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 marks the second part of my "Phantom of Atlantis" series, an AU take on "Stargate Atlantis" where John Sheppard, instead of being the city's military commander, is a mysterious masked figure who has been living in Atlantis and fighting the Wraith for almost two decades prior to the expedition's arrival in the city; reading the first story- "The Phantom of Atlantis"- will be required to understand what's going on here in greater detail

AN 2: Thanks are due to Manic Penguin, whose story 'Connections' inspired some of the plot elements in the upcoming few chapters (All of which are naturally used with her permission)

Mystery of the Phantom

Sitting in the SGC conference room opposite the newly-appointed General Hank Landry- General O'Neill had apparently left for his new Washington assignment shortly after their return from Atlantis; he claimed that he'd only stayed around as long as he had to make sure everyone got back all right-, Elizabeth was already beginning to feel anxious about this meeting.

The traditional check-ups in the infirmary had proceeded fairly smoothly, which was something that Elizabeth was definitely grateful for. McKay had complained about the needles, of course, but that was just something she'd come to expect by this point; the only truly frustrating detail had been the sheer length of time they'd spent there as everyone's medical records were updated to compensate for their year away, and that was only because going over your health for the past year had never been something Elizabeth had particularly enjoyed doing.

The subsequent debriefings as she and the rest of her staff went over some of the details in the respective mission reports of their various department members proved to be rather difficult at times, of course. Kavanagh alone seemed to be complaining that he had been unjustly forced out of his position despite the fact that it was hardly anyone else's fault if nobody liked him, while Peterson seemed to alternate between being grateful to be away from Atlantis and being angry at the fact that everyone seemed so unsympathetic towards the fact that he'd nearly died when those nanites had infected him…

Even with all those issues put aside for the moment, however, now that she was actually being called upon to justify their latest request for new staff and resources, Elizabeth couldn't help but feel grossly out of practise at this particular type of meeting. As much as she might like to regard herself as an accomplished diplomat, the fact remained that she hadn't actually been engaged in any actual large-scale diplomatic relations since she found herself in Atlantis; what negotiations she had carried out had been relatively 'small-fry' compared to what she was dealing with at present.

Negotiating some temporary treaties and alliances with people in the Pegasus Galaxy to gain food in exchange for their promises of future protection wasn't the same as talking to the SGC on Earth, no matter how much she might want to act like it was. For one thing, if she didn't manage to make her case in Pegasus the worst that could happen was the people of her city had to go without food for a short while; if she failed to make her case here, she stood a very good chance of access to Atlantis being cut off for good, or at least losing some of her staff if her superiors decided that they'd prefer to cut back on the military or scientific divisions of the city (The presence of the Wraith might prompt some people to either cut back on sending out teams to other worlds, thus lessening the need for a military division, or the need to deal with the Wraith might prompt them to withdraw some of the scientists; Elizabeth couldn't know which would turn out to be the case).

"Right then," Landry said as he looked at her, his tone an interesting combination of seriousness and a light trace of humour, "first things first, while there's an expected level of cannibalism from the SGC, take into account that we do still have issues to deal with in this galaxy even with the Goa'uld having been virtually eliminated, so have your people keep that in mind when attempting to poach my people."

"I'll remember that," Elizabeth replied, allowing herself a slight smile at the general's response. The earlier debriefings on mission reports had been conducted in front of a larger group of SGC officials to make sure everything was covered from all relevant angles, but with the current meeting it had been decided that a more individual approach with both leaders bringing their staffs' concerns and requests forward would work best. "Of course, the advantages of access to a fully-powered ZPM make it easier for us to recruit further staff, given that Atlantis is no longer such an uncertain long-term project."

"Yes, Homeworld Security has already noted the obvious benefits in your requests to get additional resources supplied now that you've established what we might need for further reconnaissance efforts in Atlantis," Landry said, nodding slightly at her before his expression became somewhat grimmer. "On that topic, Colonel Carter asked me to confirm that you are aware that not all the scientists on your list can be made available to you; the red flags that would go up as a result of that many major names disappearing would attract too much attention for anyone to conceal."

Having already anticipated a comment like that- she might have been out of touch with current events on Earth but she doubted things had changed that much-, Elizabeth responded with the more cautious reply.

"Given that we now have the ability to regularly maintain contact with Earth, both through the Stargate and the Daedalus's ferry runs, the general cover story of a scientific expedition of a classified nature should prove sufficient in most cases," she said, looking back at the general with a casual gaze. "Coupled with the fact that we're actually able to provide an effective time frame of how long we're expecting the staff to commit to the project, I don't foresee any serious problems with getting further staff. Besides, at present Atlantis is barely operating on more than a skeleton staff at this time, and I think we can all agree that an endeavour of this magnitude requires more than that."

"Quite," Landry said, nodding briefly at Elizabeth before he looked at her with a far grimmer expression. "On a related topic, more than one member of those government agencies aware of the SGC has expressed… concern… about the continued presence of the individual known as 'the Phantom' within Atlantis."

"The Phantom?" Elizabeth repeated, trying to sound casual even as she was inwardly crossing her fingers; she had to remember to watch what she said about this particular issue…

"While nobody can deny that his actions did indeed prove helpful towards us during the siege of Atlantis, as well as providing you with other assistance while you were isolated from Earth," Landry continued, his expression becoming increasingly solemn as he stared at her, "we also have to keep in mind the possibility that his agenda might change at some future date; just because he's worked to our benefit so far doesn't meant that he'll continue to do so."

For a brief moment, Elizabeth wished that she could mention what she knew about the Phantom to try and act in his defence, but quickly stopped that thought before it could go any further; the last thing she wanted was to give away how she knew the Phantom wouldn't do anything against them (Especially when even she had to admit that her 'knowledge' was based more on feelings than anything else).

"As my reports have indicated," she said, trying to bring the conversation away from a potentially dangerous area, "Colonel Sumner and I are working to do what we can to apprehend the Phantom, but so far he has proven exceptionally skilled at evading capture; even when he returned one of our gateships after using it to detonate a naquadah generator, he somehow managed to evade our teams without anyone even seeing him depart from the gateship in the first place despite an entire team being dispatched to apprehend him as he returned."

"Yes, I read that in the files," Landry continued, his expression becoming increasingly grim as he looked at her. "Actually, the issue with those nanites is actually a particular example of one of the main points of concern at this time; some of my superiors are naturally… uncomfortable… about the obvious implication that he was aware of their existence and chose not to warn anyone about them."

"If you'll consult the reports, you'll note that Doctor McKay stated that the nanites were released due to flooding damage sustained in the storm," Elizabeth responded, folding her arms as she looked at Landry. "Admittedly, it would have been helpful if we had been made aware of their presence regardless, but given that, if it hadn't been for the storm, we would have simply discovered the nanites while they were still contained, and hence no danger to anyone who knew enough about what they were doing."

"True," Landry said, nodding slightly in recognition of Elizabeth's point. "However, there are other factors to consider, most notably the issue of that shield he programmed to activate whenever you dialled this galaxy."

"Again, the files clearly explain that that program was installed before any of us even arrived in Atlantis; the obvious assumption would be that the Phantom set that up to prevent the Wraith from gaining access to this galaxy after learning where they went after leaving Pegasus after he consulted the city's databanks," Elizabeth replied, already cursing herself for her last statement as soon as she finished saying it; speculation like that wasn't the best way to avoid attracting attention to her opinion on the Phantom.

"I don't deny that it would have been far more beneficial for us if he had deactivated that program as soon as he could," she continued, knowing even as she spoke that she was walking a fine line between being objective and giving away more than she might like about her… interest… in the Phantom, but nevertheless resolved to continue, "but when you consider that we are technically the intruders in this situation- he has lived in Atlantis, according to all reports, for almost two decades before we arrived there-, the fact that he has taken no action to drive us out of the city since our arrival- indeed, he has taken action more than once to allow us to remain in this city when he could have easily driven us out- is something that we shouldn't overlook just because he operates independently from our own command structure."

"Nobody is denying that the Phantom's presence has proven vital to your expedition's survival at crucial moments, Doctor Weir; what they object to is his continued status as an independent element rather than operating within a defined command structure," Landry replied; for a moment he seemed to be looking at her in an apologetic manner, but then the moment passed and he was simply staring grimly at her once again. "Your point about him having lived in Atlantis for longer than us is a valid point, don't get me wrong, but many people feel that, if he's willing to have us live there in the first place, he should be equally willing to allow us greater access to whatever knowledge or information he has to share. The fact that he has so far told your team nothing about his knowledge of Atlantis beyond what you needed to know at a time of crisis has several people understandably concerned that he has some hidden agenda that we are as yet unaware of."

"You can assure your superiors that we are making all possible effort to apprehend and question the Phantom about his knowledge of Atlantis; as we have already mentioned in our reports, that knowledge of the city that makes him such a valuable target also makes him rather difficult to have a conversation with in the first place," Elizabeth replied, trying not to think about those moments when he'd visited her on the balcony; in the end, it couldn't exactly count as questioning him when he was always the one who made the decision to initiate contact in the first place. "Should they need further details about our plans regarding the Phantom, Colonel Sumner is the person to ask for information; he has final call in military-related matters, after all."

"Naturally," Landry said, nodding briefly back at her, a slight smile visible at the corner of his mouth- Elizabeth chose to take that as a good sign; hopefully she'd given him something to think about-, before the smile faded and his expression became more solemn once again. "Getting back to the matter of staff…"

Even as she responded to Landry's words, however, Elizabeth couldn't shake the concerns that his earlier comments had sparked off in her mind.

What would happen to the Phantom now?

Sumner might have allowed him to escape once, but would that decision reflect a new policy towards the Phantom's existence overall, or was it strictly a one-time method of 'repaying his debt' (Or something like that; Elizabeth would be the first to admit that she wasn't up on the fine details of military terms even if she had spent a significant portion of her life working to achieve negotiations to prevent military action being required by anyone) to the Phantom for helping to protect Atlantis?

Elizabeth didn't know.

More to the point, she didn't know why it mattered to her so much; how could this man have captured her interest like this when she didn't even know his name…?