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

The Phantom of Atlantis

With the last of the expedition members- with the exception of the gateship containing Lieutenant Ford and Doctor Beckett; the last small group of Athosian hunters were apparently taking their time getting back- having left for Manaria, and the two remaining marines left on guard in the control room in the event of any attempted uninvited guests, Elizabeth soon found herself in Doctor McKay's laboratory, standing opposite Colonel Sumner around a table in the laboratory as McKay went over the information on his laptop one last time.

"Right then," he said, his fingers rapidly flying over the keyboard as he spoke, "one last time for the non-scientists here; there are dozens, possibly hundreds of lightning rods placed strategically around the city. Now, normally all the energy these things capture is routed into four main grounding stations. In turn the stations ground all that energy into the ocean below."

"So," Sumner said, looking over at McKay, "once we disable those grounding stations…"

"We use the energy to power the shield," McKay confirmed, smiling slightly at the general.

"The city can handle that?" Elizabeth asked, looking uncertainly at McKay.

"Yes!" McKay replied, his voice displaying his eagerness at what they were about to accomplish.

"…Theoretically," he added, spoiling the effect in Elizabeth's eyes.

"When you say 'theoretically'…" Sumner said, looking questioningly at McKay.

"I mean theoretically; you are aware we're on a time limit at the moment?" McKay asked, looking pointedly at the colonel before he continued. "Anyway, Elizabeth, you take grounding station two; I'll take grounding station one, and Colonel, you take stations three and four."

"Which are where?" Sumner asked, his folded arms demonstrating his dislike for McKay's attitude; in all fairness, Elizabeth herself acknowledged that the Canadian scientist's habit of sometimes assuming you knew everything he did about a situation could be frustrating, but at least he always got the job done in the end.

"Oh, here and here," McKay replied, indicating the points in question on a screen displaying the city that was up on a nearby wall.

"And we are currently…?" the colonel continued, his gaze still fixed on the astrophysicist before him.

"Here," McKay replied, indicating an area in approximately the middle of the city. "I need to get done quickly so I can start working on the subroutines, and Elizabeth was complaining about her knee the other day-"

"Would any of these generators be near transporters?" Sumner asked, cutting off the scientist before he could continue (Elizabeth was already fairly sure that McKay had given Sumner the hardest part of the job for more personal reasons, particularly given that she'd never complained about her knees in her life; the two men might work together well enough on the team, but personality-wise they clashed surprisingly often about relatively trivial matters).

"Uh… yes, Elizabeth's is," McKay replied, looking at Sumner in a slightly sheepish manner, although Elizabeth couldn't tell if it was genuine or not.

"And mine?" Sumner asked pointedly.

"Uh… it's a brisk walk away," McKay replied.

"And by 'brisk' you mean 'far'."

"And by 'walk' I mean 'run'," McKay admitted, before continuing his explanation as though nothing had happened. "You'll need to radio in once you've got to your first station."

Sighing slightly, Sumner shrugged and stood back from the table.

"All right, let's do this," he said, looking over at the other two. "I'll see you later."

With that, he turned around and walked out of the lab, leaving Elizabeth and McKay to look at each other in shared frustration.

As a military commander, Sumner's record was excellent.

As far as his ability to form personal bonds with those under his command went, however, he definitely had a lot to learn.

"Well… best get to work," McKay said, shrugging slightly as he turned back to study the display before them. "Now, Elizabeth, the nearest teleporter to your grounding station is here…"


As the figure watched and listened to the two men standing on guard in the gateroom from his usual spot in the upper tunnel leading to the jumper bay- really, when there weren't that many people in the room sound could carry surprisingly well even without his use of the radio to listen in in case of a last-minute change of plan-, he couldn't help a slight smile crossing his face as he took in their conversation.

It was inane, it was pointless, it served no purpose in the current situation…

And that's why he liked it, really; he rarely got the chance to listen to any kind of conversation that didn't involve plans against the Wraith or something like that these days. The opportunity to kick back as discuss something as inane as what the expedition members missed from home was something he hadn't had the chance to enjoy that much, and he was grateful for the opportunity to do so now even if he couldn't contribute himself.

"Bacon," one of the men said in response to the other's question.

"The one thing you wish you brought with you is bacon?" the other guard said.

"Hey, it's the food that makes other food worth eating," the first man replied (Not that their unknown observer could disagree with his opinion; he'd always enjoyed a decent bacon sandwich himself back in the days, and he'd yet to encounter any meat the Pegasus Galaxy had to offer that was anything like as good…).

"You wish you brought bacon to another galaxy?" the second guard said

"Yeah," the first one replied. "You asked me-"

Before he could continue, the Stargate began to activate, the first three chevrons rapidly illuminating even as the two guards and their unknown observer turned to look at the sight.

"Offworld activation," the guard said, the original topic of discussion instantly forgotten as the two of them hurried over to the control panel.

"Doctor Weir said no one should be coming back until tomorrow," the other guard said, the confusion evident as his colleague activated the laptop positioned beside the DHD.

"There's been an attack on Manara," a woman's voice- one that the figure watching the scene below didn't recognise- said over the now-activated radio link. "We've got wounded incoming. Lower the shield."

The first guard took a brief glance at the console. "They're broadcasting an Athosian IDC."

"Please, before it's too late!" the woman's said on the other end of the communication.

The man watching the scene from above them was rapidly beginning to dislike the situation he now found himself; what were the odds of the Wraith attacking Manara just when the Atlantis expedition were present?

But, on the other hand, it wasn't entirely impossible to assume that

"We are lowering the shield," the first guard said into the radio before him

"Whoa," his colleague said, reaching out to grab his arm before it could reach the switch to deactivate the shield, "let's get the OK from Doctor Weir-"

"They're under attack," the guard countered, his tone clearly allowing for no argument in the current situation. "Lower the shield."

After a moment's hesitation, the other soldier reached over to punch in the code to lower the shield, the Stargate subsequently 'opening' to the world on the other side of the wormhole even as the guard who'd voiced the initial objection activated his radio.

"Doctor Weir," he said, as he and his colleague got to their feet and began to hurry towards the lower level to greet the new arrivals, "there's been some sort of an attack on Manara. We have an Athosian party incoming with wounded."

"We're on our way," Elizabeth replied briefly, before her radio connection terminated as well, drawing the man's attention back to the cloaked figures currently coming through the Stargate carrying a couple of stretchers.

They definitely looked Athosian, he couldn't deny that, but something about them didn't seem right… the woman currently speaking to the guards just didn't strike him as someone he'd seen before…

Then a tall figure dressed in a familiar uniform of dark green with brown edges swung off one of the stretchers, got to his feet, pulled out two pistols, and shot the guards before him with as little regard as a Wraith would show for its latest victims.

As the rest of the new arrivals shrugged off their cloaks, revealing identical uniforms and similar weapons- a lot less sleek and significantly bulkier than the expedition's weapons from Earth, but nevertheless a step up from some of the technology he'd encountered during his travels throughout the Pegasus Galaxy-, the true identity of the new arrivals became clear to their unknown observer; only a few civilisations had reached the level of technological development necessary to make weapons like that, and only one of those groups had a reason to come after Atlantis.

Great… the man above groaned, slumping against the walls of the tunnel as he took in what had just happened. We've got a small Genii army inside the city, only one military and two civilian members of the expedition left to even try and defend it from them, and a massive storm bearing down on all of us; to say the situation is discouraging is a serious understatement.

Even as the Genii began to spread out- their exact words eluded him due to their lack of a radio he could tap into, but all he needed to hear was "Cover the entrances!" to know that they were planning to settle in for a prolonged period-, his mind raced over his possible options in the current situation. He could jump down there and try to take out the Genii while they were still contained in the gateroom, of course, but right now he only had a couple of handguns on him against approximately two dozen trained Genii soldiers- he hadn't had time to take a more accurate count yet- and they were already too spread-out for him to see them all clearly enough from his current position. All it would take was for one of them to get in a lucky shot- he wasn't going to count on his presence being enough to shock them into submission; if these guys were gutsy enough to invade Atlantis they clearly didn't put much faith in the tales he'd tried to encourage to stop people looking for him- and he'd be dead, or at least wounded enough to make his continued attempts to help impractical at best.

However, while direct attack wasn't an option, a more subtle approach might at least put him in a better bargaining position to… encourage them… to leave the city without too much fuss. Given that this was the Genii he was dealing with, based on Sumner's report of their encounter, their most likely reason for being here was the acquisition of explosives with which to perfect their own nuclear weapons technology, thus allowing them to strike back at the Wraith (He briefly contemplated telling the Genii that there were too many hive ships for that to work but swiftly decided against it; even if they did believe he was real, their commander struck him as the kind of person who totally ignored anything that didn't fit his view of the world, which in this case almost certainly included the idea that the Genii alone deserved to live and defeat the Wraith).

With that in mind, his best bet to get them out of the way would be to move the C4 to a secure location- fortunately, his long time in the city had acquainted him with several locations that would probably fit the bill-, and then try and force them to surrender the hostages and leave the city in exchange for at least some of the explosives (Giving the expedition's entire supply of C4 to these guys would definitely be giving the child in the tinder-box the lit match; if they actually thought that the radiation was harmless to them with the kind of shielding McKay had described in his report, they'd probably blow up quite a few innocent planets before they realised how much they were screwing up with their experiments, but with a limit amount they might at least be more inclined to limit their tests).

Plus, of course, he mused, another couple of thoughts occurring to him as he took one last glance at the Genii forces gathered in the gateroom, I'll need to make sure that the Zero Point Module doesn't fall into their hands; even if they can't use it as a power source for anything, the last thing we need is them trying to use it as a bargaining chip of their own…

Oh, and there's still that other puddle jumper left on the mainland; might as well get off a message while I can


As she and McKay walked hurriedly towards the control room, their own individual grounding stations and the first of Sumner's already deactivated, Elizabeth had already activated her radio to inform Sumner of the latest turn of events; even if it turned out to be nothing significant, she had a duty to make sure that her military commander was kept up-to-date on the situation.

"Apparently there's wounded incoming," she said as she walked.

"You're saying that we have people who were injured in a Wraith attack?" Sumner's voice said over the radio, his tone clearly reflecting his scepticism.

"Yes, I acknowledge that it's odd-" McKay began.

"'Odd' is not the word, Doctor; this goes against everything we have learned to date about the Wraith's M.O.," Sumner replied. "Given what we know of the Wraith, if they'd attacked Manaria I wouldn't have expected much in the way of wounded; if they knew we were there the entire population of Atlantis and the Athosians would have either been culled or-"

The sound of guns cocking in Elizabeth's face drove her attention away from her conversation with her military commander and to the more immediate issue of the group of unfamiliar soldiers standing over the fallen bodies of two of her staff, in strange uniforms consisting of dark greenish-grey and brown lining, pointing some primitive but nevertheless dangerous-looking guns directly at her and McKay.

If Elizabeth had been the type of person to do so, she would have sworn.

As it was, as two of the soldiers before them walked forward to grab her and McKay by the arms and force them into the centre of the gateroom, all she could do was hope that this latest turn of events would be explained sooner rather than later.

"Doctor Elizabeth Weir," a voice said from off to Elizabeth's right. Glancing up the stairs in the direction of the speaker, Elizabeth watched as a tall man with a weather-beaten face and an (In her opinion) ridiculously prominent nose stepped forward, looking at her with an annoyingly smug expression on his face.

"Yes," Elizabeth replied simply; if she'd learned anything from the hostage negotiations she'd conducted in her time in the U.N., it was that it was important to avoid antagonising the hostage-takers- and she and McKay were hostages; she wasn't going to assume otherwise- until you had a better idea of what they wanted.

"And you must be Doctor McKay," the man continued, looking over at the Canadian scientist. For a moment, McKay simply looked silently back at the man who seemed increasingly likely to be the leader of the soldiers, but then one of his people- a young woman with shoulder-length light red hair- stepped forward to stand beside him.

"That is him," she said, glaring coldly at the astrophysicist.

Before Elizabeth could ask the man who he was, he had suddenly reached out to take the radio she wore over her ear away, slipping it slightly uncertainly over his own as he spoke into it. "Would this be Colonel Sumner?"

For a moment, even as Elizabeth cursed herself for continuing to talk to Sumner as she approached the gateroom- this man must have overheard the colonel talking over the radio; he'd never have suspected that somebody else was inside the city otherwise-, there was nothing but silence on the other end of the radio connection, until the man spoke again.

"Do not attempt to deceive me; my men and I heard you talking to Doctor Weir when she entered the room containing the Stargate," he coldly said into the radio; whether he was bluffing or being honest Elizabeth couldn't be sure, and wasn't sure what she could do about it in the first place. "If you do not reply immediately, I will be forced to take… action."

Elizabeth might not know what this man meant by that comment, but, at the same time, she knew that she definitely did not want to find out what he was planning. After another brief silence,

"This is Colonel Marshall Sumner," the military commander said on the other end of the radio. "What do you want?"

"Simply return to the Gateroom via the shortest possible route," the commander said. "My men and I will be waiting for you."

With that he terminated the call and casually handed the radio back to Elizabeth, who took

"You seem to know a lot about us," she said, staring coolly at the man before her. "Who are you?"

"They're Genii," McKay said off to her left, his voice clearly showing his disgust at the soldier's actions (Not that Elizabeth could blame him; they'd been willing enough to help the Genii before they'd tried to steal the gateship and the Wraith data recorder).

"There's only one thing you need to know, Doctor Weir," the man before her said, his tone as self-satisfied as it had been when he first spoke. "As of right now, we are in control of Atlantis."


As she sat anxiously in the gateship with Lieutenant Ford, Doctor Beckett, and the last group of hunters, Teyla couldn't help but wish that she was already back on Atlantis, if not having already travelled through the Stargate to Manaria to be with her people. She was confident that they would be safe, of course- the Manarians were a good people, if somewhat reluctant to give something without any guarantees of receiving something in return- but that still didn't prevent her from feeling concerned…

Before that train of thought could progress any further, however, something came up on the viewing window at the front of the gateship, prompting Teyla, Ford and Beckett to look at the new display in surprise. Teyla swiftly abandoned her own attempts to read it- she recognised the written language as that used by her new friends, but she was still working on learning more than the essential basics of it; her training for becoming a member of Colonel Sumner's team had been more focused on military tactics and use of weapons rather than languages and writing-, but evidently Ford and Beckett understood what it said all too well.

"What the Hell…?" Lieutenant Ford muttered, as he glanced over at Beckett. "Am I reading this wrong, or is this thing in English?"

"Not just English, son… a totally coherent message…" DoctorBeckett replied, his eyes rapidly scanning the information before him even as they reflected his confusion at this latest turn of events. "'Genii in Atlantis… Weir, Sumner and McKay captive… get back here ASAP… P.'."

After a moment's pause, during which the three sitting in the gateship's control room processed what Doctor Beckett had just read, Lieutenant Ford voiced what they were doubtless all thinking.

"'P.'?" he said, looking over at Teyla. "You think this came from that 'Phantom' of yours?"

"He is hardly 'my' Phantom, Lieutenant; he has been the guardian of almost the entirety of this Galaxy for the better part of the last ten to fifteen years," Teyla countered, looking pointedly at her teammate as she spoke; she understood Colonel Sumner's reasons for disliking the Phantom's presence, but she still felt that the military commander would do well to show the man more respect than he had done so up until to this point. "In any case, it would appear to be the only logical explanation; according to this letter, Colonel Sumner, Doctor Weir and Doctor McKay have all been captured, and I cannot think of any soldiers in the last group whose names begin with 'P'."

"Look, whoever it's from, I think it's safe to say we can trust it; these 'Genii' buggers- they're the ones who wanted us to help them build nuclear weapons, right?- wouldn't have anything to gain by letting us know they're there," Doctor Beckett pointed out, before he sighed slightly as he stared at the message once again. "Too bad we can't actually do anything about it right now…"

"What?" Lieutenant Ford said, looking incredulously over at the doctor. "What are you talking about; we have to do something-"

"Take a look outside, hot shot," Doctor Beckett said, indicating the storm still raging around them with a wave of his hand at the main viewscreen. "We're not flying through this."

"Sumner, McKay and Weir were taken hostage, Doc!" Lieutenant Ford protested. "I'm not just gonna sit here while some guy who won't even let us know if he's really there-!"

"Neither one of us are real pilots," Doctor Beckett countered, pointedly ignoring the younger man's comments about the Phantom as he looked at his colleague. "It was a bad idea an hour ago; it's an idiotic one now."

"We're gonna have to take our chances-" Lieutenant Ford began.

"Doctor Beckett is right, Lieutenant," Teyla cut in, her own anxiety about this latest turn of events concealed as she looked at her friend. "You are of no use to the hostages if you are dead; we must remain here until the weather improves and we can safely depart."

She had thought about saying that he was no use to the Phantom dead, but Teyla knew well enough that such a line of argument wouldn't work; Lieutenant Ford was a good person, but he was in many ways Colonel Sumner's man, and had already made it clear more than once that he agreed with Sumner's view of the Phantom as a potential danger to the expedition.

She trusted that the Phantom- and this message was from the Phantom; Teyla was convinced of that much at least- could handle himself until they could make their way back to the city; she simply knew that mentioning such a fact to Lieutenant Ford would do little to help him the way he currently felt about the situation, given his commanding officer's own stance on the Phantom.

All that she and the rest of the people in the gateship could do now was wait and trust that the Phantom would do what he could for the hostages that remained in the city in the hands of the Genii…


AN: To anyone who thinks I'm making Ford a bit too 'military' as opposed to his more relaxed, somewhat jocular attitude in the show -, given that he could be VERY 'military-minded' when the situation called for it- such as when giving the rest of the team that briefing about the weapons they'd be using to capture 'Steve' in "Suspicions"- I'm assuming that part of the reason for that attitude was that Sheppard was the kind of military commander who was comfortable with informality, and didn't insist on people maintaining a 'professional' attitude unless the situation called for it, while Sumner is less relaxed about his duty even when he's not dealing with the latest crisis. Ford's still fundamentally the same person, it's just that in this timeline he's been more encouraged to be 'professional' rather than to be 'casual' even when he's off-duty in Atlantis