Mystery of the Phantom by Marcus S Lazarus
Summary: (AU, Part 2 of series) As their second year in Atlantis begins, Elizabeth finds herself drawn ever further into the mystery of the Phantom of Atlantis, while John finds himself constantly torn between what he has become and what he wishes to be...
Categories: Fanfiction Characters: None
Genres: Action & Adventure, Alternate Universe, Drama, Mystery & Suspense, Romance
Warnings: None
Challenges: None
Series: The Phantom of Atlantis
Chapters: 50 Completed: Yes Word count: 164646 Read: 667875 Published: September 15, 2009 Updated: August 09, 2014
It's a New Bond by Marcus S Lazarus
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
Mystery of the Phantom

“All right,” Elizabeth said as she sat around a table in the commissary, looking at Sumner, McKay and Beckett as they ate their various lunches; no matter how good some of the food in the Pegasus Galaxy had been, there was no real substitute for the foods they’d grown up with over the years. “Now, everyone’s clear on the current timetable?”

“Seems straightforward enough, anyway,” McKay confirmed, tucking into a plate of something Elizabeth couldn’t immediately identify save for the fact that it definitely wasn’t lemon chicken (McKay had practically emptied out the commissary of everything but the aforementioned food upon his arrival). “I spend a few days in Area 51, Sumner and Carson go over personnel files and any new equipment they’ve picked up here while we’re away, and you’re off to Washington to get everything straightened out regarding how many people we can request for the upcoming year?”

“Essentially, yes,” Elizabeth confirmed, nodding briefly back at McKay and wondering how much longer she could allow him to get away with repeating himself before she could legitimately tell him to stop it; she was fairly sure she’d gone over the timetable at least a dozen times by this point. “We’ve only got around a couple of weeks before the Daedalus gets back to Earth and gets checked over for the return trip; given that it should take the better part of the first week for me to sort out specific numbers for you all, that time is generally free to do what you will with it.”

“Well, that’s good to know at any rate; been meaning to visit my family since I got back here,” Carson said, smiling briefly at the thought even as he continued to chew his sandwich. “A few days back should be enough for her, anyway…”

“Quite,” Sumner said, nodding briefly at Carson before he looked back at Elizabeth with an expression that she couldn’t quite identity. “I’d… well, I’ve got a few people I need to see myself.”

“Colonel Everett’s family?” Carson asked, looking at Atlantis’s military leader with a slightly uncertain tone; the colonel had yet to discuss his feelings on Everett’s sudden loss of approximately a decade’s worth of life energy, but Elizabeth had been informed that Sumner had been seen in the medical bay looking at the bed where Everett had been examined before his return to Earth.

“Among others,” Sumner said briefly, evidently uncomfortable with taking that conversation any further. Elizabeth briefly thought about asking him for further information, but swiftly decided against it; as McKay had pointed out more than once, Sumner wasn’t the type of military commander who spent much time in social conversation with the rest of his team.

“Right…” Elizabeth said, glancing down at her watch before she sighed and stood up. “Well, I’d better be off; I still have to make sure everything I need from here is packed before my flight.”

“Have a good trip,” Carson called after her, prompting Elizabeth to nod in response before she walked out of the commissary, heading for her office as the rest of the Atlantis senior staff continued to eat their assorted foods.

For a moment, as she paused at the door to look back at the small group of people who’d almost become a new family to her over the past year- Sumner was admittedly more of a distant cousin than a particularly close relative, but Elizabeth had been surprised to find that she’d actually become rather fond even of Rodney McKay despite his occasional arrogance, and Carson was rather like a slightly-distant-while-still-fond-of cousin-, she allowed herself a smile at the sight of her three department heads back on Earth at last, but then shook it off and turned back to head down the corridor.

Nostalgia for life back on Atlantis and any bonds she’d formed there- even if she doubted that Sumner would regard there being any particular ‘bond’ between them; he might have grown comfortable in the city, but his attitude when off-duty made it clear that she and the others were only colleagues to him- could wait until she got back from Washington; right now, she had business to attend to.

A few hours later, as Elizabeth sat in the airport waiting area for their plane to be ready- why was it that her transportation always seemed to be delayed these days?-, she was almost grateful to have an opportunity to study an actual newspaper; it might not be the kind of leisure reading she preferred for a long flight, but it gave her a good chance to catch up on some of the events that had been happening on Earth since she was last present.

The only problem was that none of the stories she was reading could successfully hold her attention for any length of time now; no matter how hard she tried, her mind still kept on drifting back to concern for the man who had saved the city she already considered ‘hers’ without her ever having seen more than the lower left side of his face.

She just wished she knew what it was about the Phantom- it was best to think of him as ‘the Phantom’ right now; if she started referring to him as ‘John’ regularly in her head there was a chance she’d say it to someone and give away the time she’d spent with him- that constantly kept her thoughts coming back to him; he was just so… different from the people she normally-

The people she more regularly found herself spending time with, was the best term she could come up with to describe her relationship with him; certainly she’d never met anybody else who could control Ancient technology with that kind of ease, to say nothing of his evidently exceptional knowledge of the city itself…

“Something up?” General O’Neill’s voice said, breaking into her train of thought.

“Pardon?” Elizabeth asked, looking up at him in confusion.

“You’ve been staring at that page for the last few minutes without ever turning it; either there’s a very engrossing photograph there or you’ve got something on your mind,” O’Neill said by way of explanation. “So, which is it?”

“Just… wondering how things are back in Atlantis,” Elizabeth replied; it was, after all, almost the truth, even if she was thinking more about a specific individual than the city as a whole.

“Got pretty attached to the place, huh?” O’Neill asked.

“More than I expected, really,” Elizabeth admitted. “I actually miss the waves more than anything else; I had trouble getting to sleep the last couple of nights because my room was too quiet.”

“Yeah, it’s funny what gets to you; when I was stuck on this planet Edora for a few months some years ago, it took me a while to get used to sleeping there regularly because it was too quiet and I wasn’t expecting anything to try and kill me,” O’Neill replied, smiling briefly at the memory before he noticed Elizabeth’s inquiring expression. “Y’know, when I was doing overnight missions through the ‘gate I always had to be ready in case something tried to sneak up on me during the night, but with the ‘gate being buried and the Edorans being perfectly friendly I didn’t even have that concern…”

“Oh,” Elizabeth said, nodding slightly in understanding- she thought she understood where the general was coming from with his last statement, even if she didn’t quite see things that way herself-, before she glanced over at the transport plane visible through the windows of the waiting area. “How long is that going to take?”

“Depends on what’s up with it,” O’Neill said briefly, before he looked back at her in a more pointed manner, a slight smile on his face as he spoke. “Anyway, getting on to a more… interesting topic, how does it feel to be Atlantis’s answer to Commissioner Gordon?”

Elizabeth blinked.

“Uh… excuse me?” she asked, looking at the general in confusion; she couldn’t exactly see where the similarities were between her and the chief of police in the Batman series.

“Y’know, be the person in a position of official authority who’s pretty much the only guy trusted by the local masked vigilante?” O’Neill elaborated, waving a hand promptingly at he smiled at her. “C’mon, you’re telling me the analogy never occurred to you…?”

“I’d hardly say that I could be considered someone the Phantom ‘trusts’,” Elizabeth replied, even as her mind raced to try and work out what had led the general to make that comparison; nobody else was aware of her secret meetings with the Phantom aside from the two of them, and they’d barely spent any time alone together during the Wraith assault to encourage the idea that there was anything between them…

“Yeah, I’m not sure I’m buying that,” O’Neill replied, his smile assuming a slightly teasing aspect as he looked at her. “From what I’ve read about the guy, the Phantom certainly sounds pretty ‘Batman’-y; after all, a guy in a mask with a lot of training but no other apparent powers- disregarding his apparent Ancient gene; when you get down to it that just makes it easy for him to use what he’s got rather than giving him anything extra- guarding a city? Add on the fact that he specifically asked for you to be left ‘in the loop’ during the siege when- according to all reports- Sumner and Everett would have been perfectly willing to take complete control of the situation themselves…”

His voice trailed off as he looked at her, evidently trying to prompt her into continuing his line of reasoning, but Elizabeth simply stared back at him with an expression that Jack would later describe to his friends as being ‘more neutral than Switzerland’.

“Your point about the… ‘Batman’ similarities makes a certain sense when you explain it like that,” Elizabeth said at last, nodding slightly in concession at the general, “but I have to disagree with your description of me as the ‘Commissioner Gordon’ to the Phantom’s ‘Batman’; he simply requested my presence during the siege because he felt that I was the only member of the expedition’s senior staff he could trust to work with him without attempting to take advantage of his presence to try and capture him at some point.”

Privately, Elizabeth wished she could come up with a better way to phrase what she’d just said- she might not have explicitly said that she agreed with the Phantom’s assessment of the situation, but she still felt as though her opinions on Atlantis’s military commanders made itself fairly clear in her words-, but she couldn’t change the facts; John had specifically said during the siege that he trusted her.

Admittedly, Elizabeth had to confess that she would probably have taken his side in that confrontation even if his appearance in the conference room before the siege had been their first ‘proper’ meeting (Discounting the incident during the Genii invasion); her diplomatic background would have practically insisted that they cooperate fully with a man capable of offering them the kind of assistance that John had been able to provide them with…

“Still proves my point,” General O’Neill said, smiling briefly at her as he spoke. “Somehow, I get the feeling you’re going to be seeing a bit more of that guy as things go on in Atlantis; you might want to look into getting a ‘PhantomSignal’ so he knows when you need his help with something…”

“I’ll keep that in mind, general,” Elizabeth replied, already noting to herself that the ‘signal’ concept might not even be needed; she might not have a ‘Bat-signal’ as such, but the memories of her conversations with the Phantom on her balcony made it fairly self-evident that she did have a connection to the Phantom beyond what she was claiming to have…

“So,” she said, realising that the current topic of conversation at least made it easy to address one of her own issues, “what’s… your opinion on the Phantom?”

“My opinion?” O’Neill replied, looking at her with a suddenly serious expression. “Officially, I have to agree with the general ruling of Colonel Sumner; the Phantom is a dangerous independent operative in a situation where stability and security are paramount, and the colonel’s efforts to capture him so that we can find out where he acquired his knowledge about Ancient technology remain paramount.”

“And… unofficially?” Elizabeth asked, looking at him with a slight smile.

“Unofficially?” O’Neill replied, shooting another brief smile at her. “Quite frankly, I’m just jealous that you guys managed to get yourselves your own personal superhero; do you know how many planets I visited and there wasn’t even a single heroic myth about somebody with superpowers?”

“Right…” Elizabeth said, smiling slightly at the general before she assumed a more serious expression. “So… if, for example, I’m a bit… lax… in arranging patrols to find his hiding place?”

“Eh, it’s not like anybody’s here’s going to be that concerned about you not finding the guy; so long as he doesn’t do anything to hurt your chances of survival out there you’ll probably be fine with the whole ‘live and let live’ policy where he’s concerned,” O’Neill said reassuringly. “Of course, so long as you can give tomorrow’s delegates some interesting stories about one of their countrymen having saved a dozen or so people at some point during the expedition, everything should probably go fine there too.”

“Are you suggesting I exaggerate the qualities of members of my staff to win support?” Elizabeth asked, raising an eyebrow pointedly as she looked over at her replacement as SGC commander.

“Something along those lines, yeah,” O’Neill said, nodding slightly reluctantly under Elizabeth’s pointed stare. “Hey, I know flattery won’t get you everywhere, but every little bit helps keep the wheels turning, right?”

Elizabeth had to admit, General O’Neill did make a point; if nothing else, after the Phantom’s presence had caused so much upheaval in the city- she’d overheard more than a few conversations among the staff about the implications of Atlantis having its own ‘superhero’ in the mess hall-, anything she could do to improve her image in the eyes of the diplomats would probably be a good thing.

She just hoped that she could get through the next couple of days without too many problems; even after her meeting with the diplomats was over, she still had more than a few… personal issues… to deal with once she was finished in Washington.

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