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: 667867 Published: September 15, 2009 Updated: August 09, 2014
A Fit of Jealous Rage by Marcus S Lazarus
Author's Notes:
AN: This takes place after "Coup D'Etat" and a bit before the opening scenes of "Michael", so the Atlantis Expedition have only recently helped Ladon establish himself as leader of the Genii, and are currently experimenting with the retrovirus to transform the Wraith that will come to be known as Michael, although they've only gone so far as to acquire their test subject; Beckett's still testing the virus on live cell samples rather than injecting it into 'Mike' himself

AN 2: It's not my longest chapter, but I think it has its interesting points nevertheless; hope you like it.
Standing on her usual balcony, Elizabeth once again wished that she knew what she'd done wrong; it seemed like the last couple of major missions that had been undertaken by the expedition had been far more morally ambiguous than she was comfortable with.

The situation with the Genii might have improved from what it had been before thanks to Ladon's apparent gratitude to them for saving his sister, but Elizabeth couldn't shake her apprehension about old examples of revolutions against dictators often ending up being just as bad as the government they were replacing; the fact that Ladon had been willing to go through with Cowan's plan until they had something to offer him left a part of her wondering what would happen if the day came when Ladon found something that he could take from them more easily than he could ask for it.

Of course, compared to the main project they were undertaking right now, an issue like diplomatic relations was quite frankly the least of Elizabeth's worries; her main concern right now was the current test of Carson's retrovirus.

She couldn't deny the obvious benefits of being able to remove the Wraith's need to feed on humans- particularly when it meant that they could eliminate the threat posed by the Wraith without having to actually kill anything-, but the ethical issues involved in the decision didn't make her feel particularly comfortable; however you dressed it up, she was essentially taking away another species' free will for her own benefit.

The Wraith might be killers, but they were killers because of what evolution had made them; even if it was to save lives, their current actions put Elizabeth in a moral quandary that she was far from comfortable with, and that was even before they knew if the retrovirus Beckett had developed was actually going to work...

Still... as much as those issues troubled her, the only real question that had been plaguing her mind for the last few weeks was, as much as she hated to admit her selfishness even to herself, far more personal; her recent revelation about what John's face- or at least part of it- looked like under his mask.

She might not have Phoebus's first-hand experience of war zones or serious injuries, but she knew enough to be reasonably sure what bone felt like on her own, and what had been under John's mask, located approximately where his cheekbone would be, had definitely felt like bone to her fingers even if she hadn't been the one controlling them at the time.

She knew that John actually had skin, of course- what she'd seen on the exposed left cheek and around his eyes had confirmed that much to her satisfaction-, and she'd definitely felt flesh on the rest of his cheek, which meant that what she'd felt was some specifically-focused injury on that particular part of his face...

So, she mused to herself, John wears that mask... because of an old injury?

It made a certain sense, but it still didn't explain what kind of injury it was; what could have happened to John's face to make him feel like he had to wear that mask? Was it just out of a sense of personal vanity, or was there something more...?

"You're making a mistake," a voice said behind her.

For a moment, Elizabeth wondered if someone had found out about her association with the Phantom- it might not actually have endangered the city so far, but it wasn't like that would be enough to convince Sumner to leave it alone if he learned that she'd been secretly meeting with someone he was still suspicious about-, but then she recognised the voice and her fear was replaced by surprise.

"John?" she said, turning back to look at the man who'd just been dominating her thoughts, his cloak draped around his body in a manner that concealed almost everything underneath it apart from his feet, a cold stare in his eyes as he glared at her. "What are you-?"

"The Wraith in your doctor's lab," John said, glaring at her with an intensity she could only recall seeing directed at her when she was being held hostage by Kolya. "You cannot go through with the retrovirus experiment; it's a mistake."

Despite the fact that she'd been having her doubts about that very experiment only moments before, Elizabeth couldn't help but feel indignant.

"Excuse me?" she said, raising an eyebrow as she stepped forward to address the man before her, her arms folded as she glared at him. "Correct me if I'm wrong, John, but as grateful as I am for your help over the last year, you don't actually have any authority over what I decide to do in this city; the retrovirus is a legitimately-arranged experiment that gives us a chance to end this conflict bloodlessly by actually helping the Wraith get rid of their hunger-"

"I've been fighting the Wraith since before anyone on your planet even knew that the Goa'uld existed; I think that gives me the right to voice my opinion as an expert witness regarding this 'experiemnt'," John retorted with a firm glare, practically spitting his sentence out as he looked at her. "That... thing in your isolation area is an animal, Elizabeth; even if there are a few Wraith out there who just eat to survive without taking any actual pleasure in it, I've never met a Wraith whose goals extended further than finding food supplies when they need them, and that kind of drive doesn't go away just because you change a few things."

"We'd be erasing his very need to feed-" Elizabeth began, hoping she sounded more resolved than she felt; John wasn't looking at the same arguments against the use of the retrovirus that she'd thought of, but that didn't make his points invalid.

"You can take out a lion's teeth, but that won't stop them trying to chew," John countered, an almost stone-like glare behind his mask as he glared at them. "He's been a monster for possibly centuries, Elizabeth; you're not going to get rid of that just by giving his DNA a tweak-"

"And what's the alternative, John?" Elizabeth asked, slamming her hand against the railing as she tried to stop herself giving into her doubts; she'd come too far in their research to turn back now. "Just keep on trying to blow up the Wraith on a hive-by-hive basis?"

"Why not; at least we can guarantee they won't hurt anybody again-!" John began.

"So you'd rather just kill them rather than give them a chance-?" Elizabeth tried to say, concealing the slight fear she felt at John's abrupt dismissal of the Wraith's right to live; they weren't perfect, but they were still living creatures essentially operating on instinct-

"THEY DON'T DESERVE A CHANCE!" John yelled, cutting off her train of thought as he suddenly reached out and grabbing Elizabeth by her shoulders, yanking her forward with such force that she found herself almost nose-to-nose with him in a manner that she'd never been before (She couldn't count how close-up they'd been when Phoebus was in control of her body as that hadn't been her).

For a moment, even with their current argument still practically filling the atmosphere around them, Elizabeth could only stare at the man before her, his eyes displaying anger mixed with a pain she couldn't quite place, the sudden shock of the scent of him- some combination of the sea and Atlantis and sweat and flesh and something uniquely John- filling her nostrils...

Then, as suddenly as it had been initiated, John's grip on her was released as he stepped back, his hands briefly shaking before he slipped them back under his cloak again, his gaze so cool that Elizabeth could almost believe nothing had happened if she couldn't still feel his fingers gripping her shoulders, the moment so unexpected that it felt as though he had taken hold of her on a level she'd never expected...

"I'm... I'm sorry," John said at last, his voice tainted with a bitterness that Elizabeth couldn't identify the reason for. "I just... I can't... they don't..."

Before Elizabeth could ask for John to elaborate on what he meant by that strange last comment, he had turned around leapt off the balcony, vanishing into whatever passage or location he used to return to the city when he did that before Elizabeth could even look over the balcony herself.

Elizabeth wasn't sure if it made her feel better or worse to know that John had the same doubts about the experiment as she did, even if he'd expressed in a more aggressive manner than she would have done herself...

But it was too late to start worrying about that now.

For all of John's talk about how they 'couldn't' use the retrovirus to 'rehabilitate' the Wraith, they'd progressed so far in their experiments with the virus that the expedition had to least attempt to use it; if they could turn the Wraith into humans, it could end the war in a matter of weeks by eliminating the very reason the Wraith wanted to kill in the first place.

If the alternative was just to kill every Wraith out there...

Elizabeth wasn't sure she could do that.

Actually, if she was honest, the fact that John was willing to do that...

It scared her a little.

Did whatever had happened to his face have anything to do with his vendetta- it was the only appropriate word- against the Wraith, or were the face and his anger at the species completely unrelated to each other?

Damnit, damnit, DAMNIT! John mentally berated himself as he crawled along the maintenance tunnels leading to his 'room' in Atlantis, cursing himself for the way he'd so abruptly lost control in those last few moments of his meeting with Elizabeth.

If only he'd given himself a chance to think about what he was doing, he might have been able to figure out a better way to phrase it... something that stopped him from showing all that emotion to the point where he'd almost lost control of himself...

God... if he'd hurt Elizabeth, even only slightly...

He couldn't believe he'd done that... to her. It might just have been grabbing her shoulders- it wasn't even anything serious-, but still...

He just... couldn't let them use that retrovirus against the Wraith; they were nothing but animals who didn't deserve to be 'cured' of their condition after everything they'd done to the galaxy...


He had to stop this.

He might have been able to bring himself to lie to Elizabeth for a few moments, but if he couldn't bring himself to lie about his motives to her for longer than a few minutes, he certainly couldn't keep on lying about his motives in his own head.

In the end, however, no matter how much John fought to deny it even to himself- he hated it when he admitted to something so selfish; it wasn't like he didn't try to be better than that-, there was only one reason he objected to the idea of the expedition using the Wraith retrovirus.

Why them... and not me?

What kind of a world was it that gave the creatures he'd dedicated his life to destroying a chance to become human after they'd caused centuries of suffering to this part of the universe... and yet left him in a position where his only way to survive was to become a monster almost as bad as they were?

How was it fair that the Wraith could just be given a 'clean slate' and have their sins 'wiped away' just because of some lucky break in genetic research, and he got left with nothing but memories and dreams of a life he'd once had and could never have again?

The retrovirus could give the Wraith a chance at a normal life... but what were the chances that he'd ever have that kind of opportunity himself?

Even if the accident hadn't happened, leaving him with no other option but to live like this, what he'd become as a person in order to survive this long...

In the end, all he was nowadays was a monster, no matter how much he tried to deny it; all he could do was ensure that, whatever he had become in his time in Pegasus, he continued to channel it in a manner that would help those who couldn't help themselves...

As far as the retrovirus went, with his attempt to talk to Elizabeth having failed, all he could really do right now was try to stay out of her way until he'd seen how the retrovirus experiment worked out.

If the retrovirus worked, he'd just accept it and hope that Elizabeth could forgive his 'rant'- although he'd need one hell of an apology if a chance occurred for them to meet before Atlantis experienced its next crisis-, and if it went wrong...

He'd be here to stop it.

He might be a monster himself, but he was a monster who would defend Atlantis- and Elizabeth Weir, of course- to the last; it was all he could do...

End Notes:
Short, but it was mainly intended to set the scene; the next chapter starts during "Michael", featuring a confrontation between John and the infamous future Hybrid...
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