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 begins shortly after the end of "Progeny" before leading into "The Real World"; hope you like it.

As always in these cases, what I don't specifically record happened essentially the same way that it did in the show and will be referenced appropriately, although changes have been made that you'll notice when the time comes; I had a few ideas that I had to include

Mystery of the Phantom

Looking out at the city before her, Elizabeth found it hard to fully believe what she'd just been through.

After all of the times they'd wished that they could find Ancients who had never Ascended, their most promising lead ever had turned out to be a group of deranged early human-form Replicators who couldn't accept the rejection of their 'parents' and had subsequently attempted to destroy the entire city of Atlantis just to eliminate them.

She supposed they should consider themselves fortunate that Ronon had come along; even with McKay's attempt to hack the Asuran network, everything they'd done to try and escape would have been worthless without the temporary advantage provided by Ronon's gun.

Elizabeth ignored the part of her mind that noted that the weapon's use in a fight at least meant that John would be able to fight the Asurans if the situation called for it; she didn't want to have to rely on him for everything, even if she appreciated the fact that he was always there when she needed him (It was one reason that she was doing this rather than writing her reports; she wanted some time to think and put everything in its proper context, rather than run the risk of relating something back to John).

Besides, hadn't today proven that she didn't need to fall back on John for help whenever things became unpleasant? She might have been nearly strangled by Niam, but that was only because of some last-minute modifications that Oberoth had made to his programming; prior to that unfortunately turn of events, she liked to think that the team had everything under control, with the Asurans defeated, their city-ship destroyed, and their attempt at a direct assault averted...


As she opened her eyes and looked up at her new surroundings, Elizabeth didn't understand what had just happened.

One minute she'd been on the balcony of Atlantis in her uniform, thinking about what had just happened, and now she was lying on a bed in a white room that she'd never seen before, dressed in loose white clothes that put her in mind of something that a patient in a hospital would wear, with a simple plastic chair and a blue blanket-coloured bed the only sign of furniture. The sound of an ambulance outside startled her, but not nearly as much as when her attempt to look out of the sunlight-illuminated window covered by a conventional venetian blind revealed a brick building that was clearly nowhere on Atlantis.

Retreating from the window in shock, Elizabeth glanced down at herself once again, and this time noticed a plastic medical bracelet around her wrist. Glancing at it failed to reveal any clear information- apparently the old joke about the illegibility of doctors' handwriting was accurate in this case-, so, with nothing else available for her to do, she turned to the door of the room, but an attempt to open it quickly revealed that it was locked, and her look through the window in the door revealed nothing more than a corridor on the other side that looked far more appropriate to Earth than Atlantis.

"Hello?" Elizabeth called out, banging urgently on the door in front of her, until she saw two people walk around the corner. Quickly realising that she didn't recognise the new arrivals, Elizabeth stepped back, but she soon realised that what she'd done had been enough to attract their attention as they walked up to her door, the man- dressed in a dark blue suit over a light blue shirt, along with a neatly-trimmed beard- taking out a set of keys and opening her door as she retreated to the opposite side of the room.

"Good morning, Doctor Weir," the man said, smiling politely at her. "I'm Doctor Adam Fletcher."

"Where am I?" Elizabeth asked, taking care to keep her distance from the man; maybe her time with John had made her overly paranoid, but she wasn't comfortable with a stranger getting into her personal space like this man was.

"You're in the Acute Care Unit of Willoughby State Hospital," Fletcher replied.

"Willoughby?" Elizabeth repeated, her mind recognising the name even as she looked out of the window to give herself time to confirm her memory. "That's… that's a psychiatric hospital."

"Outside D.C., yes," Fletcher said, smiling at her in that frustratingly encouraging manner that doctors always seemed to use when dealing with patients who'd done something simple after so long being ill.

"I'm on Earth?" Elizabeth said, choosing to ignore Fletcher's slight smile at that statement. "When did I get back?"

"You mean, back to Earth?" Doctor Fletcher repeated, looking apologetically at her. "Doctor Weir, you never left."

Elizabeth didn't know what this man meant by that statement- it could have been anything from a plot to trick her to him simply lacking security clearance to know about the expedition-, but she was starting to feel very uncomfortable about this situation…


As she sat in the doctor's office a few hours later, Elizabeth had no idea how she was meant to feel after everything she'd heard and learned since she woke up.

According to what everyone was telling her, she had collapsed during a treaty negotiation that she hadn't given more than a passing thought to since she'd been appointed the new head of Stargate Command, it was over two years earlier than she thought it was, General Jack O'Neill had no idea what she was talking about when she told him about the Stargate, there was that… moment… when General O'Neill's head had done… something

And now, Doctor Fletcher was telling her that everything she'd experienced- everything she remembered of her life since she'd received that fateful phone call from Vice-President Robert Kinsey up to her recent confrontation with the Pegasus Replicators- was nothing more than a delusional breakdown caused by the stress of a treaty negotiation on top of Simon's death in a car accident?

She'd coped with worse than that and she was fine…

But, if they were telling the truth- and so far she had no reason to think otherwise; this was too detailed to be some kind of deception set up by the Genii or something like that, it was too vivid to be a hallucination or dream, and their escape had been too elaborate to be another Asuran trick-, all of her more serious experiences had occurred in an elaborate delusion she'd experienced since her collapse; they hadn't actually happened to her.

God… how had her mind come up with all that?

"It's actually… rather fascinating, when you think about it," Doctor Fletcher said, looking thoughtfully at her from the other side of his desk, having been studying her file in a thoughtful manner since before she had entered the room. "With your stress already higher than the average due to the particular demands of your job, with peoples' lives sometimes depending on your actions, your mind helped you escape the dual burden of your stress and your grief by creating a world where you could get away from everything associated with their causes, drawing on your old interest in space- you expressed an interest in being an astronaut when you were a child, based on some of the people I've spoken to-"

"People you've spoken to?" Elizabeth repeated, looking sharply at him.

"You came here in a virtually catatonic state; I had to talk with some of your associates to get an idea of your background so that I could help you when you came back to yourself," Doctor Fletcher explained, looking apologetically at her. "I assure you, everything I heard will be treated with strictest confidence; even what we heard you muttering-"

"I muttered?" Elizabeth repeated again, trying to make sense of the story that she was hearing even as she knew that nothing about this situation could ever hope to make sense to her.

"Bits and pieces, anyway; we checked in on you to see if you were making any progress, and managed to pick up some interesting details about your dream," Doctor Fletcher said, pulling out a file and studying his notes. "We weren't aware of the context, of course- all this stuff about the Stargate is completely new, as an example-, but we had managed to piece together that you were dreaming about being in the city of Atlantis, under attack by an enemy force of some sort, and that you were spending time with this… vigilante… who lived in the city?"

"The Phantom?" Elizabeth said, so shocked at this casual revelation of their awareness of her greatest secret that she couldn't even feel bothered to resort to her usually instinctive efforts to lie about her association with John.

She'd actually been… talking about him in her sleep?

"Ah yes, the 'Phantom'," Doctor Fletcher said, looking over his notes for a moment before he turned his attention back to her. "A man whom, according to what we heard, is also known to you as 'John'- a highly generic name, creating the suggestion of it being an alias to limit the possibility that you have actually been told his real name and therefore limiting the true depth of your connection to him-, and a hero who can handle virtually everything that this new galaxy has to throw at him?"

"Yes..." Elizabeth said, looking uncertainly at the man who claimed to be her doctor, suddenly uncomfortable at hearing John being analysed like that.

"Well, it's simple enough, isn't it?" Doctor Fletcher said, smiling at her in an understanding manner that made her want to punch him. "With your fiancé dead, your mind sought to create a new romantic partner for you; someone who could be just as devoted to you, but who would be simultaneously remain distant from you- I assume that nothing actually… well, happened, by the way?"

"No…" Elizabeth said, feeling suddenly embarrassed at the assumption that it was possible for something to have happened between her and John in the first place.

The very idea of what Doctor Fletcher had suggested was ridiculous; John was her friend and ally, he wasn't a potential anything...

Was he?

Elizabeth felt almost ashamed to admit it, but now that she thought about it, there was something there that she'd always shied away from exploring in depth; even before Phoebus had attempted to use her body to seduce John- something that she never liked to think about for several reasons, the least of which was what she'd felt under his mask; John wore that mask for a reason and it wasn't her place to question him about it if he didn't want to talk-, there had been a part of her that had… thought about it…

But that was only natural; John was an attractive man- even if she had never seen his face, he was physically strong and had a good character; that made up for the fact that he'd always worn a mask, as far as she was concerned- who had done a great deal for Atlantis without ever asking for anything, it would have been strange if she didn't feel grateful

Unfortunately, even if she knew that it didn't actually matter what she thought or felt about a man who didn't actually exist, she couldn't quite bring herself to identify what she really felt about him; John defied so many attempts at categorisation that it didn't seem right to try and do it when he wasn't there, even if he….

He never would be…

"Actually, going over some of these notes, the Phantom's presence in Atlantis is one of the most interesting parts of your experience," Doctor Fletcher said, drawing her attention back to the matter at hand as he looked briefly at the file in front of him before turning his gaze back to her. "After all, you're not only living in a legendary city created by an ancient race, but you've formed a connection with a vigilante with a Batman-like reputation who's been protecting that city single-handedly for an unspecified amount of time before you arrived in it."

"So?" Elizabeth asked, looking at Doctor Fletcher in confusion. "It's a bit… outlandish, I know, but what does that have to do with the idea that I… created the Phantom as a substitute?"

"Without meaning to be insulting, why, exactly, would a warrior like the Phantom be interested in spending so much time with a diplomat when there are women like this... Teyla Emmagen on Atlantis as well?" Doctor Fletcher said, looking at her with that pointed stare that doctors always used when they were trying to be comforting while delivering direct news.

"Teyla?" Elizabeth repeated in confusion; she didn't understand what Teyla would have to do with her relationship with John.

"Well, from what we gathered from your dreams, she's basically a native of the culture that has grown up around the idea of Atlantis's creators as… would 'gods' be accurate?" Fletcher asked.

"They… Teyla's people had a lot of respect for Atlantis's creators, but I don't think I'd go so far as to say that…" Elizabeth said, suddenly feeling awkward at Fletcher's analysis of this whole situation.

"Well, the point is, she's from a society that regarded Atlantis as a legend even before the Phantom became a factor, correct?" Fletcher said, allowing Elizabeth to nod awkwardly at him before he continued. "So… if she's a warrior who's been brought up in full awareness of the Phantom's legend, why would he ignore someone who has basically worshipped him in favour of someone who has just shown up in the city and doesn't necessarily share his views on how to deal with his enemies?"

"His goal is the protection of Atlantis; he's not interested in me just to get laid-!" Elizabeth protested automatically.

"But surely, considering the lack of help you can actually give him without 'exposing your connection', it would make more sense for him to contact Teyla if he wanted to offer advice to the expedition, considering how you already trusted her and his own experience allowing him to come up with various explanations for how she came to those conclusions given her… primitive background," Fletcher said, smiling sympathetically at her. "You created this relationship with the Phantom to protect yourself from getting hurt again by creating someone you could be attracted to who would simultaneously never actually be with you, because he could never share everything with you."

Elizabeth wanted to protest at the idea, but she was already finding herself lost in thought at the scenario that had just been suggested to her.

As much as she hated to think that she was as messed up as Doctor Fletcher's scenario suggested- how could she do her job if she couldn't even trust her own mind?-, it did make sense…

After all, she'd never really understood why John had given her that shield device that she still kept in her jacket pocket; didn't it almost make more sense to consider the idea that she'd been hallucinating…?

But she couldn't do it.

Even if Doctor Fletcher provided all the statistics he wanted to confirm that people could live out years in dreams and wake up after only a day or so, what she'd experienced with Atlantis was too vivid to be dismissed as a hallucination so quickly, even if she had yet to see anything to suggest that the hospital staff were lying to her.


Lying in bed that night, her father's pocket-watch on her side table and her medication down the sink- that part might not be appropriate, but she wasn't going to develop drug dependency at a time like this-, Elizabeth tried to rest her practically buzzing mind.

Seeing her mother again had been pleasant, of course- it had been too long since she'd been able to spare time to visit her home-, but that didn't help her escape what she was thinking of; everything she'd been through in Atlantis just felt too vivid to be a dream, but at the same time everything she'd experienced here fundamentally made so much more sense.

She wouldn't live in a delusion, but why couldn't she shake the feeling that this wasn't as simple as she was being led to believe?

Looking up, she could only stare at the sight of a shadowy figure, crouched in the ceiling despite the lack of places for him to be standing, some kind of opaque surface between her and the stranger, looking down at her with a sense of what Elizabeth could only describe as protective malice; he was clearly dangerous, but, at the same time, she could tell that he wasn't going to attack her.

"John?" she said, the name slipping out without her thinking about it.

She might not be able to see him clearly, but something about the manner of the person above her just made her think of the Phantom, the way she always felt secure in Atlantis just because she felt that he was there, the way she knew she could count on him to help when he was needed…

Even if everything she'd seen so far told her he couldn't exist, something about that presence just… made her feel safer…

But it didn't make sense; John didn't even exist, and even if he did, Fletcher had been correct that his 'interest' in her didn't actually fit anything that she knew about him…

Even if John, the Phantom of Atlantis, was somehow real where everything else she'd created in her hallucination was fake, why would he have ever wanted to spend time with her in particular?


AN 2: Hope everyone enjoyed that; coming up next, we return to Atlantis, and witness John's own thoughts on Elizabeth's current predicament…

AN 3: I acknowledge that Fletcher may have had too much detail about Atlantis for something he overheard and 'translated' from Elizabeth's mutterings, but I felt it appropriate considering the nanites' objective; they need to undermine Elizabeth's sense of self to take control of her, which here involves undermining her certainty about her relationship with John.