Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now

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: Bonus points to anyone who notices what's different about Elizabeth's conversation with Doctor Grodin in this chapter before they encounter McKay and Ford

The Phantom of Atlantis

A couple of days after the Athosians' arrival in Atlantis, as Doctor Elizabeth Weir sat in her office, Colonel Sumner and Lieutenant Ford practiced on the shooting range, Teyla Emmagan helped her people adjust to their new home, and Doctors Rodney McKay and Carson Beckett attempted to perfect a process to give non-ATA-gene positive expedition members the ability to control Ancient technology, a figure clad in a black cloak and a silver mask crouched in his old observation hole in the tower and watched Elizabeth as she sat in her office.

He had to admit, it was good to see that he hadn't misjudged her at the beginning; she may not have been a military woman by nature, but she was nevertheless viewing her current situation from a military standpoint that he could easily approve of, even if he felt her unease about the Athosians was unwarranted.

He'd visited the planet once or twice (Using a cloaked puddle jumper, naturally), and he knew for a fact that none of them were Wraith worshippers; indeed, none of them would so much as even think of doing such a thing. Unlike some of the cultures he'd encountered in his time here- the Wraith worshippers aside, the Olesians, who just sat back and let the Wraith have anybody who stepped outside the rules of the little verging-on-Big-Brother-style regime they'd set up there, would always get on his nerves- the Athosians were genuinely good people, and he would always remain grateful that they, rather than anyone else, were the first civilisation that the expedition had made contact with.

In many ways, the two were exactly what the other needed; the Athosians provided the expedition members with local knowledge of both the civilisations and the food to be found in this galaxy, and the expedition provided the Athosians with a more secure location than the original Athos. He'd seen them settle in to work with each other so far, and they had done well; he had a strong feeling that things were going to work out well for the expedition as they began to settle in to their new home.

Now…

Taking a slight breath to prepare himself for his next move- what he was about to do would officially end any possibility he had of keeping his existence a total secret, after all-, he turned around and returned to the service tunnels that he'd used to access the area in the first place.

It was time to give Elizabeth his little discovery; if nothing else, it would make him feel better to know that she had it on her from this point onwards.

He just hoped he'd judged what her reaction to it would be correctly; if he was wrong, than his time in Atlantis was going to become far more complicated than he was prepared to deal with at the present moment…


Unaware of her silent observer as she sat in her office, Elizabeth's attention was current focused on the recent discoveries of their MALP excursions to date while trying to determine where would be the most appropriate location to send one of their teams to, to say nothing of considering the structure of the teams in question to see if there were any changes that she could suggest should be made to them.

She had to admit that, if nothing else, Colonel Sumner had put together a fairly effective collection of men and women when selecting his teams for offworld travel, particularly when selecting his own. Despite the lieutenant's own doubts about himself after killing the Wraith hive-keeper, Sumner had decided to keep Lieutenant Ford on the team to provide him with another military man to balance out the other two members; the lieutenant had, after all, displayed great presence of mind in coming up with a means of killing the Wraith when under pressure and conventional measures had failed, even if it had turned out to be a bad decision. Acknowledging the benefits of local knowledge of the Pegasus Galaxy and the need for a science expert in the event of them discovering any Ancient technology during their travels, Sumner had also selected Doctor McKay to serve as the team's scientist and Teyla Emmagan as a guide and unofficial diplomat.

All in all, Elizabeth had to admit that he'd chosen well; Teyla still needed some lessons in understanding Earth military weapons and tactics to ensure that she didn't unintentionally jeopardise one of Sumner's plans due to her not knowing what he was attempting to do, and McKay still needed to learn to pull his weight more in their shooting and hand-to-hand training sessions, but that aside the group was generally settling in with each other fairly well.

Now all Elizabeth needed to do was work out how to deal with the fact that she potentially had the Pegasus Galaxy's resident superhero hiding out in her city without anyone knowing about it.

'Superhero'…

On the surface of it, it was such a childish term- mention it anywhere back on Earth and people automatically thought of men and women in spandex costumes beating up criminals and saving people's lives from impossible situations-, but Elizabeth could think of no other term to describe the Phantom after what Teyla had told her about him.

Having appeared seemingly out of nowhere over a decade prior to the arrival of the Atlantis expedition, stories of the Phantom seemed to have spread throughout the Pegasus Galaxy ever since. Nobody was ever entirely sure how he did it, but it seemed that, ever since his first appearance, whenever the Wraith were known to be attacking a village that had little to no chance of effectively fighting back, glowing golden lights were always launched at their ships from nowhere, eliminating the ships and ending the Wraith's attack in a matter of moments. Sometimes, if some damage had been done to the location where the attacks had taken place, a figure clad in black clothes with a silver mask covering most of his face would appear on the ground to aid in the recovery of anybody who might have been trapped or injured in the attack, but with the last of the injured recovered he vanished without even waiting to be thanked. Nobody had ever been able to determine why the Phantom wore the mask that had become his most defining characteristic, and Teyla had no theories to offer Elizabeth either. Whether it was a simple disguise or served some other purpose, nobody could say; even exact descriptions of the mask seemed to vary, as nobody had ever managed to come close enough to see what it looked like beyond the facts that it was silver and seemed to cover most of his face.

On a more positive note, however, the more Elizabeth turned over the facts that she'd gathered about the Phantom in her mind, the more sense it seemed to make, particularly when she considered some of the Ancient technology they had discovered so far. Discovering trapped victims of a Wraith attack would practically be child's play with the use of a 'Life Signs Detector', and according to Sumner and Ford's reports of the recent rescue, the gateships used drone weapons much like had been deployed against Anubis's ship from the Antarctic base back on Earth, which would certainly account for the 'golden lights' that the Phantom was meant to use against the Wraith.

Admittedly, they had yet to discover anything that might give the Phantom the ability to know when the Wraith were mounting an attack, but Elizabeth was fairly certain that this last fact didn't mean anything; she was fairly sure it was little more than a coincidence. After all, it wasn't outside the realm of possibility that the occasions where the Phantom provided aid against the Wraith occurred simply because he visited those planets at approximately the same time as the Wraith ships arrived, and people simply never heard about the attacks where he wasn't involved because…

Elizabeth halted that line of thought instantly, not liking where it was going in the least; the thought of innocent people dying in the manner that had been described to her by Sumner and Ford wasn't something she felt like contemplating right now.

Sighing, she leant back in her chair for a moment, only to change her mind and leave her office; maybe a walk would help her think on what she'd learnt about the city's possible 'owner' better than simply sitting around.


As she walked through the corridors of what she was already beginning to think of as 'her' city- even as a part of her tried to remain cautious in case the 'Phantom' was real and expressed a desire for them to depart-, Elizabeth allowed herself some slight satisfaction as she took in her staff's continued efforts to sort out the equipment they'd brought along from Earth and work out how to incorporate it into the city's systems, or at least where to place it now that they'd had more opportunity to explore the city. To date, Elizabeth and Sumner had decided to confine the expedition to the area immediately around the control tower in order to limit any risks of leaving people behind in case they needed to evacuate Atlantis on short notice for some reason (Exactly where they'd go instead had yet to be determined; finding an appropriate planet to set up an Alpha Site would have to be one of their first priorities once they were settled in), but with the Athosians to take into account, they'd need to step up their exploration schedule as soon as possible to try and find enough rooms for everybody to be comfortable in.

"Doctor Weir!" a voice said from off to one side as Elizabeth walked down one of the corridors. Glancing back in the direction of the voice, Elizabeth smiled slightly as she saw Doctor Grodin walking towards her. The young man's honest enthusiasm about their discoveries in the city was something that Elizabeth was always grateful to hear; McKay may have been just as enthusiastic on being in Atlantis, but his habit of trying to take exclusive credit for the discoveries they'd made somewhat negated the pleasure she felt at seeing an inquiring mind find the answers to various questions.

"At ease, Doctor," she said, silently wondering even as she spoke when she'd begun to so easily slip into military vocabulary; even after so short a time in the Pegasus Galaxy, a part of her was already waiting for the other shoe to drop and the Wraith to find them. "Have any of the teams discovered something since we last spoke?"

"Well," Grodin said, as he turned around and began to walk back towards the control room, prompting Elizabeth to follow him, "some of the other scientists and myself have discovered what seems to be the Ancients' water treatment plant; as far as we can determine, it works by desalinizing the sea water and storing them into tanks big enough to supply the whole city.

"Good," Elizabeth said, nodding briefly in approval at him. "So fresh water won't be a problem."

So long as she avoided thinking about the fact that food was still going to be an issue until they were able to stop the shield activating whenever they dialled Earth, she could at least rest easy on that particular score.

"It seems that some Ancient technology requires the use of the active gene," Grodin continued as he walked. "Other things merely require initialisation; once activated, like the control room, anyone can push the buttons to make it work-"

Further conversation was temporarily interrupted as three Athosian children hurried past them, one of them- Jinto, Elizabeth noted with a slight smile- wearing the silver mask of the Phantom as he led the others.

"Good morning, Doctor Weir," Jinto said briefly as he and his friends hurried between her and Grodin.

"Good morning," she called after him, "and careful!"

As soon as the children had vanished around another corner, Elizabeth assumed a more professional expression and glanced back at Grodin. "I think we need to dedicate some recreational areas."

"Agreed," Grodin confirmed, nodding in agreement at her as they continued to walk up the stairs.

"And," Elizabeth added, indicating a box of equipment slightly further along the corridor they had just come along, "we certainly need to clear the hallway and get everything put away as soon as possible."

"Of course," Grodin confirmed, as they continued up the stairs. "We're still in the process of making sure that everyone's been assigned living quarters; Colonel Sumner seems to be taking his time OK-ing enough space."

"Well," Elizabeth continued as they finally entered the control room and she began to walk back towards her office, "the safety and security of this expedition are his-"

"OK, I'm ready!" McKay's voice suddenly said from off to the side. Glancing in the direction of the voice, Elizabeth just had enough time to see Doctor McKay and Lieutenant Ford standing on the balcony outside the Atlantis conference room before Ford literally shoved McKay over the balcony, sending him hurtling towards the floor of the gateroom to hit it with a powerful thud.

"Woah!" Ford said, grinning slightly as he glanced over at where Elizabeth and Grodin were now standing at the balcony outside the control room. "Did you see that?"

"Yes…" Elizabeth said, looking at Ford and wondering if he'd had some kind of pre-existing mental imbalance that the SGC psychiatric evaluations hadn't picked up on beforehand. "What the-?"

"I'm fine," McKay suddenly said, picking himself up from the floor as though nothing had happened, raising his hands reassuringly as he looked up at them, revealing some kind of glowing green… Elizabeth could only think of it as a gem, even as she knew that it was clearly more than just a jewel McKay had found somewhere… on his chest.

Her curiosity roused, she turned around and headed for the stairs leading down towards the floor of the gateroom, Grodin close behind her as Ford hurried over to join them.

"Look!" McKay said, grinning broadly as he indicated the device on his chest. "Beckett's gene therapy worked; I was able to activate this! It's a, uh, personal shield; acts like a protective skin, and it must have inertial dampening features too, because-" he indicated the area where he'd just landed with one hand, "-I didn't feel a thing. Watch this."

Before Elizabeth could ask him to elaborate further, McKay had turned to look at Peter, a clearly eager expression on his face. "Hit me."

Elizabeth wasn't sure what startled her more; the fact that McKay had just asked someone to punch, the fact that Grodin didn't seem to hesitate before doing so, or the fact that, the second his fist made contact with McKay's face, a greenish energy shield appeared around McKay- accompanied by a faint sound that reminded her of the traditional noise made when Ancient technology activated.

"AHHowww… GOD!" Grodin yelled, clutching his hand as some of the Athosian children behind him laughed at the sight (Elizabeth had to admit, there was a part of her that found it hard to restrain a slight smile herself).

"You didn't have to swing so hard," McKay said nonchalantly before he glanced over in her direction. "And notice he didn't even hesitate."

"I'm still trying to understand how you thought it was a good idea to test this device by having someone throw you off a balcony," Elizabeth stated, trying to get the conversation

"Oh, believe me," McKay said, grinning slightly at her as he indicated the balcony once more, "that's not the first thing we tried."

"I shot him," Ford said, a broad grin on his face as he looked over at Elizabeth, the grin only fading slightly as she stared incredulously at him. "It was just in the leg."

As Elizabeth turned back to look critically at McKay, the scientist simply shrugged and grinned back at her.

"I'm invulnerable!" he said happily.

"Aren't you the one who's always sprouting off about how proper and careful scientific procedure must be adhered to?" Elizabeth asked.

"In-vul-ner-able," McKay replied in a sing-song voice, clearly unconcerned about his superior's evident unhappiness with his actions.

"Alright…" Elizabeth sighed, deciding to give the matter a rest until a better opportunity to discuss it came up, "take it off; let's go have this meeting."

"Just jealous…" McKay muttered as she began to walk up the stairs.

"Oh yes; green with envy," she said, turning back to look at him as she paused mid-way up the stairs. Just as she turned around, McKay was raising his hand to his chest…

Only to be unable to touch the shield in question as the force field prevented him from reaching it.

"Oh," he said, as he attempted to reach the device again, "this could be a problem…"

As the small group that had gathered around him earlier turned to look at the scientist, McKay once again attempted to reach the device, only for the shield to once again block his hand as he looked anxiously up at them. "I can't get at it."

Raising an eyebrow, Ford reached out in an attempt to grab the device himself, only for the same thing to happen; his hand could make contact with McKay, but it couldn't actually touch his skin.

"Just checking," the lieutenant said, raising his hands apologetically as McKay glared at him.

"All right…" Elizabeth sighed, quickly going over the possible ways to deal with this new problem. "Doctor Grodin, please accompany Doctor McKay to the medical wing; maybe Doctor Beckett can offer some suggestions about whether or not this is related to the gene therapy. Lieutenant Ford, you're with me; Colonel Sumner and Teyla are waiting for us in the briefing room."


An hour later, the meeting with Sumner on base security over and the self-destruct codes should the base ever be penetrated assigned to their respective owners (McKay stating that they not bother offering him one due to his current predicament; Elizabeth strongly wished he wouldn't go on about that as much as he did), she was once again heading for her office, her mind going over everything that had been discussed in the recent meetings in case she'd missed something important at the time.

In general, she felt that the situation was going well. Admittedly, she was still uncertain about trusting Teyla until the issue of whether or not one of the Athosians had tipped the Wraith off to their arrival in the first place had been satisfied one way or the other, and they were still no further along in determining the password that would allow them to shut down the shield whenever they tried to dial an address outside of this galaxy, but those questions aside the expedition were settling in fairly comfortably. The naquadah generators that they had brought with them from Stargate Command were helping to limit the amount of power being used by the ZPM, the search for living quarters was coming along well, and they'd already managed to track down rooms that could serve as a medical wing, an armoury, a mess hall, and even food storage.

If it weren't for the issue of the head of the science division facing death by starvation due to his apparent inability to calm down enough to turn his personal shield off- and Elizabeth was convinced that it was McKay's subconscious fears keeping that thing on; she wasn't a medical doctor but she was confident that the Ancient gene therapy wouldn't just grant someone the ability to turn the technology on without being able to turn it off-, Elizabeth would even go so far as to say that they already had the city running perfectly.

As she reached her office and moved to sit down in her chair, thoughts of McKay's current predicament occupying her thoughts- was there anything that they could do to make Atlantis more comfortable in the short term that might ease McKay's subconscious fears about their current situation enough to allow his subconscious to turn the shield off?-, she saw something on the table, and her eyes widened.

It was another Ancient Shield Device…

With a note attached?

Raising a confused eyebrow, Elizabeth picked up the note and studied it, instantly discovering that it almost presented more questions than it answered. Not only was it written in English- which effectively ruled out anyone but the rest of the expedition as being the ones to write it in the first place- but it stated on it, in clear, albeit sketchy letters, as though the person who'd wrote it hadn't done anything like this for a while,

"This one works for you.
Keep it secret, and be safe…
for me."

What? Elizabeth thought to herself, looking in confusion at the Ancient shield she now held in her hand.

What could the writer have meant when he said that it would 'work for her'? She didn't even have the Ancient gene and had yet to authorise full distribution of the gene therapy; how could she be expected to operate this thing?

Still…

Maybe it was just the tales she'd heard of the Phantom since she came here- the idea of one man managing to make that kind of impact on an entire galaxy, even if not every tale she'd heard about him could be true, was somewhat inspiring in its own way-, but there was a part of that was beginning to feel that, when it came to Atlantis, it was possible that nothing was impossible.

Despite everything she knew about Ancient technology telling her that this wasn't going to work, Elizabeth picked up the shield device and, after a moment's thought, placed it on her chest, the shield turning bright green as soon as it came in contact with her jacket.

Blinking in shock as she stared at the device, Elizabeth quickly reached up to remove it, grateful when it simply shut down and came away in her hand rather than preventing her from taking it off as its counterpart had for McKay. Whether this device was simply easier to turn off than McKay's was, or she simply had a greater degree of control over her subconscious mind than McKay did, Elizabeth wasn't sure and didn't feel like questioning in any great detail.

All that did matter was that somebody had given her an Ancient shield device that she could somehow control despite her lack of an Ancient gene, they wanted her to keep its existence a secret, and they wanted her to stay safe… for them?

Elizabeth was rapidly beginning to feel like she'd ended up in the middle of a bizarre mystery novel; every discovery that she made only left her with even more questions to be answered about the city and its near-mythical 'guardian'.

Who could have left this shield for her?

How was she able to control something that, according to McKay and Grodin, required the Ancient gene in order to work at all?

And more importantly… why would whoever have left the shield here for her in the first place be particularly concerned about her safety over everyone else they might have given the shield to?


AN 2: If anyone's wondering about how Elizabeth can work the shield device despite not having the Ancient gene, I took my inspiration from 'Irresponsible', when Lucius Lavin mentioned that he managed to get his one working by tracking down someone with the Ancient gene and getting them to activate it for him, subsequently using it for himself. Since Lucius was able to turn it on and off- as well as permit John to use it when he faced off against Koyla and his men - without having the Ancient gene himself, I'm assuming that, like most Ancient technology, the gene is simply required to turn the shied on in the first place and isn't required in the long term. I'm also assuming that McKay's belief in 'Hide and Seek' that the shield imprints on the wearer is, like turning the thing on or off, mainly controlled by the user's will rather than being a fixed fact of the shield's design; if the wearer wants someone else to be able to use the shield, the shield will automatically program itself to respond to that other person