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: Not entirely certain about this chapter, but things should pick up later; I have more definite plans for future episodes (Particularly relating to my new take on such classics as "Conversion" and "The Long Goodbye")

The Phantom of Atlantis

Even as he sat down in the chair, John wished that he was as confident in his ability to use the chair as he'd claimed to be when talking with the colonels to convince them to work with him.

He'd tested it out now and again in the past when he'd had nothing else to do, of course, but he'd never gotten into the habit of regularly practising with firing the drones or raising the shield like he might have liked; the only thing he'd regularly done from the chair was pilot the jumpers by remote, and that had mostly been for the sake of it to see if he could control the jumpers that way.

It wasn't like he hadn't had his reasons for not practising using the chair in greater depth, of course- his drone supply was limited and he couldn't do much with the shield without risking water damage to the city-, but he'd still given the others the impression that he was better-trained with this thing than he actually was; he could only hope that his practical abilities would be enough when the time came. He'd practised enough with other Ancient technology that he was fairly confident he knew what he was doing, but that still didn't mean he felt entirely comfortable with his first time genuinely trying to control something this big and powerful being in the middle of a combat scenario…

He didn't even need the subconscious access to the sensors the chair gave him- just enough to know where enemy objects were going to be so that he knew where to strike- to know that the city was even now preparing to fight back against the Wraith darts; all he needed to know right now was a clearer picture of where the darts were so that he could be sure he wouldn't be wasting drones.

On the bright side, the drones themselves were nigh-on indestructible, which at least limited the possibility of them being taken out by friendly fire; the problem for him right now was that finding the darts when they were far enough away from the city that he could be sure he wouldn't be taking out something that the conventional guns were about to destroy themselves- there was no point using drones on something that could just as easily be shot down by the rest of the expedition members-, while still being close enough to ensure that he could use the city's sensors to accurately direct the drones towards the darts…

Then the lights went off around him- the chair responding to his decision to conserve energy; he was going to keep the shield deactivated until the time was right and otherwise work on making it hard for the Wraith-, and John allowed his mind to 'sink' into the chair, reaching deep into the city's sensors as he prepared for the upcoming assault.

As the darts reached the outskirts of the city's sensors, John sent a few quick drones up into the air to eliminate the first wave of darts as soon as possible, only for the next wave to get past the city's outer limits and within range of the gun batteries before he could bring the city's sensors to focus on them. For a few moments, all his attention was focused on the darts as they ducked and weaved around the towers, his mind not even registering the presence of Colonel Everett as the new colonel yelled at him to do something…

Well, OK, maybe I am aware that the guy's yelling in my ear all the time… John reflected, the part of his mind that was still aware of his immediate surroundings rather than the city's sensors registering Everett ordering him to stop lying around and do something…

Fine, John reflected, his hands clenching the chair as he focused his attention on the sensors. Firstly, make sure I know where those rail guns are

A few seconds' analysis of the sensors was enough to allow him to determine where the guns that Everett had installed were located- he'd been initially more concerned with making sure the pilots knew how to operate the jumpers rather than looking at where the guns had been installed, trusting the colonels to establish a suitable defence perimeter- based on such details as where the darts were being shot down and other such factors, subsequently deploying another dozen or so drones to target the darts that were heading for the more vulnerable areas.

Even as the other darts began to fall to the expedition's own weapons, the drones targeted the darts that had evaded the main assault and quickly took them down, destroying the darts' propulsion systems and sending them hurtling to crash into the sea around the city (A couple of darts had begun to attempt kamikaze runs, but he managed to aim the drones at the front of the darts just in time to knock them off-course and send them either into the sea or at the very least divert them to the less vital parts of the city).

After another few moments of waiting and monitoring the city sensors, the man known as the Phantom allowed himself a slight smile.

There was no sign of any further darts approaching the city.

The first wave of the Wraith assault had been defeated.

They'd won

Then he registered reports that one of the gun batteries had gone silent despite sensors showing that area to still be intact, and he couldn't help but curse.

So much for that hope; they had taken casualties in the first wave…


"Why didn't you raise the shield?" Everett asked, looking pointedly at the Phantom as the city's five leaders- Doctors Weir and McKay, the two colonels, and the Phantom- sat around the conference room table, the Phantom currently attracting the glares of his Earth 'counterparts' as he sat at one end of the table.

"Well, in case you hadn't noticed, we are rather low on power-" the Phantom began.

"What are you talking about; our ZedPM has more than enough power to raise the shield-!" McKay began incredulously.

"And, given that we have two hive-ships on their way, no idea how much firepower they possess- I've never exactly been in a position to see what those things can do if they really 'let rip', you know- and even less idea how long we have to wait until we receive any kind of word from Daedalus, it seemed more sensible to save that power until we have no other choice but to use it," the Phantom countered, leaning forward slightly as he glared pointedly at the Canadian scientist. "We've sustained losses, yes, but it's nothing we can't recover from; on the other hand, if we start using the shield energy indiscriminately with just over ten percent of our full power capacity available to us, we run the risk of being defenceless when the main assault arrives."

Once again, Everett wished that he could accuse the Phantom of being irresponsibly reckless, only to be forced to remind himself that he would have done almost the exact same thing in the other man's position; sometimes you had to let some die to save the majority…

In the end, though, the part that really struck him about the Phantom at this point was the expression in the other man's eyes; a look of loathing and hatred that he barely seemed to be keeping under control.

It wasn't for the Wraith, Everett was fairly certain- he didn't display any signs in his voice when talking about them to suggest he felt that strongly about them, even though it was clear he was dedicated to defeating them-, and apart from the initial complications of his arrival the members of the expedition had generally been fairly civil towards him after his presence had been made official, but that still left him no further along towards answering the question of who the Phantom hated so passionately…

Everett shook it off; trying to get inside the head of the kind of man who'd wear a mask on a full-time basis wasn't something he had the time or inclination to deal with at this moment in time.

"Getting back to the issue of those hive-ships," he said, drawing his focus back to the main issue facing them at this time as he looked over at the Phantom, "you're certain you can send the gateships by remote up to those hive ships?"

The Phantom shrugged. "Should be straightforward enough; all I need to do is manoeuvre the ships to avoid the darts and then send them straight into the hanger of the hive-ship when they're not expecting it-"

"Uh… are you sure they won't expect it?" McKay asked, looking uncertainly at the Phantom as though reluctant to question someone with the other man's attitude but feeling obligated to make the point. "I mean, if you've been practising doing this kind of thing…"

"I only practised it in the vicinity of Atlantis; the chair's 'range' to control something under these conditions is relatively limited," the Phantom explained, looking briefly over at McKay. "Even if I kept the Stargate open while attempting this strategy, the ships would have eventually shut down or the drones exploded when they went too far from the Stargate for the control chair 'signal' to reach them; the connection between the chair and the gateship drones is… fragile over long distances, to say the least."

"But you are certain you can maintain control over the distance required under the present circumstances, right?" Sumner put in, his eyes narrowed as he looked pointedly at the man before him, bringing the conversation back to the matter he was interested in.

"Oh, that's not a problem; once the hive-ships get into position, I'll just need a minute or so to work out the quickest route possible to get the fine details worked out-" the Phantom began.

"I'm sorry; go back to the part where the hive-ships need to be in position before you'll be able to pull this off?" McKay cut in, looking in more-than-slight fear at the Phantom. "Couldn't you send them out now-?"

"The gateships were never meant to be flown that way, Doctor McKay; it's stretching things to their limits to expect me just to maintain control of them after sending them to the upper atmosphere," the Phantom interjected, his eyes demonstrating a more-than-slight frustration at the other man's fear. "They have to be in position there or it won't work-"

Further explanation on his part was cut off as Teyla ran into the conference room, anxiety clear on her face as she looked at Elizabeth.

"Doctor Weir," she said, looking urgently at the expedition leader, "we have an urgent problem; the Wraith have managed to gain access to Atlantis."

"What?" Everett said, standing up to look at the Athosian woman in shock. "How-"

"The darts…" the Phantom cut in, realisation and frustration apparently warring for supremacy on what they could see of his face. "I stopped the darts themselves from hitting the city, but a few Wraith must have managed to beam out before I was able to do any serious damage to their systems; if they've managed to gain access to Atlantis to any degree…"

The man in the mask didn't need to finish the sentence; everyone listening to him clearly understood what this latest implication meant for their future attempts to defend this city.

"We need to prepare search teams to find them before they can do any damage," Sumner said, getting to his feet and glancing over at Ford. "Get everyone organised; we need to find them as soon as possible-"

"And position guards around the ZPM room and the naquadah generators; we can't afford to take the chance that the Wraith will figure out what's powering what," the Phantom cut in (Sumner briefly wondered how much the man knew about which parts of the city were powered solely by the ZPM and which parts were maintained by their backup naquadah generators, but decided he almost didn't want to know the answer; the fact that he'd known enough to remove a generator that wouldn't disrupt the city's daily operations during that nanite thing was more than enough for him). "Any chance I could be on one of those teams?"

"Excuse me?" Everett said, his initial shock shaken aside as he turned to look at the Phantom. "In case you'd forgotten, you're needed here for when those hive-ships-"

"The hive-ships aren't going to be here for a while, Colonel Everett; even with the sensors screwed up like they are at present, it's not going to be difficult for you to get enough of an advance warning of their presence for me to get here in time," the Phantom pointed out, even as he pulled out his weapon and examined his power cell before putting it back in its holster. "From what I detected from the sensors, I'd say that around twenty darts managed to make it into a position to beam something into the city; the city's sensors themselves can't distinguish between Wraith and human life signs- the Ancients never really considered the possibility that anything that wasn't one of them would get into the city without their permission so they never programmed the sensors to compensate-, so we're going to need to rely on those 'Life Signs Detectors' to specifically identify the Wraith during our search."

Everett couldn't believe it; bad enough that this… this vigilante had taken over defence of the entire city, but did he have to be so goddamn good at it? He'd only agreed to having the guy around in the first place to use his information until the point came when he didn't need it, and now it seemed like he barely managed to get by for ten minutes without this masked bastard taking over…

"Fine," he muttered, standing up and looking over at Sumner. "Let's get going; we've got Wraith to track down…"

"You shall not be alone," Teyla put in, stepping forward slightly to draw attention back to her. "My people and I are willing to aid in the search in any way we can."

For a moment Everett thought about turning them down- he already had one amateur to worry about; the last thing he needed was more of them to worry about-, but quickly pushed that thought aside; if these people had managed to survive in a Wraith-dominated galaxy all these years- coupled with what the files had mentioned about some of them being able to 'sense' the Wraith-, they must have some skills that could be useful in this situation.

"Very well," he said, nodding in brief resignation at this latest turn of events. "We'll get you some weapons; we'd better get moving as soon as possible."

"Uh… we'll just… get to work on those time devices for the bombs, shall we?" McKay asked, looking uncertainly at the group around them.

"Good call," the Phantom said, nodding in confirmation at McKay. "Get the timers installed but don't program them with a specific time-frame just yet; I still need to work out a time estimate before you start anything decisive."

"Uh… sure," McKay said, as the military members of the expedition stood up and walked out of the conference room, leaving him alone with Elizabeth as they silently exchanged glances.

Finally, after a few moments of uncertainty, Elizabeth broke the silence.

"Well," she said, shrugging slightly as she looked over at McKay, "you can't say the Phantom doesn't have some interesting ideas, can you?"


As he stood in the corridor leading to an uninhabited area of the city that the sensors had identified as the location of unexplained life signs, John couldn't help but smile slightly under his mask.

He knew that it wasn't exactly healthy, but he couldn't help it; after so long having to hide from the people he'd long ago sworn to protect in the city that was regarded as his home by practically everyone who knew of his 'legend', it was really rather refreshing to be able to get back to where he'd started, going after the Wraith as they sought their prey.

Admittedly, he wasn't used to dealing with them in these conditions- the Wraith had never managed to make it into Atlantis before; that iris was really a brilliant means of defence; even without the sea above the city preventing the Wraith finding anything if any of them had managed to track down the planet he was dialling from, they couldn't even come through the gate if he didn't want them there-, but that didn't mean he couldn't adapt.

Hell, if anything, hunting the Wraith here was easier than his previous hunts; here he was on territory he knew like the back of his hand (Probably better, now he thought about it; that phrase had never made any sense to him), while the Wraith were completely unfamiliar with the layout of Atlantis.

Plus, of course, he reflected, glancing ahead of himself to where Lieutenant Ford was walking ahead of him, his weapon drawn as he looked around himself with an anxiety that was only visible to John after such a long experience with human hunters, the back-up helps.

He wasn't going to say that it was actually easy for him to start working with other people after so long doing his own thing, but it was rather nice not to have to worry about watching his back…

As a Wraith warrior- one of the big guys with those stupid masks; John had never understood how those suckers saw anything in that headgear- out of the shadows to throw the young lieutenant down a nearby corridor, John didn't hesitate; raising his own gun, he stepped out behind the Wraith as it advanced on its latest would-be meal, fired a couple of quick kill-shots at the Wraith- no sense doing things halfway, after all- before walking over to crouch down to check on the lieutenant.

"How are you?" he asked casually, as Ford turned to glare at him while wincing slightly at the pain in his skull.

"Not bad," the younger man said briefly, narrowing his eyes as he looked pointedly at the masked man before him while indicating his gun. "How about next time I be the one to shoot the Wraith?"

"Wouldn't work; if I was bait, these guys would just kill me," John said, shrugging nonchalantly as he slid his gun back into its holster. "You're just another human to them, and that means they'll take their time to make it interesting; with me?"

He smiled slightly. "They know the only way they're ever going to feed on me is if they take me out straight away; taking their time with me would only get them killed."

Ford didn't look like he entirely believed the Phantom's explanation, but that wasn't important right now; all that mattered to him was that they were working together to deal with the Wraith.

"Attention all teams," Sumner's voice suddenly said over the radio, the colonel sounding slightly breathless. "Three Wraith just attempted to attack generator number two; whichever team is closest to generator three, report there as soon as possible to provide further assistance."

Quickly thinking back on the briefing where team layout had been allocated, John remembered that Teyla's team- a predominately Athosian one with just one marine- was the closest team to that area; at least that meant they'd have a clear idea what the Wraith they'd be facing would be capable of, rather than a traditional Earth-originated team.

"We are on our way," Teyla said, her voice cutting through his radio, the sound of running in the background as her team moved into position.

Going over the 'grid' he'd created of Atlantis in his head, John smiled slightly as he turned around to hurry towards the area that was most likely to be the location of any as-yet undiscovered Wraith, barely registering the sound of Lieutenant Ford behind him (The Wraith were traditionally heavier than humans so he was fairly confident he'd be able to hear it if any of them attempted to sneak up behind him and Ford without even needing to look).

If any remaining were in that area, he'd prefer to take care of them as soon as possible…

Even as he ran, however, a part of him couldn't help but feel somewhat concerned about the ease with which he'd slipped back into 'combat mode'; even after all the time he'd spent hiding on Atlantis, it still barely took him a matter of minutes to shift back into combat mentality.

For all his attempts to convince himself he was more than a guy who killed Wraith, he kept on slipping back into that roll far too easily for his own comfort…

Then another Wraith began to charge down another corridor towards him, and he forced his mind back on topic as he fired his gun at the creature's face; he could worry about what his eagerness for combat said about his psychological state when this Wraith invasion had been dealt with.


An hour or so later, the senior staff found themselves back in the conference room, the colonels going over the aftermath of the recent 'invasion'- they'd managed to get by with only a few casualties in the teams, mainly since the Phantom's advice about establishing themselves around the generators meant that they'd managed to catch some of the Wraith off-guard and thus limit the available opportunities for the Wraith to take people by surprise- while McKay reported on the progress with the bombs.

"Getting the bombs set isn't the problem; the problem is in disabling their original motion-detection settings and reprogramming them to accommodate a timer," the Canadian explained as he glanced around at the others. "We think we've managed to calibrate everything to work correctly with the new systems, but these are fairly complicated devices; it's going to take time to make sure we've got everything wired up correctly…"

"In case you didn't notice, Doctor McKay," Colonel Everett said, looking pointedly at the man before him, "those hive-ships are only a day or so away from us in a best-case scenario; we need to be certain those timers are going to be ready by then-"

"Look, these are nuclear bombs we're dealing with here; we need to be careful if we're going to avoid blowing anything up-" McKay countered.

"Look, just do what you can and then get everything together; this is not the time to start arguing about this stuff, OK?" the Phantom said, standing up to glare pointedly at the two men before turning to look at Elizabeth. "If you don't mind, I think I should get to the chair room right now and get a little practise with that remote control thing; let me know when the hive-ships are within range."

"Already on it; we have a gateship keeping an eye on things ready to let us know when the ships come within range of the planet," Sumner put in, looking at the Phantom in a very pointed manner, evidently almost insulted that the Phantom had addressed a military-based announcement to Elizabeth rather than to him or Everett.

"Ah, good," the Phantom said, moving past the initial discomfort like it didn't exist as he looked at the other man. "He does know he's to time approximately how long it takes him to get from the ship to Atlantis once they take up orbital positions, right?"

"Yes," Everett said, his teeth gritted slightly as he looked at the Phantom, once again insulted at the other man's casual assumption of command even as he was unable to contradict any of the orders the man was giving. "He's even going to go at regular speed to ensure the… conditions… are accurate."

"Good," the Phantom said, nodding once more before he glanced over at McKay. "Let me know when those timers are ready; once I know how long it takes to get to the hive-ships from here I'll let you know what time I need."

"Uh… check," McKay said, his comment apparently only being registered by the Phantom's back as the man stood up, turned around and left the conference room, his black cloak trailing behind him as he walked through the door.

After a moment's silence, McKay spoke again.

"Blunt kinda guy, isn't he?" he said, indicating the door where the Phantom had just left.

"He knows when to cut through the crap and get to the point," Sumner said, his tone admitting a brief, if grudging, respect for the man. "Have to respect that, when you get down to it."

"Whatever you think of his methods, he makes a valid point; if we don't keep on working, we're going to have a problem when the Wraith get here," Elizabeth said, looking around the table before her gaze focused on Sumner. "Colonel, I assume your men are still ready and able to man the defence?"

"What they can work, they will," Sumner said, nodding in confirmation at her.

"Then we need to make sure everyone who can fight is ready to do so; we've dealt with everything from the first wave, but that still leaves the second wave on their way and no sign yet of the Daedalus," Elizabeth said, looking pointedly at everyone around her to make sure they understood what she was saying. "Prepare to evacuate the injured to the alpha site- we can't afford to waste the energy needed to dial Earth at a time like this-, and then get everyone else into position immediately; we have to hold this city."


As John sat back in the Ancient control chair, his mind keeping a close 'eye'- for lack of a better term; keeping a close 'thought' always sounded slightly stupid to him- on the sensors for any sign of the Wraith hive-ships, Doctor McKay monitoring the chair's systems- he insisted on making sure everything was working right in this situation personally no matter how many times his team assured him everything was fine-, he allowed himself a brief smile as he heard Elizabeth's voice begin to address the city; something about her continued presence there made him feel… better, somehow (He knew why that was, but wasn't too keen to analyse it in great depth; things were complicated enough without that getting involved right now).

"This is Weir," she said, her voice clear as she spoke to her people. "Now I know how tired you all are, and how much we have asked of you these past few days. Hopefully the Daedalus will arrive soon, but until that happens our fate is in our own hands. If during the course of this battle our mission fails, I will give the order to evacuate to Earth; we all hope that won't be necessary, but we are not to hesitate if it does. That is all."

John barely had the time to smile in approval at her statement- effectively covering everything they needed to know about the current situation while also encouraging them to hold on and not give up-, before a less welcome voice spoke to him directly.

"Sumner to Phantom?" a voice said over the radio, breaking him out of his brief reflections and bringing his attention back to the matter at hand.

"Yeah?" he said, reaching up to tap the radio they'd given him (He'd deactivated the one he'd installed in his mask; as long as he was working with the rest of the expedition, he didn't think it would be the best idea to let them know just how much he knew about them).

"Gateship Four just contacted me," Sumner explained. "They said that, allowing for the assumption of a gradual speed to adjust for potential dart impact, it should be possible to reach a hive-ship in around four minutes."

"Right, got that; tell the pilot thanks for his assistance," John said, quickly shifting the radio link- Sumner would understand; with the city itself at stake he didn't have time for a polite goodbye- to address the scientist currently overseeing the placement of the bombs. "Doctor Zelenka, program the timers on the bombs for four minutes forty seconds, to begin when I give the signal; that should be enough time to reach the hive-ships' main hangers."

"Affirmative," the Czech scientist replied briefly before returning to his original task, leaving John to sit patiently for another few moments, his mind briefly drifting to thoughts of Elizabeth- she'd really been brilliant in that conference room; quietly but firmly exerting her authority over the colonels almost without them realising it- until…

"They're sending in another wave!" Elizabeth's voice yelled over the radio, spurring the part of John's mind that would always think like a soldier back into action.

Shifting his focus back to the short-range sensors, John noted that she was right; darts were already approaching the city, in far larger numbers than the first time around.

Fortunately, this time around they were closer together…

John didn't hesitate; with their drone supply depleted, his original strategy wouldn't work, so it was time to go back to something he'd wanted to do the first time around. As soon as the darts were close enough, he activated the shield, sending the darts crashing into it before they could pull away, only dropping the shield when the last few darts in the wave pulled up to avoid striking the shield like their predecessors had; from what he could tell, there were enough darts left for the city's Earth-originated defences to pick them off in relative comfort.

He jut hoped that there weren't enough darts left to beam a few decent-sied Wraith strike teams into the city before they were all destroyed; they did not need another round of hand-to-hand with those assholes…

"Wow…" McKay muttered- admittedly in a low voice; clearly he didn't want to admit to being impressed by something someone else had done- before he turned to look at the man in the chair as another thought occurred to him. "Hold on, what happened to 'not wanting to waste power'?"

"Well," John said, shrugging slightly as he looked at the Canadian standing beside him, "I figure that, given how long we've got until the Daedalus is meant to arrive, we can afford to waste a little energy at this juncture."

"And if the Daedalus doesn't arrive?" McKay asked, glaring critically at the other man.

John shrugged. "If it doesn't arrive in time, we're probably going to be dead; what good will power be to us then?"

After a brief silence, McKay sighed.

"Y'know, do you ever wish you weren't right all the time?" he asked.

"That depends; how do you feel when you realise that you were wrong about something?" John asked, raising an eyebrow at McKay before he leant back in the chair. "On second thoughts, don't answer that; I really need to concentrate at this point…"

Reaching out with his mind for the jumper that they'd loaded the first bomb into, John activated the gateship's drones at their lowest level- just enough to get them moving without being so powerful that they'd risk blowing something up-, and, after receiving confirmation from Zelenka that the time had been activated and he was clear of the ship, sent the gateship up through the tower, his mind fixed on monitoring the sensors to avoid incoming darts even as he pushed the ship onwards and upwards as quickly as he dared.

Here we go… he reflected, allowing himself a slight smile as he drew in ever closer to his target. Scratch one more hive-ship

Right

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