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 if anyone identifies the song where I got this title from (Chapter titles will now alternate between various lyrics from various songs that I feel reflect John and Elizabeth's relationship in this universe or whatever best describes the situation; one of my last reviews left me re-thinking my original thoughts regarding ceasing using song lyrics)

The Phantom of Atlantis

As McKay studied the information he'd managed to pull up on his laptop from the Ancient computers, he found himself liking the situation that he and his team had just stumbled into less and less with every passing second. Not only did they have to face the possibility that they were going to die of some horrible unidentified Ancient virus, but so far he wasn't having much luck in tracking down anything that they could actually use in the current situation. He might have been able to confirm that they were in an Ancient viral lab where the computer systems were cut off from the rest of the Ancient database, thus restricting them to hear if they wanted to learn more about the virus, but what they were actually dealing with was still a mystery to him; he didn't even know if the Ancients had created the viruses or were just studying them after finding them on some planet in this galaxy.

"OK," Zelenka's voice suddenly said from almost right behind him, breaking into McKay's train of thought as he studied the information he'd discovered so far on the screen before him. "I think that we…"

"Yes, yes, yes, yes, yes…" McKay interrupted, quickly running over what little of the conversation taking place behind him his subconscious mind had overheard- Zelenka, Ford and Dumais been talking about what container could have held the virus that killed Wagner and Johnson and expressed the possibility that the Ancient database could hold the answer about what kind of virus they were tackling-, before he continued. "It doesn't appear to be networked in with the rest of the Ancient systems-"

"Doctor McKay?" a voice suddenly said over his radio, cutting the Canadian off mid-sentence as he glanced down in surprise at the radio; he hadn't recognised the speaker's voice, and he'd assumed that he'd already met everyone in the expedition after spending the last few months in the city with few people to talk to apart from each other.

After a moment's confused hesitation, McKay shrugged and activated the radio.

"This is Doctor Rodney McKay; who is this?" he asked, noting from the confused expressions of the other scientists around him that they had no more of an idea about who was speaking right now than he did.

"I am the Phantom," the voice replied simply, a slightly amused tone in the voice as though the speaker found it rather amusing to say that line. "I'm here to help."

McKay blinked.

Whoever else he'd been expecting to contact him, he hadn't expected it to be that guy…

"Hold on; you're the Phantom?" he repeated, trying not to look as shocked as he knew he felt. "As in… the Phantom? The guy who took out that Genii invasion force a few weeks back?"

His eyes narrowed and his voice lowered as something else occurred to him. "The guy who stunned me while taking out the invasion force in question?"

"The same," the voice- the Phantom's voice- replied at the other end; unlike earlier, the speaker's tone now sounded almost embarrassed. "On that topic, I would like to take this opportunity to apologise for stunning you like that; I had very little time available to me and could think of no other way to guarantee that the Genii would not continue to attempt to take you as a hostage other than rendering you unconscious and thus making you more difficult to move-"

"I'm sorry, is that last comment meant to imply something?" McKay asked pointedly; if he'd been holding the radio the other people in the room had little doubt that he would have been glaring at it. "You know, a weight related something-"

"This is not the time to argue about my opinion of your physical condition, Doctor McKay," the Phantom's voice said, interrupting the Canadian scientist mid-sentence, the tone grim as he spoke. "We have to get past that particular issue; if we don't act quickly then people will be dead in-"

Before the Phantom could continue, the sound of someone whimpering audibly prompted McKay to turn around, his eyes widening in shock as he saw Dumais standing away from her laptop, her mouth wide open and her hands raised as she took deep, rapid breaths, an expression of terror on her face.

"Dumais?" McKay said, stepping forward slightly as he looked uncertainly at her. "Dumais? Dumais?"

Before he could say anything else, Dumais had turned to look in shock at Peterson, the other scientist standing in clearly-growing fear off to the side, and let out a small scream.

"It's all over you!" she screamed, before she rushed towards him, her hands desperately flailing all over his chest as though trying to brush something off his chest. McKay barely even registered Peterson's protests as Dumais continued to yell about something covering the other scientist; ignoring the Phantom's requests for information over the radio, he and Zelenka hurried over to pull Dumais off Peterson, only for the woman in question to clutch her head almost as soon as she'd been pulled away from the other scientist.

Before McKay could do more than remember that this was almost exactly what had happened to Johnson, Dumais let out a brief scream and collapsed to the ground, alternating between screaming and grunting as McKay and Zelenka lowered her to the ground, only to fall silent as they lay her down on the floor.

McKay didn't need to see the blood trickling from her ears and nose to know that she was dead; after the Genii invasion- to say nothing of that mess caused by the Hoffan drug-, he'd managed to get a very clear picture of what death looked like, and he was practically staring it in the face right now.

Staring grimly at the sight before him, McKay stood up, briefly shifting channels on his radio to send a quick message to Elizabeth.

"Tell Beckett to pick up the pace!" he yelled, unconcerned about manners; the situation was too serious to be concerned about minor social niceties like that. "I've just lost another member of my team!"

"Where's Peterson?" Ford's voice suddenly said, his tone low even as the words prompted McKay to glance up at his younger teammate.

"What?" he asked, almost hoping he'd heard the other man incorrectly.

"Peterson!" Ford replied, glaring back at McKay before he hurriedly walked over to the door, glancing briefly around the corridor before he turned back to look at the others. "He's gone!"

"Let me guess; someone has run off?" the Phantom asked; to McKay's relief- the Genii invasion had made it pretty clear to the Canadian scientist that he did not want this guy pissed at him-, the other man- or whatever he was; just because he seemed human from what brief glimpses they'd caught of him so far didn't mean he was- gave no indication of anger or frustration at being ignored like he had been earlier.

"Yes," McKay replied, turning his attention back to his radio, making no effort to conceal his frustration with the man on the other end; given that the guy wasn't angry at being ignored earlier, he felt slightly more comfortable at the idea of losing his temper at the man in question. "As you have oh-so-correctly assumed, one of my team has run off, potentially endangering this entire expedition if he is carrying this virus, and the last thing I need right now is you calling me to apologise for stunning me a month ago-"

"I did not just call you to apologise about that; I called you because I know what you are dealing with," the Phantom's voice cut in, sounding at least slightly frustrated at McKay's initial assumption about his reasons for calling the Canadian scientist.

McKay stopped yelling instantly.

"Excuse me?" he asked.

"The 'virus', as you assumed it was, is actually a nanovirus that was created by the Ancients as part of a plan for an anti-Wraith weapon that didn't work out like they'd hoped it would," the Phantom continued, evidently refusing to give McKay a chance to interrupt him as he spoke. "It was designed with the intention of being released into Wraith hive ships and attacking the Wraith on the cellular level- the theory being that the Wraith's natural ability to heal from pretty much anything would translate into an inability to cope with such 'attacks' due to their lack of medical technology rendering them unable to identify the nanites-, but the Ancients activated the nanites before the programming was complete; they'll kill anything that doesn't at least possess the Ancient gene around six hours after the initial exposure-"

"Hold on; six hours?" Hays suddenly yelled, looking in shock at McKay in the absence of being able to look at the person who had actually told them this latest information. "But… but I ran into Dumais shortly after she met Wagner and Johnson!"

"Hey, I was with you-" McKay began.

"As I recall, you underwent the Ancient gene therapy during your first few days in Atlantis, Doctor McKay; given that the nanites only target those without the gene, you will be perfectly safe," the Phantom cut in, his voice slightly raised as he tried to call attention back to himself. "However… Hays, correct?"

"Uh… yeah," Hays replied, nodding slightly before he stopped himself as he remembered the person who'd asked the question wasn't in the room to see that part of his response.

"Thank you… Hays, on the other hand, will be dead in a short amount of time unless we can come up with a plan to shut the nanites down before that happens," the Phantom continued. "Tell me, Doctor McKay, would the EM pulse generated by detonating a naquadah generator in the upper atmosphere possess sufficient power to shut down the nanites without the explosion itself damaging Atlantis?"

"Hold on; you want to blow up a naquadah generator?" Ford cut in, the sole military member of the group in the lab speaking up for the first time since the Phantom had first spoken. "You can't do that; you don't have the authority-!"

"In case you haven't been paying attention, Lieutenant, if I don't try it then you- the last time I checked you lack the Ancient gene- and at least a third of the population of this city face the very real possibility that you will all be dead within a matter of hours, particularly if Peterson makes it to a more populated part of Atlantis," the Phantom countered, his voice cold as he spoke to the young military officer. "You can either worry about how Colonel Sumner will react to the loss of a naquadah generator later, or suffer an aneurysm when the nanites that have almost certainly infected you by this point finish incubating and fulfil their pre-programmed function, thus rendering the issue of Sumner's reaction to my actions academic; the choice is yours."

After a moment's silence as Ford considered what the Phantom had just said, the voice on the other end of the radio spoke once more. "Shall I take your silence as meaning that you have acknowledged that I made a valid point?"

"Fine…" the young lieutenant groaned, glaring pointedly at McKay in absence of being able to glare at the Phantom himself. "Just so you know, I still don't like this; you're an unpredictable element in a situation where we need stability-"

"You don't have to like me, Ford; you just have to let me do what I have to do if this city's going to survive with most of its population intact," the Phantom replied simply, before he turned back to McKay. "Now, Doctor, getting back to the matter at hand; would the EMP generated by a naquadah generator being detonated in the upper atmosphere be sufficient to shut down the nanites, or wouldn't it?"

"Well, given that their small size would probably translate into them being a bit more vulnerable to an EMP than conventional Ancient technology, I suppose it's possible…" McKay replied, nodding thoughtfully before his eyes widened as he realised something. "Hold on; putting aside the fact that we only have a certain amount of generators, how the Hell are you meant to detonate a generator at the safe distance you'd need to be at to stop the radiation from hitting us just as much as the EMP?"

"All I require from you is to direct me to a generator that you can spare; I'll do the rest," the Phantom replied simply. "Just tell me this; how high up would I need to be to prevent radiation from the blast damaging the city?"

"Uh… twenty miles, give or take," McKay replied, looking over at Zelenka in a bemused manner that clearly demonstrated his own uncertainty at trusting the fate of the entire city to somebody they still knew relatively little about. "But look; if this goes wrong you could destroy our own computer equipment-"

"If you have another plan that you guarantee will generate the necessary EMP, I'd like to hear it," the Phantom countered briskly. "Otherwise, let me do what I have to do, understand?"

After a moment's quick thought- just in case he could come up with something safer in the time they had available to them-, McKay sighed and nodded in resignation.

"All right…" he groaned, looking in frustration at the radio. "Just… don't damage anything else while you're doing that, will you?"

"Of course not," the Phantom replied, once again sounding slightly amused at the implication. "Now, where's a decent generator for me to use?"


A few minutes later, John found himself standing inside the jumper bay- he would always consider it the 'jumper' bay; 'gateship' just sounded so unimaginative to him (And that wasn't just the fact that he'd come up with it that prompted that opinion)-, a naquadah generator in his hands as he headed for the nearest jumper to his entrance tunnel. He'd managed to acquire the necessary generator quickly enough- McKay hadn't been able to just give him an inactive generator as the pulse would have taken too long to 'charge up' for detonation that way-, but he had been able to direct him to the generator currently responsible for powering the southern end of the city; as the least habited area of the city, disconnecting the generator from there would have the least amount of impact on the day-to-day activities of the expedition, particularly with the ZPM available to 'pick up the slack' until a new generator could be installed.

It hadn't been easy getting to this area, of course, but with Peterson currently occupied getting through the doors in the eastern part of the city, John had been able to save time by using the transporter to get to the southern end, recover the generator, and then transport to the central tower. So long as Peterson remained in that part of the city- which, with the transporters deactivated, would be his location for some time-, the city's damaged internal sensors couldn't detect the nanovirus and activate quarantine procedures, leaving power on in the rest of the city for John to travel from one part of Atlantis to the other.

He hated leaving the guy loose like that- there was always the possibility that he'd reach the control tower while he was otherwise occupied-, but he had to face facts; right now, the only thing he could do that could definitely help anyone was detonate the naquadah generator and hope that his and McKay's calculations were correct about the effect the blast would have on the nanites.

"Elizabeth?" he said, reaching up to activate his radio as he walked into the jumper, crouching down to activate the 'bomb hatch'- as he called it- where the generator could be placed and subsequently ejected when he reached the proper location above the city. If he understood the generator instructions correctly- and he was sure he had; after spending the last few years learning about Ancient technology by a combination of the Ancient database and trial and error, the generators were easy-, once he triggered the necessary overload, he would only have a few seconds to get out of the way before the thing blew up; he'd need to be fast when the time came…

"John?" Elizabeth replied, her voice low in his ear as she drew his attention back to the conversation at hand; he'd been so caught up in his thoughts about the generator's explosive potential that he'd almost forgotten that he'd contacted the Atlantis leader. "What is it?"

"I'm in the jum-the gateship bay-, and I'm just about to take the generator out to detonate it," he said, looking grimly around himself as he placed the generator in the hatch before he stood up and headed towards the cockpit. "You need to let the rest of the city know what's going to happen as soon as possible; when this thing goes off, the hard drive of every piece of Earth technology currently active will be wiped unless you shut them down."

"Hold on; you want me to tell the rest of the expedition about this?" Elizabeth asked, evidently surprised at the latest turn of events. "The last time I checked at least half the expedition- mostly the military half, I admit, but there are definitely some civilians here who agree with them- would like to see you locked up-"

"You cannot afford to lose any kind of technological advantage that might be gained by keeping those computer active; if that means I have to risk being captured, so be it," John replied, his tone direct as he activated the jumper and opened the outer hanger door that would take him out of the city. "If Sumner asks you how you know what I'm planning, tell him that I only contacted you to tell you to turn off your computers in order to prevent data loss; McKay and his group only know that I need to use a naquadah generator, but they don't know that I spoke to you before I contacted them."

"What?" Elizabeth asked, evidently confused at this sudden apparent change of topic. "But if he knew that you were willing to speak to me-"

"He would most likely try and have you removed from command for willingly engaging in conversation with a potential enemy of the city on the grounds that your judgement could have been compromised by your personal thoughts and feelings regarding my continued presence in Atlantis; I will not allow you to risk your position on the chance that it might improve my own," John countered, his concentration equally divided between the conversation with Elizabeth and flying the jumper; it might have become second nature to him over the years, but a few months out of practice could make all the difference unless he paid close enough attention to what he was doing. "For the sake of the expedition, do not give him a reason to doubt you; simply say that I called you and told you what I was about to do before I turned off my radio, and you decided to go along with it just to make sure.

For a moment Elizabeth sat there in silence, most likely reflecting on what he'd just asked of her, before she sighed over the line.

"All right," she said, her tone making it clear that she wasn't sure about this but would respect his wishes nevertheless. "If that's what you want me to tell him… that's what I'll tell him."

"Thank you," John replied, allowing himself a slightly grateful smile- Atlantis needed a leader like Elizabeth if the expedition were going to make any allies in the Pegasus Galaxy- before another thought occurred to him. "Talking of capturing people, where's Peterson; McKay told me that he ran off, but I didn't gather anything else about what happened to him?"

"He's still on the move, but so far we've managed to contain him in the eastern part of the city; the doors might only slow him down- apparently he has a good knowledge of Ancient technology-, but they're slowing him down enough to make a significant difference," Elizabeth replied, her voice still low. "John, are you sure about this? I mean, what if the generator knocks out the gateship as well…?"

"I'm sure," John replied, a grim expression on his face under his mask as he set a course that would take the jumper to a point high above Atlantis, forcing himself to ignore his relief at being in the air once again- it had been way too long since he'd been able to fly these things; it had been the first thing he'd ever discovered that he was really good at, and he still felt the same joy at being in the air that he'd felt when he first took one of them around the planet to scout it around- as he focused his mind on the task at hand. "This is the only way to be sure of saving the city; just give me a few minutes to get into position…"


"You're trusting the Phantom to do something like this?" Sumner's voice yelled as the control room staff around Elizabeth closed their laptops and disconnected them from the Ancient computers; she had no sooner issued a city-wide broadcast to alert the rest of the expedition to the fact that they were about to trigger an EMP before the colonel had contacted her from the gym where he and Teyla had been training before the quarantine began. "Do you even realise how dangerous that could be, given how little we know about that man? Not only do we have no idea why he's doing all this, we don't even know that he's telling the truth about this virus; maybe it is just a biological infection-"

"Doctor Beckett has already contacted me with the results of the autopsies his staff performed on the bodies of Wagner and Johnson; both of them were killed by a ruptured sacular brain aneurysm located in exactly the same part of the brain, directly above the visual cortex," Elizabeth interjected before Sumner could finish his rant; if he was going to accuse people of anything, she was going to make sure that he had all the facts available to him before he did so. "I'm not a medical doctor, but I think we can both agree that the odds of two different people suffering an aneurysm in the same part of their brain at the same time as the result of a biological infection are so remote that it's practically impossible for that means of death to have anything but an artificial cause, wouldn't you say?"

For a moment, Sumner was silent on the other end of the line, before he sighed in resignation.

"All right," he groaned, evidently unhappy about having to acknowledge that he would have to rely on the Phantom in order to save Atlantis. "Just keep an eye on that gateship; I want a security team in the gateship bay as soon as this virus has been eliminated."

"What?" Elizabeth said; she couldn't believe that, even at a time like this, Sumner couldn't stop focusing on his near-obsession with capturing the Phantom. "Colonel, if this is about your concerns regarding the Phantom taking action without consulting us, I'd like to point that he did inform Doctor McKay and myself what he was doing-"

"We wouldn't even need his help if he had just told us that this virus was there in the first place," Sumner coldly pointed out, his tone making it clear to Elizabeth that this was another occasion where no argument she could come up with would manage to convince him to change his mind (Or, at least, wouldn't allow her to change his mind in the time available before John's gateship landed). "Even if he's been willing to consult with you before he took such significant action, if he'd just been less independent we wouldn't have to deal with this problem in the first place."

"It's not like he did it on purpose-" Elizabeth began.

"Purpose doesn't matter; the final results are all that I'm concerned with right now," Sumner countered. "In his own way, the Phantom's potentially as dangerous as the Wraith. We might know the Wraith's motives for culling other worlds, but we still have little to no idea what actually motivates the Phantom's actions, and his knowledge of the city could be dangerous if he ever decided to use it against us; hell, for all we know he could have released this virus himself-"

"Enough," Elizabeth interjected; she might have promised John that she'd inform the city of the situation as though he'd only called her to tell her what he was doing rather than asking her if he could do it in the first place, but that didn't mean she had to allow Sumner to insult him like that. "I acknowledge that you have a point regarding our lack of knowledge about the Phantom's motives, but voicing unfound suspicions won't accomplish anything but creating paranoia in this city; I will not have your efforts to find the Phantom turn Atlantis into seventeenth-century Salem. Understood?"

"Understood," Sumner replied, a slightly hostile edge to his voice before he terminated the connection, leaving Elizabeth briefly worried that she might just have pushed her military commander slightly too far with the reference to the Salem Witch Trials. She knew that it might have been pushing her luck, but she'd honestly meant what she said; even if a part of her could see the value in Sumner's arguments about the Phantom's independence being potentially dangerous in the long run, if Sumner started thinking that the Phantom had done things when there was no proof that he'd had anything to do with them he was approaching the point where he'd have to be dismissed on the grounds of exaggerated paranoia.

Elizabeth didn't want to have to resort to that; as much as she and Sumner might clash on occasion about how best to run the city, he was the most qualified person to organise its defences in the event of the Wraith ever managing to find their way to Atlantis. John would do his best, of course, but he was only one man, to say nothing of being a man whom at least half of the military staff would like nothing better than to see out of the way…

And when had she come to depend on John for safety to that kind of extent? He may have saved the city from the Genii and that shadow creature- to say nothing of saving Sumner's team when they were trapped on the other side of that wormhole in the early days- but you could hardly get used to someone doing something after they'd only done it three times…

"I'm almost in position," John's voice suddenly said in her radio, breaking her train of thought as she turned her attention back to the more immediate matter of stopping the virus.

"I hear you," she replied, keeping her voice low as she slowly moved off towards her office; at least this way she wouldn't give any anti-Phantom members of the current control room staff any reason to further rquestion her ability to make decisions in that matter. "Would the EM pulse have any effect on the Gateship?"

"The jum- the gateship is shielded from the effects of an EMP; it's the shockwave that concerns me right now," John replied briefly.

For a moment Elizabeth simply stood silently off to the side, noting the deactivated equipment around the room- they'd done everything they could do protect their equipment short of actually sending it through the Stargate-, before she spoke again.

"Good luck," she said simply.

"Thanks," John replied briefly, before there was a brief crackle of static and he was suddenly broadcasting across what sounded like the city's public address system. "Attention Atlantis, this is the Phantom. Ensure that all computers and electronic equipment has been deactivated; I am releasing the generator… now!"

For a few seconds there was nothing but silence throughout the city- baring Doctor Grodin's voice as he counted down the seconds that followed the Phantom's statement, until, the moment Grodin said "One", the world outside the city windows was briefly illuminated in a brilliant white glow, so dazzling in intensity that everyone in the control room was forced to look away for the few seconds that the light lasted.

For a few moments, Elizabeth simply stood in the centre of the control room in silence, unwilling to try and contact John even as she wished she knew how he was- had he managed to escape the blast in time?-, before she finally heard his voice.

"This is the Phantom," he said, his tone neutral once again; evidently he didn't want to give away anything that would risk showing weakness given his official fugitive status. "The generator has detonated, and I have safely cleared the blast."

"Good," Elizabeth replied, privately satisfied with herself for choosing such a neutral expression; it could have been taken as meaning that she was glad the generator detonation had worked out as planned, or that she was glad the Phantom had escaped the resulting explosion.

As John terminated the connection- Elizabeth took that as a good sign regarding his faith in the plan; he was so certain that it had worked he felt no need to ask about it-, she turned to look at Grodin, who nodded as he activated the computer in front of him.

"Just to make sure you know," McKay's voice suddenly said from her radio, "the pulse only lasts a couple of microseconds; once it's over-"

"The computers are all fine, Rodney," Elizabeth said, smiling slightly as her staff around her moved to activate the various computers. "Once Doctor Beckett's checked you over to confirm that the nanites have deactivated, you have a green light to return."

With that said, she terminated that radio connection and turned to look at Sergeant Bates. "Bates, take a security team to Doctor Peterson's location; escort him to the medical wing if he needs more convincing that he is no longer infected."

"Understood," Bates said, nodding briefly at her before eh turned and hurried down the stairs, signalling to a couple of the surrounding marines. They had only just begun to advance towards the door leading to the corridors where Peterson had last been seen- Elizabeth hadn't had the chance to check the monitors to see where it was now-, when Sumner's voice suddenly cut in over the broadcast system.

"This is Colonel Marshall Sumner," he said, his voice making it clear that he expected his current orders to be instantly obeyed. "All available security teams report to the gateship bay immediately; once the Phantom's gateship arrives keep all guns trained on it until my arrival."

To Bates's credit, Elizabeth was gratified to note that he didn't automatically obey the order; he raised one hand to his ear to activate his radio even as he and his marines stopped walking. "Sorry, sir, but Doctor Weir ordered-"

Elizabeth couldn't hear Sumner's reply over the radio, but she was hardly surprised when Sumner's voice appeared on hers. "I apologise for circumventing your authority, Doctor Weir, but Doctor Peterson can wait a few minutes; this is our best chance to apprehend the Phantom, and I will not allow him to slip through our fingers again."

"Understood," Elizabeth replied briefly, terminating the connection as she turned to walk after Bates and the other marines.

Her issues with Sumner countermanding her like that would have to wait; right now, she had to make sure that any anti-Phantom soldiers with itchy trigger fingers didn't try to shoot John the second he tried to walk out of that gateship…

As Elizabeth walked into the gateship bay- taking care to keep a respectful distance behind the soldiers; she didn't want to appear overly anxious-, she glanced upwards just in time to see the gateship begin to descend into the bay as it entered through the currently-open hole in the roof, the ship already rotating to land in the only currently-empty slot in the entire bay…

It was only when the ship actually reached the ground, allowing Elizabeth and the marines before her to see through the cockpit window into the rest of the ship, that Elizabeth realised something she hadn't been expecting.

The gateship was empty.

Admittedly, it wasn't impossible to assume that John- the Phantom; she couldn't afford to risk slipping up and saying his real name at a time like this- was hiding somewhere in the ship where he couldn't be seen from the window, but she doubted it; what would he have to gain by attempting something that… well, pathetic? There was nowhere for him to go but out of the ship, and she doubted even Jo- the Phantom- could easily take out this many marines when they were all prepared and ready for him; his main advantage when fighting off the Genii had been surprise, which was something he'd only have a slight amount of here in relation to the amount he would have possessed during that confrontation.

Despite herself, as the marines stated in confusion at the empty ship before her, Elizabeth smiled.

She might still lack any knowledge about John's long-term motives, but she could say one thing for certain; since she'd learnt of his existence, her time in the Pegasus Galaxy had never been boring.


If anyone had been able to see the city from the outside at that point, they would have swiftly learned what had just taken place. Clinging to the highest part of Atlantis's central control tower, his long black cloak flapping in the wind as he looked down at the descent that awaited him, estimating the distance between here and the outer entrance to the emergency tunnels that he'd once discovered, was the black-clad form of the Phantom, a slight smile on his face as he listened to Sumner's shock over his radio.

Sorry, Marshall, he mused to himself as he began to climb down; in many ways, the Atlantis military commander's adherence to the rules made him almost worryingly predictable when presented with an opportunity like the one he'd almost been provided with. But right now, I'm just not ready to sacrifice my independence; I can accomplish a lot more on my own at the moment.

Maybe he'd make full contact with the expedition at some future date, but for the moment, he felt that he worked best 'undercover' in the event of something like the Genii invasion happening again; sometimes, a city like Atlantis needed somebody who was willing to go against authority and do what they had to do rather than what they were ordered to do.

Until he felt that Atlantis had a commander who understood the value of that- much like what Elizabeth had told him about General O'Neill during their all-too-brief time together after he'd first arrived in the city; now there was a guy who knew that you couldn't win by sticking to the rules all the time- he'd risk getting in even more trouble if he made contact with Sumner than if he remained independent.

At least he was operating outside of the chain of command Sumner couldn't get more angry with him; if he even seriously tried to make an effort to work under Sumner- and it would be 'under'; he was sure of it- the two of them would end up fighting it out in a matter of days because John couldn't obey his orders…

As he finally reached the hatch that would allow him back into the maintenance tunnels, and thus into Atlantis itself, John shook his head as he opened the hatch before him.

He could worry about the future later.

Right now, his immediate priority was getting to a comfortable spot and having a decent sleep after his latest near-death experience (If having to set off a nuclear explosion and get away from it in thirty seconds wasn't a near-death experience, he didn't know what was).


AN 2: Well, the next chapter explores the aftermath of this particular escapade; I can assure you, Sumner and Elizabeth are going to have words next time around…

AN 3: If anyone's wondering how the jumper managed to land without anyone in it, I read somewhere that the jumpers apparently operate on automatic pilot when they're within a certain distance of Atlantis, hence explaining how Ford was able to use one to leave in "The Siege- Part Three" despite him lacking the Ancient gene. With that in mind, it seemed reasonable to assume that John would be able to set his jumper on autopilot once he drew in close enough to the city, subsequently jumping out the rear hatch and climbing down the tower from the outside while the security team kept an eye on things inside the gateship bay