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: Thanks are due to Manic Penguin, whose story 'Connections' inspired some of the plot elements I'll be using in the next few chapters and subsequently gave me permission to use whatever I wanted for my own work (Although I'm naturally putting my own spin on things)

The Phantom of Atlantis

A few days after the conclusion of the siege, the last remnants of the Wraiths' temporary presence in Atlantis cleared away and any damage caused by their attacks already being repaired, Elizabeth sat in her office going over the files and messages- many preferring to 're-do' the more grim messages they had sent to their families prior to the siege- her staff had prepared in response to the news of the upcoming trip back to Earth.

Although the Daedalus was already on its way back to Earth- a round trip of almost a month without a ZPM available to enhance their power-, the new SGC commander General Landry- along with a new group referred to in the paperwork Elizabeth had received as the 'International Oversight Agency'; apparently General Landry had been - had requested the presence of Atlantis's senior staff to go over some details about resource and personnel allocation in light of their renewed ability to contact Earth… which, Elizabeth was already certain, would result in her facing several questions about her command decisions that she was not looking forward to, starting with her actions regarding allowing the Athosians access to the city and working their way up from there.

In spite of that particular complication, however, everything was going fairly well in Atlantis at the moment; even the latest revelation regarding Teyla's Wraith DNA had gone down fairly well once it had become known to the general population. A few expedition members had been slightly uncomfortable about the implications of that particular genetic quirk at first, but in general everyone had accepted the view that Teyla was no more a Wraith than those with the Ancient gene were Ancients and left it at that.

It was probably going to cause some problems with the 'IOA', of course, but after Teyla's genes had helped them save the city from the Wraith, and with Teal'c and Jonas Quinn to serve as an example of a precedent of an alien serving in a prominent role on an SG team- to say nothing of their long-term alliance with the Jaffa-, she was fairly certain she could convince them to leave the Athosians where they were…

Quite frankly, even with most of the expedition focused on nothing more than sending messages to their loved ones- or, in the case of those coming with her and the senior staff back to Earth, making arrangements to visit their loved ones; organising files and mission reports were the sole responsibility of the department heads at this time-, the issue of the Phantom remained the biggest problem facing Elizabeth; she had no idea how she was going to deal with the complications that would arise regarding the SGC's opinion of his presence in Atlantis. Admittedly, General O'Neill seemed to be on his side based on his comments when they'd first regained contact with Earth, and the aid he'd provided for them during the siege would go a long way towards proving that he could cooperate with them if the situation called for it, but she somehow doubted that the rest of the SGC would see things that way…

On the bright side, the recent collaboration with the Phantom seemed to have gone some way towards improving his relations with the expedition's military division, particularly in regard to Sumner's opinion of him. Elizabeth acknowledged that the colonel was never going to be John's biggest fan, but he at least seemed to be prepared to try and give the other man more leeway than he had in the past; the fact that he'd allowed John to escape when he could have easily at least attempted to capture him said a lot for his new willingness to consider tolerating the Phantom's presence in the city.

In the end, she supposed that all she'd have to do was keep her fingers crossed and hope for the best; John had helped them out so far when there'd been no reason for him to do so, given their status as the 'aggressors' (They may not have taken any explicit action against him, but they had 'invaded' his home and set themselves up there without asking him), as well as avoiding actually doing any damage to them in retaliation, but whether that would count for anything in the eyes of some of the bureaucrats back on Earth was something Elizabeth just didn't know.

Hell, when you got down to it, it hadn't been long ago that she'd been one of those bureaucrats, hiding behind official forms and regulations while making decisions- she'd tried to negotiate witha group of Goa'uld, for God's sake-; she knew all too well how easy it could be to hide behind what seemed good on paper to avoid having to make the more 'risky' decisions, and trusting someone they know as little about as they knew about the Phantom was definitely a risky decision. General O'Neill might have told Sumner to ask the Phantom for assistance during the Siege, but aid during a crisis was one thing; expecting the SGC overseers back on Earth to trust the Phantom on a long-term basis might be more difficult…

"Doctor Weir?" Sumner said, prompting her to glance up from the paperwork to see her military commander standing at her door. "The science teams have almost finished sorting out the artefacts for the archaeology departments back on Earth, and McKay tells me that the science teams have organised everything they think Earth would be interested in; we're ready to go whenever you are."

"And I assume that McKay's got everything he claims he needs to get the SGC convinced that he requires more than the already-large scientific team he's been provided with already, correct?" Elizabeth asked, smiling slightly as she stood up from behind the desk. "For a man who always goes on about how he doesn't need the staff he already has, he does seem to want a lot of help…"

"Probably an ego thing," Doctor Beckett added as he walked into the office, smiling slightly over at the two of them; evidently he'd finally managed to guarantee that those left in charge of his department during his time on Earth would manage fine in his absence. "You know, like some people get big cars to… compensate… for other areas, Rodney likes a big department to… well, just to show off, really."

"Right…" Elizabeth said, nodding uncertainly at the Scottish doctor- the implications of his theory weren't something she was entirely comfortable with; the idea of Rodney McKay having sex wasn't something she was sure she'd ever be comfortable thinking about- before she looked back at Sumner. "Well, we'd better be off; they're waiting for us back… at the SGC."

Neither of the men before her bothered to ask what she meant by that last comment; Sumner may have made it clear that he primarily saw Atlantis as another assignment rather than anything else, but even he had evidently come to see Atlantis as more of a home than a simple place of business.

Earth might be the place where they had been born, but Atlantis- for all that they had only been here for a few months- had already become their home (Even if Elizabeth at least was starting to consider herself more of a tenant; John might be officially a 'renegade' in this city from Earth's perspective, but she couldn't help but regard him as the real owner who just let them live there).

Actually, looking over the personnel files before her as her visitors returned to their tasks- Carson shooting her an apologetic smile-, so far Elizabeth had only discovered one request for transfer back to Earth, and given that the request came from Doctor Kavanagh- the man had been frustrating even before she'd rejected his initial suggestion to raise the shield during that incident when the gateship got stuck half-way through the Stargate, and had just become ever more insufferable afterwards- nobody was that concerned about his departure (Although Elizabeth had found herself wondering why he'd become rather more jumpy than annoying ever since they'd sent messages back to the SGC; every time she entered a room where he was working, Kavanagh always seemed to go out of his way to get out of it as quickly as possible…).

Shaking thoughts of that frustrating doctor aside, Elizabeth turned her attention back to the matter before her; they were going back to Earth tomorrow, and she still hadn't finished sorting out who'd be coming back with them and who would remain in charge of the city in their absence. Teyla would have been her first choice as her 'stand-in', but Sumner- no matter how much he respected Teyla as a teammate or with his recent collaboration with the Phantom- still felt uncomfortable entrusting Atlantis to someone who hadn't come from Earth, which meant that Elizabeth had to make a choice between Zelenka, Doctor Viro- Carson's selected 'second'-, or just attempting a compromise by the previously-mentioned men and Teyla in charge all together.

In the end, that one would probably work out more efficiently; at least that way she wouldn't be left worrying about how one of her staff would cope with a workload that even she had trouble with, given that they'd all be focusing simply on taking more direct responsibility for their own departments (Especially since all 'gate activity would be suspended until their return from Earth to focus on reconstruction of Atlantis)…

Sighing briefly at herself, Elizabeth returned her attention to the more immediate matter of tying up the last loose ends left to her; if she didn't sort out specifically who was responsible for what soon she'd reach the point where she was too tired to properly concentrate.

She was just grateful that she didn't have far to go to talk to her family while also trying to accommodate talking to the political support in Washington, given that Simon and her mother were both in that city; Carson going away to Scotland for a few days to visit his family was already more of a separation than she was entirely comfortable with (Although she freely acknowledged that it was mainly increased familiarity after spending so long with the same group of people that was responsible for that issue), and she'd prefer to remain as 'on-sight' as possible when discussing something as important as Atlantis's future.

After spending so long struggling just to survive out in the Pegasus Galaxy, it would be nice to be able to guarantee for her staff that they would no longer have to worry about struggling for some of the necessities like food or clothing in order to operate on a daily basis like they'd been trying to do ever since they used up their initial supplies (Which wasn't to say trade wouldn't continue; some of the clothing they'd acquired in their more recent deals was actually rather comfortable…).

Finally, after filling in so many forms that she felt like her wrist was going to come off from exhaustion, Elizabeth signed her name on the last dotted line of the last form before her- she'd had to go back over a couple to make sure she hadn't missed something from fatigue, but in general she was comfortable with how things had turned out- and stood up to head for her room.

Right now, after the stress and challenges of the last few weeks- even with John's help they'd lost far too many people- , she just wanted to curl up in her bed and get away from the stress of running a city as elaborate as Atlantis for a while.

If she could just get a few hours' uninterrupted sleep, away from Sumner's military-fixated mindset and McKay's occasional panic/frustration attack about everything from the 'incompetence' of his staff to his own health, she was sure that she'd feel far better in the morning…

As she stood in front of the Stargate the following morning, however, despite being well-rested and secure in the knowledge that she'd dealt with everything she could deal with in order to make it as easy as possible for her 'replacements' to cope with whatever paperwork they might have to tackle over the next month, Elizabeth knew that she'd been kidding herself.

No matter how hard she tried, she couldn't stop her thoughts from coming back to the central issue she'd be facing when she got back to Earth; the presence of the Phantom at the SGC. The issue of their reaction to the Wraith was a definite danger, but there was no way anyone could blame her for their 'waking up'- even Sumner would have nothing to worry about, given that the Wraith had only 'activated' because of Lieutenant Ford's actions and the lieutenant certainly wasn't around to deal with the consequences of that decision-, and her dealings with the Genii only turned out badly after they betrayed Sumner's team, which meant that the presence of the Phantom in the city was the only issue she would really have trouble dealing with.

The Wraith might be dangerous, but in the end the IOA could be relatively certain how they were going to act, especially after learning about their interest in Earth; Elizabeth could already predict multiple 'lectures' about the dangers of an independent renegade element like the Phantom operating in the city…

Pushing those thoughts aside once again- she could worry about how she'd deal with those questions when she was actually in position to answer them-, Elizabeth took a deep breath and turned around to look at the group of expedition members who had gathered together for their trip back to Earth.

"It's been a long year for all of us," she said at last, her mind briefly flashing back to all the faces who hadn't lived to see this day (She knew that it was actually a couple of months short of a year, but now was hardly the time to get bogged down in details like that). "We've seen and accomplished things that none of us would have believed possible even after learning about the Stargate program, confronted an enemy more ruthless than even the Goa'uld, and found ourselves learning that even the place we thought would be our exclusive home has a few… surprises… in it for us," (She avoided specifically naming the Phantom even if she knew that everyone would know who she was talking about; that particular issue was one area that she wanted to keep out of the 'public eye' as much as possible), "but, in the end, we've not only managed to survive, but we succeeded in fighting off a foe so powerful that they all but totally defeated the Ancients. It's been an incredible experience, and I'm proud to have shared it with all of you…"

She swallowed for a moment, briefly wishing that she had the freedom to say what she really wanted to say- that she'd come to respect and admire so many of them as friends-, but knowledge of Sumner's preference for emotional detachment, combined with the risk if she said something that might even hint at her contact with John, kept her from saying anything.

"…and now," she continued, her composure regained once more, "it's time to return to Earth so that others know what we have discovered here, and give the rest of humanity a chance to benefit from what we've learned. We've all come a long way since we first arrived here; it's time to let the people we left behind know what we've accomplished."

Glancing up at the balcony where Teyla and the rest of the control room staff were watching her- everyone else was presently too busy with the repair work and checking out some of the newly-activating systems that were becoming available with the new ZPM to be here-, Elizabeth gave the Athosian woman a brief smile of approval, before she turned back around to walk through the Stargate, ready to return to the world that now was only her home due to the location of her birth…

As Elizabeth led the small group back through the Stargate, she was unaware of the darkly-clad figure watching her from his usual position on the other side of a small hatch near the ceiling of the room, a slight smile on his face under his mask as he watched her.

He'd done it.

Even when faced with a Wraith fleet on a scale this galaxy hadn't seen since the Ancients, Elizabeth had lived to make it back to Earth…

John tried to restrain the brief pain he felt in his heart at the thought of what was coming next, but he couldn't help it.

She hadn't just made it back to Earth (Although that was the most obvious part of the trip she'd just taken through the Stargate); she'd made it back to Simon.

Even if the Elizabeth he'd met all those years ago had only briefly mentioned the man she was planning to marry before she was given command of the Atlantis expedition during her talk with him, the possibility that the Elizabeth he would meet when the time came for the expedition to arrive would go back to Simon in the end- to say nothing of his own feelings about that particular issue- had always been one of the many little personal issues he'd struggled to overcome during his time alone (Along with other matters such as his reaction when he found himself dreaming about Elizabeth… that way… in the first place and working his way up from there).

If she couldn't persuade Simon to come back to Atlantis with her now that they had the ability to regularly return to Earth…

Would she stay with him?

Atlantis might be the most incredible experience of a person's life, but it didn't exactly make it easy to create a normal life for yourself; if Elizabeth had a chance at happiness…

If she had a chance with Simon, she deserved to take it.

She deserves better than a life with a monster

Shaking that thought aside- the last thing he wanted was to start getting negative about his own sense of worth when Atlantis was due to get a serious personnel upgrade in a matter of weeks; no matter what Sumner had done for him at the end of the siege there was no guarantee his superiors would be as tolerant, which meant he'd probably have even more soldiers to avoid-, John turned around and began to head towards one of his old storerooms.

If he was going to figure out what to do with himself if the worst came to the worst and Elizabeth did leave Atlantis (Thus costing him his only real ally on the senior staff; even without Sumner's evident discomfort at anything related to him, McKay still clearly wasn't entirely certain about him and Teyla and Beckett's authority over the kind of situations he might create by his presence was limited), he might as well do it somewhere comfortable…

AN 2: Well, that's the first part of this series over; the next part, "Mystery of the Phantom", will be up as soon as possible, I can assure you (I just can't give you a specific time-frame at this point)