased weight to the idea that he was on their side.

She just wished she could identify why she felt so… strange… whenever she thought about him; what was it about that man that interested her so much…?

AN 2: I'm not entirely happy with this chapter, but we get on to more straightforward territory next up; just consider this a 'filler' before the main events