Mystery of the Phantom by Marcus S Lazarus
Summary: (AU, Part 2 of series) As their second year in Atlantis begins, Elizabeth finds herself drawn ever further into the mystery of the Phantom of Atlantis, while John finds himself constantly torn between what he has become and what he wishes to be...
Categories: Fanfiction Characters: None
Genres: Action & Adventure, Alternate Universe, Drama, Mystery & Suspense, Romance
Warnings: None
Challenges: None
Series: The Phantom of Atlantis
Chapters: 50 Completed: Yes Word count: 164646 Read: 667567 Published: September 15, 2009 Updated: August 09, 2014
Lost Boy Found by Marcus S Lazarus
Author's Notes:
AN: Hope you like what I've come up with for this chapter- and what's happening in Atlantis will be explored in the next one, I promise-; things are getting a bit more complicated right now, but I feel that this sets the scene for the next chapter or so rather nicely...
As he took in his surroundings as he woke up, John groaned at the sight around him; as it had been the last few times he'd woken up, it hadn't changed from the basic laboratory that Michael had established on whatever planet this was after they'd landed here in the gateship, John strapped down to an examination table of some sort and allowed 'out' only after he was stunned and taken to another room to eat and attend to hygiene-related issues.

He'd been here for a couple of weeks already- assuming that Michael's comments about how long he'd been drugged had been accurate; he'd done his best to keep count after regaining consciousness, but some time had definitely gone by before he'd managed to completely wake up that he couldn't account for-, and so far Michael was showing no signs that he was going to give John any clue about what he was trying to accomplish here. John had tried to remain silent so far in the hopes that Michael would answer his questions for the sake of hearing himself talk rather than anything else- most of the Wraith John had encountered were fairly egocentric when dealing with captives, after all-, but he had yet to say anything more than the news that he'd been unconscious for 'a while' after he woke up and otherwise leaving the matter alone.

God... he'd tried to trust Michael, and then the bastard went and knocked him out because he 'couldn't take the chance' that John would take him back to Atlantis; John could have just dropped him off on a decent planet and let him make a life for himself, but Michael hadn't even given him the goddamn opportunity to even do that much!

Even if the hybrid had turned against him, however, John was grateful that Michael had been able to steer the jumper to this planet- judging by the pain in his wrists, he assumed that Michael had made him keep his hands on the controls so that the ship still sensed that he was physically giving orders even if he wasn't conscious; the jumpers might be primarily controlled mentally, but it wasn't like they'd stop if the pilot was knocked out-; he might be a prisoner here, but at least he wasn't dead in space.

The situation might be grim, but where there was life, there was still hope; he had to focus on that if he was going to get out of this situation at some point.

Plus, of course, he could at least be grateful that Michael hadn't removed his mask; he probably couldn't have done much to the technology inside it even if he'd been able to get past some of the anti-Wraith measures John had installed- including humans as something that the mask would prevent removal by had been considered and discarded when John realised that he didn't know how to design sensors that would ignore all other humans but him; programming Atlantis's sensors not to track him had been challenging even when someone else had done most of the hard work in designing the systems already-, but it made John feel better to know that the other man didn't know what he really looked like under the mask.

It was unlikely that Michael would have been able to figure out what was really responsible for his appearance underneath the mask- the circumstances that had led to him looking like this were fairly unique-, but that didn't mean John wanted more people to get the wrong impression about him; his early experiences of travelling without the mask had been more than enough of that for him...

Right now, he just needed to focus on the immediate priorities facing him, which included determining his current location and the reason for their presence there. Judging by the general atmosphere of the place, they were apparently in some old Wraith research facility on a planet on the outskirts of the Pegasus Galaxy- John hadn't been able to establish whether or not it had a Stargate, but he was guessing that it was gateless or at least didn't have a Stargate in a convenient location, given that those facilities were generally established on worlds where the Stargate wasn't immediately accessible to ensure that nobody stumbled across their work by accident; the mess that resulted in Teyla and other Athosians possessing their 'gift' had taught the Wraith to avoid repeating those circumstances-, and, from what John had seen, Michael was working to access the laboratory's computers for some reason or another.

How Michael had known about this stuff was something John didn't know- had he regained some of his Wraith memories about who he'd been, or had he stumbled across something in the hive's databanks before they'd turned against him?-, but it also wasn't something he really needed to concern himself with right now. Given Michael's apparent pariah status among other Wraith after his transformation, coupled with his recent role in helping John, McKay and Ronon escape- even if he had turned on them afterwards-, he probably wouldn't have to worry about dealing with more Wraith in this situation any time soon, which meant that he still had a chance to get out if he was careful...

"Still contemplating escape?" Michael asked, his voice drawing John away from his thoughts as he looked up at the man on the other side of the door to his room (He couldn't call it a cell as the door wasn't locked; he just couldn't walk over to it), his own gun hanging from Michael's belt as though the hybrid was daring him to take it. "Haven't you given up by now?"

"I think we both know that I didn't become the thing the Wraith have nightmares about by giving up that easily," John countered, clenching his fists as he stared resolutely at Michael, resisting the temptation to try his only viable plan so far; if he tipped his hand before he knew how he was going to go any further, he'd be in even more trouble than he already was and would lose his own real advantage. "What do you even want with me, anyway? If you seriously think that I would ever help you of my own free will-"

"Let's just say that you could be... useful to me down the line," Michael said, chuckling slightly as he walked around John, flexing his fingers as though anticipating what it would be like to take John's body apart. "After all, you are a very unique specimen-"

"If you think I'll ever help you in anything-" John spat scornfully at the hybrid (How he'd ever hoped that this guy could have been a kindred soul he didn't know; the bastard was just out to destroy anything that might threaten his safety).

"You will give me something eventually," Michael said, shaking his head in satisfaction. "Even if you don't choose to aid me willingly... there are always ways to get what I'm after."

"And what would those be?" John asked scathingly. "We both know that I've endured the worst that you Wraith have to throw at me to get me to comply using your normal methods, and I always ended up turning them against you; what are you going to do that they didn't, stick some kind of implant on me or something?"

"Tempting, but imprecise and unlikely to succeed anyway," the hybrid replied dismissively. "No, what I plan for you is far more long-term than that... to say nothing of less direct-"

The sound of something yelling in pain outside the door of John's cell forced him to abandon any thoughts he had of waiting any longer to break out.

He might not know much about his current location, but he did know when something was in pain, and if Michael was carrying out further experiments in this lab, that just made it all the more important for him to stop this bastard before he could do anything else; John could take whatever this guy had to deliver if he had to, but another victim in this place was another potential ally for John as far as he was concerned.

As though he was being held down by nothing more than string, John suddenly broke the straps that had been keeping him apparently trapped, his feet landing on the ground as Michael drew the weapon he'd taken from John and fired it at him, only to be shocked when the gun's red energy shimmered over the distinctive green pattern of an Ancient shield device that John had kept concealed in his cloak, just close enough to his skin to be activated without Michael realising that it was there. Before Michael could fully process what was happening, John had punched the hybrid in the face, the additional power of the force field boosting John's already above-average strength to send Michael slumping to the ground, completely unconscious.

"Take all the time you want to rest, you bastard," John said, glaring scornfully at his enemy as he took his gun back before he turned around and ran out of the cell, hurrying down a corridor in the direction of the scream that he'd heard earlier. Finally reaching a likely-looking door- it looked fairly thick, but it was also slightly open; Michael had probably been here earlier and forgotten to properly lock it-, John opened the door, and nearly felt like throwing up at the sight that greeted him on the other end.

The entire room was filled with a massive web of purple vein-like things that put John in mind of a Wraith hive-ship, of varying thickness and length, all of them reaching out to the ground, walls, or ceiling, and all of them originating from the same source; a young man, lying bound on an operating table in the middle of the room similar to the one that John had been imprisoned on, his face immediately familiar to John despite the burns and further disfigurement around one eye.

"Lieutenant Ford?" John said, his eyes widening in shock as he took in the sight of Atlantis's most prominent MIA member; he wasn't sure if the man was even conscious in this sort of state, but addressing him directly seemed like the most effective way to establish that.

"Ugh..." Ford muttered, blinking his eyes open- the formerly-black eye now back to normal, even if the skin around it was still strange; judging by his appearance, John guessed that something had happened that made Ford briefly pass out from pain as he let out the previously-heard scream, but things appeared to be more stable now- and taking in the room around him in momentary confusion until his gaze focused on the Phantom. "You-!"

"Easy!" John said, holding up his hands in a defensive gesture; Michael would probably be out for a while, but anything that might stir him into consciousness was definitely not to be encouraged. "I know you're probably mad, but don't freak out on me before you've had a chance to think; I'm here to help you-!"

"You want to help?" Ford said, glaring over at the man he knew only as the Phantom as he tried to move his arm; John wasn't sure if Ford had fully registered where the things filling the room came from or if he was just focusing on his own anger. "Make those goddamn voices stop!"

"Voices?" John repeated in confusion, taking a brief pause to listen again in case he'd missed something earlier before he refocused his attention back on Ford. "There aren't any..."

As his gaze refocused on the tendrils extending outwards from Ford's body, John wished that he could think that his current theory was wrong; it might be based on minimal evidence, but those things looked far too much like the interior of a hive-ship for John to feel comfortable deluding himself that he was dealing with anything other than the worst-case-scenario (Besides, if he assumed the worst, anything else he encountered or learned to the contrary would be a pleasant surprise, even if he wasn't optimistic about the odds of that actually happening given some of his past experiences).

"Oh no..." he said, glancing around the room urgently for a few seconds before his eyes fell on an old Wraith computer; it was antiquated by any standard- it looked like it was from an era before they'd even fully mastered using organic computer systems and were using scavenged Ancient technology-, but that didn't matter right now; as John hurried over to the computer and began to scan through its files, all that mattered was what it had to tell him rather than how it was stored.

"What are you...?" Ford asked, turning his head to look at John as much as his position would allow him to do so.

"Looking for information on what Michael's doing to you," John replied grimly, his fingers practically flying over the controls as he searched through the database (He noticed some brief references to Michael finding Ford a day or so ago, which at least suggested that this planet had a Stargate, but then he noted Michael's reference to 'disabling' the DHD and scratched that possibility as a way of getting off this world). "If I'm right, than..."

He trailed off, realising as he spoke that he wasn't entirely sure what he could do about the situation if he was right, before shrugging and turning his attention back to the computer. "Well, on the bright side, the Wraith and Ancient written languages aren't that different from each other- and don't ask me how that's possible because I just don't know for certain any more than you do-; all I need to do is make the necessary adjustments to accommodate some of the slight linguistic differences- you don't fight the Wraith as long as I have without picking up some useful details about how they communicate-, and we should be able to..."

His eyes widened as he registered the information now displayed on the screen in front of him, and John couldn't stop himself from letting out one of the few swear-words he allowed himself to say these days. "Oh, shit."

"Bad?" Ford asked, looking at the man he knew as the Phantom with increased apprehension, his usual hostility against the man in the mask forgotten in the face of the fear and regret that was visible despite the limited amount of his face that was exposed to outside view.

"You've been infected with a Wraith pathogen," he said, looking grimly back at the other man. "I'm not clear on the how of it, but based on the references here to this thing generating an organo-metallic polymer... I'm guessing that this is going to become a hive-ship."

"A what?" Ford said, staring at him incredulously before he indicated some of the tendrils coming out of him with an awkward wave of his hand. "You're saying that this... stuff... is going to become a hive-ship?"

"It's a bit worse than that, actually," John said, looking regretfully at Ford, wishing that he had a better idea how to phrase this; he might be brilliant in a fight, but he sucked in social situations. "If the infection runs its course... you yourself will be the Hive-Ship."

"What?" Ford said, clearly incredulous at the idea.

"Well, they are essentially living things; it's not like they all started out that size," John said, smiling slightly at Ford even if he knew that it was a mistake as soon as his lips started to twitch; there was nothing he could do to lighten the mood in this situation, so he shouldn't really even bother to try. "How long it will take I can't say- Hives are always restricted by their power requirements, and in your case you're starting out with access to limited external power even if you're physiologically more capable of weathering the stress of the transformation than others might be; a side-effect of that enzyme, I suspect-, but the fact remains that you are going to become a Hive-"

"How the Hell did this fucking happen?" Ford yelled, shaking off his initial shock to focus on the immediate facts. "I'm not a fucking Wraith-!"

"No, but it wouldn't exactly be impossible to infect you with the relevant pathogen; once it gets into your system, it'll only take so much time until it finally consumes your physiology and coverts it for its purposes," John said, looking grimly at the lieutenant. "Once it reaches a certain point, it'll consume your brain and your consciousness will be replaced with that of the Hive; it's having trouble reaching that stage given the lack of energy sources available for it to draw on right now, but your enhanced strength is giving it a lot more to tap into than it would normally have in this situation, and the fact that you can hear those voices suggests that it's starting to manifest some degree of intelligence-"

"Shut up about what this thing is doing to me; just stop it!" Ford yelled in exasperation, wincing as he tried to wave one hand, the strain of even that much physical activity apparently too much for him in his current condition. "You're the goddamn Phantom; you've got to be able to do something-!"

"There's nothing I can do, Lieutenant Ford," John said, glaring at the other man. "If we had enough time and Doctor Beckett or someone like that was here, maybe we could pull it off, but my knowledge of even human biology is limited, never mind Wraith biology; I can keep myself healthy and kill Wraith fairly quickly, but treating something like this is way beyond my abilities."

"You have to do something!" Ford yelled urgently at him, panic becoming obvious as his fragile control of himself began to fall apart. "I won't become a-!"

"If I had time to put the cure together and someone had established some kind of foundation that I could use to start things off, maybe I could do something, but I can't create an antidote to something like this from scratch!" John yelled- he might be exaggerating his skills, but he liked to think of himself as fairly adaptable and he knew that he was intelligent, so he might have been able to do something if the aforementioned rules applied and someone else had given him something to work with-, before he paused and took a couple of deep breaths, trying to calm himself before he looked back at Ford. "If I could save you, I would- whatever you think of me, I've never wanted anyone in Atlantis to die; all I've ever wanted to do is protect that city-, but I can't cure this; I don't even know what could hurt it without hurting you!"

After a moment of silence as the two stared at each other, a grim expression on Ford's face and a pleading one on John's, Ford sighed in resignation.

"Fine," he said, his gaze flicking down to John's waist. "Use that."

"Wh-?" John began, before he followed Ford's gaze and realised what the other man was looking at; the gun he'd just taken back from Michael. "Are you-?"

"NO!" Ford yelled, staring with near-frantic intensity at him. "I won't become a hive; if you can't help me, kill me!"

For a moment, John could only stare silently at back at Ford, his knowledge that Ford's suggestion was all that he could do for him warring with John's simple promise to himself not to kill human beings unless he knew that they unquestionably deserved to die.

He'd avoided killing even Kolya when nobody could have blamed him for shooting the guy in the head after ensuring that Elizabeth was out of harm's way; he would not kill Ford...

"Look," John said, glaring at Ford, "I'm not going to kill you, and there's still time to cure you of this; right now, our immediate priority has to be to get out of here and find some way of helping you."

"And how would you recommend we do that?" Ford asked.

"Actually, my plan ties into what's being done to you right now," John replied with a slight smile. "Theoretically, since you're becoming a hive-ship, some part of you is already growing the components that they all possess; if we focus, you might be able to access some of them in their larval stage and accelerate their growth-"

"You want me to try and help this thing-?" Ford began.

"-focusing on the long-range communication systems that might allow us to establish contact with Atlantis," John finished, smiling encouragingly at the lieutenant; he might know how grim the situation was, but since he doubted that the lab had access to a communication system in itself, he'd have to work with what he had. "The enzyme's allowing you to better cope with the transformation; maybe it'll give you some degree of control if you focus on what you want the pathogen to generate."

"We're in a completely different solar system; we'll be lucky if we can get any kind of signal through-!" Ford countered.

"We can at least send off a Morse code message or something; once they know something's here, that's half the problem dealt with," John said, looking resolutely at Ford. "Just send concentrated pulses of information to Atlantis, focusing on the right length for each, and we should be able to pull this off..."

John just hoped that he sounded more confident than he felt; even if Ford could find the communication systems in whatever his body was trying to become and use them in the manner described, there was no way to guarantee whether or not Atlantis was in a position to respond to their request in time even if they understood it...

Still, he had to try.

Even if he was reasonably sure that he could find the puddle jumper that Michael had used to get here in the first place somewhere on the base with relatively limited effort- Michael wouldn't want to destroy the only means of transportation available to him, even if it he probably couldn't use it-, he wasn't going to abandon Ford here unless he had absolutely no choice.

It was time to see whether those meditation lessons he'd received when he was stuck in that temporal field thing were worth anything when he was trying to teach those skills to others; if he could just help Ford focus his mind on his goal, the chances of them both getting out of here might get better...
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