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

Crouching uncomfortably in the maintenance tunnel just off the room that had been designated Atlantis's quarantine facility, John once again cursed his luck.

It could never be simple, could it? No matter what he attempted to do in order to protect this city, Atlantis in particular and the Pegasus Galaxy in general just kept on throwing up a mass of unpleasant surprises, no matter what kind of lengths he went to in order to learn more about the world he'd been unexpectedly dumped in so many years ago.

God… how could he have missed an entire planet of demented nanites-turned-humanoids with a grudge against the human race? He might be limited in his ability to actually search through the database at times, but something that big shouldn't have been that easy to erase all record of, no matter how good the Ancients were at their job…

He knew that it was irrational to blame himself for missing something that the Ancients had evidently gone to great lengths to cover up, but he couldn't help it; he had made it his personal mission to protect Doctor Elizabeth Weir, and because of the Asurans he had failed so completely that he was completely stuck for how he could help her.

He'd been listening to Doctor Beckett's reports on her condition, so he at least knew what the whole coma thing was about- nanites from that 'Niam' guy had infected her when the Replicator bastard had tried to strangle her in the 'gateship' and were spreading from her brain to the rest of her body-, but that didn't help them in finding a way to stop the damn things. They'd only activated a few hours ago and already they'd spread through her body, convincing her immune system that they weren't a threat as they spread through her system, leaving them with practically free reign to assimilate her body and turn it into a new vessel for their consciousness, unable to kill the nanites biologically or technologically without risking damage to Elizabeth herself…

He knew what had happened to her, but he had no idea how to treat it; he just hadn't trained himself for something like this!

Seeing her lying on the bed in that isolation tent, scanners constantly going over her body as the senior staff of Atlantis gathered around her, McKay and Beckett trying to devise some kind of cure while Sumner and Teyla waited for some kind of news on her fate (He'd seen Ronon drop in for a visit earlier, but he'd been all-but-ordered to leave by Sumner on the grounds that he wasn't a senior member of Atlantis's staff even if he was a member of Sumner's team), John had never felt so helpless.

He'd always known what to do to help Elizabeth in the past- get to the right part of Atlantis, advise her on whether or not it was worth visiting a particular planet, show up and shoot whoever was threatening her-, but how could he stop something like this?

God, he couldn't even talk to her without risking the rest of the senior staff coming down on him like the proverbial ton of bricks, and after the brutal way he'd treated Lucius he wouldn't blame them; he'd gone way too far when dealing with a guy whose only crime was being a smug git, and now they'd seen him as the monster he'd always been trying to ensure he'd never become, which meant that Sumner would probably arrest him the second he showed himself.

He'd give everything he had to save her, but all his strength and skill meant nothing now…

She might be able to hear him, and there was definitely something going on inside her head based on Beckett's scans, but that wouldn't do him any good if he wasn't in audible range.

Sometimes, he hated his life…

Come on, Elizabeth, he said, staring desperately at her, hoping that thought would suffice when words were hopeless. Fight these things… don't let them take you from us

Don't let them take you from me…


Walking into her house, Elizabeth wished that she could explain why she was so reluctant to accept the world around her.

Even if she wasn't the person she thought she'd been for- as far as she was concerned- the last two years, what did it really matter? She had an interesting and engaging job that challenged her abilities while never pushing her to the point that she couldn't handle the task before her, she had her mother back in her life, she was forming- or should that be reforming- a good friendship with General Jack O'Neill…

But, no matter what she tried to do with her life, one thing kept on preventing her from making the last few steps to move on from her delusion.

She might be prepared to move on from Atlantis, but how could she move on from John?

Even if the relationship they'd shared didn't make sense, that just made it all the more meaningful to her, rather than less. Relationships weren't meant to be predictable, no matter how people might like to pretend otherwise; Doctor Fletcher could argue that John was a representation of what she'd been looking to escape after Simon's death, but even if that made sense, Elizabeth still felt that there was more to John's existence than that.

She could understand Fletcher's theory about wanting to remain detached by creating a man who she couldn't commit to because he wouldn't share his identity with her, but surely, if she'd created John to do something like that, he'd have actually shared something with her other than professional interaction?

It just didn't quite make sense to her; if John was a product of her imagination to fill the void left by Simon's death, surely they would have actually done something together…

Admittedly, now that the idea was in her head, Elizabeth was finding it hard not to think about the possibility of doing something like that, but she wasn't sure how to go about it-

And how the Hell she had allowed herself to get onto this train of thought she didn't know; where was the point in thinking about someone who didn't exist? She was already avoiding mentioning the dreams to her mother- the fact that she hadn't told any of her friends or colleagues went without saying-, and had rejected some of the additional medication that Doctor Fletcher had offered as she didn't want to actually lose her memories of John…

It made no sense for her to be this focused on retaining the memories of someone who'd never existed, but there was just something about her experiences with John that were more real than anything she'd ever encountered in this world, and she couldn't put that aside that easily.

Where everything else about this world left her feeling emotionally numb at best, just the thought of John left her feeling so alive…

Besides, after Doctor Fletcher and General O'Neill used the exact same term to describe her condition, completely independent of each other, she felt that she was entitled to be a bit suspicious of the situation surrounding her; she might be drugged, but she wasn't stupid.

If only she could work out what she was missing…

The sudden sense of something nearby her prompted her to turn around, her eyes narrowing as they focused on a nearby door. Walking up to the door, Elizabeth paused for a moment- what if she'd just stumbled across an intruder of some sort?- before opening the door to reveal…

Her eyes widened incredulously.

A Stargate

An active Stargate…

Reaching out towards it, Elizabeth could almost feel the event horizon…

A hand clapped down on her shoulder, yanking her away from the door before something jabbed into her arm, consciousness rapidly fading from Elizabeth's mind…


"OK," McKay said, looking around the room at the rest of the Atlantis senior staff, John watching from a small hatch in one wall that gave him a reasonably clear view of Elizabeth and the rest of the room's residents, "we think we've found a way to uncouple the nanite cells from Elizabeth's cells."

"'We'?" Beckett said sceptically.

"How?" Teyla asked, voicing John's own thoughts on the question.

"We create a distraction," McKay explained, holding up a small cylinder marked with a biohazard symbol before Doctor Beckett gingerly took it from the Canadian and put it on a nearby trolley.

"It finally occurred to me why I wasn't having any success…" Beckett began

"What were the nanites originally designed to do?" McKay said, talking over Beckett before the doctor could finish his sentence.

"Fight the Wraith," Ronon said simply.

"Exactly," McKay said with a proud grin. "So that's what we'll get them to do now."

"We think by implanting a small amount of Wraith tissue into Doctor Weir's body…" Beckett began.

"It's like a tumour," McKay said, once again interrupting the doctor.

"Aye, a small tumour, yes," Beckett clarified, assuaging John's initial concerns even if he was still alert for more information about what they were planning to do to Elizabeth. "The nanites will essentially…"

"They'll attack it," McKay explained; for a man who dismissed medicine as voodoo so often, he seemed to take a surprising amount of pride in anticipating Doctor Beckett's medical explanations for the problems they were facing. "They have to- it's what they are programmed to do-, which will draw them away from Elizabeth's cells, effectively unbinding them."

"It will only last a few seconds or so, mind you, before the nanites attack the Wraith tissue and return their focus to Doctor Weir's cells," Beckett added.

"Yeah," McKay said, acknowledging the odds with a brief concessionary nod at Doctor Beckett, "but that's all we need: momentary distraction to draw them away from her so we can zap 'em with the EM pulse."

"Very well," Sumner said, in that grim tone of his that John had never liked; it sounded far too much to him like Caldwell wasn't really that concerned about the potential risks of what he was doing, so long as there was a chance of success.

This was Elizabeth's life, and Caldwell was just treating it like another goddamn day at the office when they were planning to inject her with Wraith DNA…

He had as much faith in McKay and Beckett's skills as he could have without having actually worked with them directly on a long-term basis, but when it came to Elizabeth, he was certain that he would have been anxious regardless of who was responsible for this procedure and what they were attempting to accomplish with it.


As soon as she woke up in the hospital room where this whole experience had started, Elizabeth was already working on planning her next move.

Regardless of what had happened to her before her apparent 'breakdown', she had been making good progress with her recovery- particularly with her disinclination towards certain drugs, even if she hadn't been totally honest about her reasons for not taking them-; there was no reason for hospital orderlies to have just… shown up like that.

She might have been prepared to let it go in the past, but if her time with John had taught her anything, it was the importance of trusting her instincts in any situation, and right now the mess that she was in was too confusing for it to be reality.

"Hey," General O'Neill's voice said, prompting her to turn and look at him as he leant against her window ledge, looking at her in an unusually solemn manner for the usually jocular general. "How're you feelin'?"

"Why am I back here?" Elizabeth asked, testing the waters with the most obvious question.

"They're worried," Jack said. "Frankly, so am I-"

"So worried that they showed up in my house while I was 'hallucinating'?" Elizabeth interjected, glaring at Jack in frustration. "What is normal about that?"

"The doctors just want to make sure-" Jack began.

Elizabeth didn't even want to hear it any more; she had no idea where she was or what was happening to her, but there was no way that she was unstable enough for hospital orderlies to have been monitoring her as closely as that.

Which meant that this scenario didn't make sense.

Which meant that this world she was in wasn't real.

"You disappoint me, Elizabeth," Doctor Fletcher said, walking into the room with a pitying look on his face. "I thought you wanted to get better-"

"I am better," Elizabeth said, looking firmly at the man she was increasingly convinced wasn't even here. "I don't know what happened to leave me here, but I do know that this is not reality-"

"Elizabeth," Doctor Fletcher said, with an obviously false sense of regret in his voice, "I'm sorry, but you don't leave me any other choice…"


"Oh no…" Beckett said, as he studied the displays on the screen before them.

He'd been so sure that he'd had the solution with the EMP attack, and now there were still nanites accumulating at Elizabeth's brain…

"We didn't get them all," he said, looking grimly back at the other senior staff.

"How is that possible?" Teyla asked.

"I don't bloody know," Beckett said, his tone grim as he moved away from his position at the scanner to walk over to where McKay stood alongside the EM-generator.

"They've been using organic material to replicate, which has rendered them immune to the EM pulse…" McKay said, looking grimly at the read-outs on the screens next to him.

"So… now what?" Ronon asked.

"They've started replicating again," Beckett said, studying the screens as though praying that some kind of solution would jump out at him.

"What do we do now?" Teyla asked, even as the display screen showed the remaining nanites moving into other parts of Elizabeth's brain.

"I don't know," Beckett said, looking grimly at the city's leader as she lay before him, urgently requiring help that he couldn't give her. "We can't use the EMP again; most of the nanites have migrated into the arteries that supply blood flow to the higher functions of her brain…"

"No," a voice suddenly said.

Spinning around, the senior staff were shocked to find the Phantom standing in the corner of the infirmary, creating his usual formidable impression in his long black cloak as he glared at the group before him.

"Elizabeth Weir does not die like this," he said firmly.

"Uh… excuse me?" McKay said, overlooking his shock at the Phantom's arrival in favour of focusing on what he could control. "I don't know if you've been paying attention- although, considering your timing, I'm guessing that you have-, but we're out of options-"

"Because you've not been paying attention," the Phantom said, looking over at the Canadian. "You haven't even considered the implications of Doctor Weir's mind still showing activity in this condition."

"What are you talking about?" Beckett asked, putting his shock aside to look at the Phantom.

"What will the long-term consequences be for Elizabeth if the nanites take action in their current position?" the masked man asked.

"Well…" Beckett said, confused at the other man's line of reasoning, "reducing blood flow to those parts of her brain will put her into a state of cerebral hypoxia…"

"Exactly," the Phantom said.

"Excuse me?" McKay said, looking at the masked man as though he'd lost his mind. "Carson just told you that they're going to kill her-"

"They'll render her brain-dead, Doctor McKay, which fits the pattern of computers trying to erase an old program and work on a new one; shut down the previous hard-drive so that you can add your own program to it that overrides the pre-existing one," the Phantom corrected, a slight smile on his face as he made his announcement. "You're dealing with Replicators, Doctor; they see the human body as nothing more than another machine, so when these nanites infected Doctor Weir, they probably concluded that the best way they could get anywhere was to take control of the 'machine'."

"You mean… they've been trying to replace Elizabeth's consciousness?" Doctor Beckett said, looking at the masked man in new in understanding.

"And her mental activity reflects the conflict as the nanites try to enforce their programming on her while competing against her own mental efforts to resist them," the Phantom finished, a slight smile on his face as he nodded in confirmation at the other man's theory.

"A battle of wills," Teyla said, looking reflectively at Elizabeth.

"This is all a fascinating theory, but it's still only that," Colonel Sumner said, looking at the Phantom with his usual penetrating stare.

"Her neural activity does support… the hypothesis, Colonel Sumner," Doctor Beckett said, looking over at the colonel with a slight smile. "And besides, it certainly fits better than any other theories I've been able to come up with for what these things are trying to accomplish; we aren't exactly dealing with mindless automatons, you know…"

"Exactly," the Phantom said, smiling grimly at the staff around him. "We may be dealing with a bunch of deranged nanites, but they're still Ancient technology, which means that not only are they very smart, but also means that I'm uniquely qualified to deal with this particular mess."

"What-?" McKay began, before the masked man turned around and walked into the quarantine sheet set up around Elizabeth.

"Don't-!" Beckett yelled, only for his words to fall on deaf ears as the mysterious guardian of Atlantis placed his hands on Elizabeth's arm…


As a new wave of orderlies entered her room, clearly intending to take her somewhere else, Elizabeth quickly chose the only option left to her; she drew back her fist and punched the approaching man with everything she had, unable to resist a sense of satisfaction as she felt his nose give under her fist.

Natural diplomacy forgotten in the face of the current threat, Elizabeth, her mind racing as she recalled everything she'd picked up from watching the occasional training session or encounter with John- as well as whatever was left over from Phoebus's time in control of her body-, lashed out at the orderlies around her, knocking them down long enough for her to the run to the door of her room. Doctor Fletcher moved to try and catch her, but a violent shove forced him out of her way before she began to run down the corridor, scanning the walls for some clue about where she could go next before she dived impulsively into an elevator and hit the button for the lowest level; she could work out where to go once she was out of the hospital…

The sight of the corridors of Stargate Command when the elevator doors opened might have confirmed that she wasn't dealing with reality, but it only provided a certain amount of comfort and reassurance; knowing where she wasn't didn't help her work out where she was.

"Elizabeth…" a voice said from down the corridor, Elizabeth turning in the direction of the voice in time to see the man she'd been told was only in her head.

"John?" she said, looking at her city's vigilante guardian incredulously, the Phantom standing in the middle of the corridor that she only now registered led to the gateroom with a firm stance that made it clear he wasn't going anywhere.

She'd accepted that this wasn't real, but to see such definitive proof that he was real…

"What's going on?" she asked, looking at him in desperation, praying that he could provide her with answers the way he always had in the past.

"You've been infected by nanites," John replied,

"They're trying to take control of your mind and body."

"What do I do?" she asked, relieved to have some kind of other explanation for what was happening to her; she might not understand quite how the nanites could have infected her, but after some of the things she'd read about in the SGC mission reports, it wasn't impossible to assume that they were somehow manipulating her brain's perceptions…

"Fight this, Elizabeth," John said, staring firmly back at her, his long black cloak and silver mask a bizarre sense of normality in a world that had seemed so strange because it was too normal. "You have to come back to me…"

The pain in the last word as he looked at her, as though the idea of her not coming back was the most devastating thing that could ever happen, was enough to convince Elizabeth that she was dealing with reality.

"What do I do?" she asked him.

"Go to the gateroom," John said, still staring at her in that same intense manner that only he could achieve. "Come back to Atlantis… come back to me…"

John began to fade away even as he spoke, but Elizabeth wasn't going to worry about that; she had further proof that this wasn't real, and that was all she needed right now. Focusing on his instructions, Elizabeth ran along the corridor, the presence of two soldiers in her path with guns in their hands barely registering to her as she ran through them, her attention focused on her final goal of getting out of this place…

Finally, she came to the gateroom, and ran up to the control room, her brief time in charge of the SGC enough for her to remember how to activate the console and dial the address she needed. Looking up, she smiled at the sight of the Stargate with an active wormhole within it, all seven standard chevrons illuminated in the 'locked' position, along with the faint glow of an eighth chevron underneath the ramp leading up to the wormhole. With that done, Elizabeth ran from the control room down to the gateroom, hurrying up the ramp leading to the active wormhole, only to come to a halt as a familiar figure stepped in front of her.

"I can't let you go," O'Neill said.

"You're not General O'Neill," Elizabeth said, glaring at the man before her, her gaze not faltering even as he transformed into Doctor Fletcher; it was almost refreshing to see that whatever was behind this was willing to abandon the lies now.

"Elizabeth, listen to me-" he began.

"You see that?" Elizabeth said, pointing at the Stargate behind him. "That's the Stargate, and yes, leaving is exactly what I plan to do."

"I won't let you go," Doctor Fletcher said once more.

With no other options left to her, and whatever good humour or diplomacy she might have had exhausted by her frustration at this whole situation, Elizabeth struck Doctor Fletcher in the face, sending him flying to the side of the platform. With the only immediate obstacle in her path removed, Elizabeth took a deep breath and walked through the Stargate…


When she opened her eyes once again, Elizabeth found herself lying on a bed in the quarantine facility, looking up to see Colonel Sumner and Doctor Beckett getting up from the ground, while McKay leant against a wall in a dazed manner and Teyla and Ronon looked slightly awkwardly at each other.

"Hello," she said, looking at them uncertainly. "Uh… what just happened?"

"Well, you were being used by a bunch of Niam's nanites, then the Phantom dropped in and touched you before bailing out on us…" McKay said, looking momentarily daze before he shook his head as though trying to clear it and turned to face the nearest wall. "And just so you know, if you end up spreading those nanites because you didn't want to get checked out, I am going to make sure we shoot you in the head that you clearly don't use-!"

"Rodney?" Carson said, looking at the scientist with a slightly frustrated stare. "Can you please stop talking to the man who's probably fully aware of what he might have done to himself- and, if past precedent is anything to go by, probably already has some idea of what to do about it-, and help me make sure that Elizabeth is all right?"

Looking at the wall that Doctor McKay had been addressing- most likely it contained one of those secret passages that John was always not-so-subtly hinting he was aware of throughout Atlantis-, Elizabeth allowed herself a brief smile at the thought.

She was back in Atlantis, John was real, and he'd just proven himself to her once again…

Her smile faltered as another thought occurred to her.

Doctor Fletcher might have been a nanite-induced hallucination, but one thing he'd said had stayed with her; why was John particularly interested in her of all people…