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: 1045776 Published: September 15, 2009 Updated: August 09, 2014
The Masks We Wear by Marcus S Lazarus
Author's Notes:
This begins shortly after the end of the last chapter, with Phoebus having already made contact with Lorne's team and convinced them that she's still Elizabeth; Thalen's role at this point will be pretty much the same as it was originally, but things get more interesting for Phoebus when she's about to take out Lorne's team...
As Phoebus walked through the corridors of Atlantis, she almost couldn't believe how easy this had been so far; for soldiers, these people had no real evident concept of warfare. She'd been in control of Elizabeth Weir's body for almost half an hour already- not counting the time she'd spent feigning that Weir was back in charge to trick them into giving her what she wanted-, and not only was she still uncaptured, but she'd actually successfully managed to convince an entire team that she was still Elizabeth Weir...

Quite frankly, she was almost tempted to shoot them after she'd finished dealing with Thalen; she'd be doing them a favour getting rid of such pathetic soldiers. Obeying orders was good, but there was a point where you needed to recognise when you were obeying the wrong orders; the number of times she'd nearly been killed because a couple of commanders had defected...

"You know," Major Lorne said as they ran through the corridors of Atlantis, Phoebus grimly leading the way, "it would help a lot if we knew more about what was going on."

Phoebus didn't bother to respond to that; if push came to shove and they continued to insist on an explanation, she'd just say that there wasn't time to worry about that sort of thing when they were dealing with a hostile life-form...

"This is Caldwell," a voice suddenly said over her host's radio. "Both Doctor Weir and Colonel Sumner are under the influence of alien entities. If at all possible, subdue and contain them with non-lethal force."

Damnit... Phoebus reflected, coming to a halt as she turned to look at the small team she'd tried to bring together. So much for things being this easy...

"Ma'am!" Lorne said, he and his men arming their guns as they moved to surround her. "I'm going to need you to hand over that weapon."

"Did it occur to you that Colonel Caldwell might be under the same influence as Colonel Sheppard?" Phoebus asked, trying to sound as diplomatic as she could based on Elizabeth's memories (She was a soldier, not a diplomat; she resorted to talking only when there was no direct way to get what she wanted). "You weren't there."

"Hand over the weapon, now," Lorne said, refusing even to acknowledge the possibility of the scenario she'd just proposed; even if Lorne did have doubts about the current situation, he was evidently still going to take her into custody to make sure.

As one of the men reached for her weapon, Phoebus prepared for her chance to attack; given that they weren't expecting 'Doctor Weir' to be capable of fighting back against them, if she could just time it correctly-

Before she could even move, the four men around her suddenly rapidly fell to the ground, one after the other, surrounded by a burst of red energy that momentarily crackled around them before fading away.

"Sorry for interrupting your little 'fun'," a voice said from behind her, "but given that I know for a fact this thing won't cause any serious potential long-term damage, coupled with the fact that I had no idea what you were going to do to them, it seemed like the best way to stop anyone getting seriously hurt."

Turning to look at the source of the voice, Phoebus's eyes widened as she took in the man standing there, his distinctive silver mask and long black cloak making his identity obvious even without Doctor Weir's memories to draw on.

"John?" she said, recalling the true name she had learned about from Elizabeth's memories. "What are you talking about; Caldwell's-"

"I watched the whole incident take place, Phoebus; don't try and bullshit me by claiming that you're not some soldier hiding out in Elizabeth's body," the man known to almost all of Atlantis as the Phantom said, his weapon shifting to aim in her direction. "I'll make this simple; before you cause irreparable harm to anybody in this city, you will get out of that body."

"I have no intention of hurting Elizabeth Weir, John-" Phoebus began.

"Phantom," the man countered, his eyes narrowing as he glared at her. "Only Elizabeth can call me 'John'."

Despite herself, Phoebus couldn't help but involuntarily smile slightly at the unexpected sense of pleasure what remained active of Elizabeth's mind felt at that declaration; her host might not fully understand what she felt for this man, but she definitely had strong feelings for him...

"Well... Phantom," she continued, walking forward slightly with a reassuring smile, "we don't have to fight; we want the same thing-"

"You're willing to use an innocent woman to fight your own war; I want to see you out of Elizabeth's body before she comes to any harm," the Phantom interjected. "I'm not seeing what we have in 'common' there..."

"We both have little reason to think well of Colonel Sumner," Phoebus responded, taking a certain pleasure herself in seeing the hesitation in the stance of the man before her as he took in her last comment.

For all of Elizabeth Weir's faith in the man before her as a noble hero with nothing more than a slight pre-inclination towards more violent solutions, underneath that mask he was little more than the beast who had so brutally tortured and killed those Genii soldiers during that attempted takeover of this city over a year ago...

"Keep talking," he said simply after a momentary contemplative pause.

"He holds the mind of the man who sought my death, and his presence in this city has constantly hindered your efforts to establish yourself as its protector," Phoebus continued, trying to assume a more relaxed, open appearance as she slowly walked up to the man before her, easing her way into his personal space without making her actions obvious. "You could do so much more if he was not here; once you establish that Atlantis doesn't require him to operate, you may even be capable of moving beyond your current role and assuming his own."

For a moment the Phantom simply stood in silence as he looked back at her, but the contemplative expression in his eyes made it clear that he was thinking over her current offer.

"You don't even have to let anyone else know that you helped me do it," Phoebus continued, still smiling reassuringly at him, taking full advantage of her host's pre-existing friendship with this man to put him psychologically off-balance however much was needed for him to agree to work with her. "I can take Doctor Weir's memories of these last few hours with me when the imprinting process comes to an end; you can tell her that Sumner gave you no choice but to kill him if you were going to save our lives..."

"I don't kill-" the Phantom said weakly.

"And the Wraith that Elizabeth recalls you defeating died of what?" Phoebus asked with a casual shrug.

"They would kill me whatever I did; Sumner isn't himself right now-" the Phantom countered, his tone demonstrating a greater resolve than he'd shown previously.

"And what if you'd only had one weapon available to you and didn't realise what you'd grabbed until after you'd fired it?" Phoebus asked, indicating the various guns lying around them from where Lorne and his men had dropped them after they'd been stunned. "A simple enough mistake, isn't it; you grab the wrong gun in the heat of the moment, you regret what happened in the aftermath, there's nothing you can do to change what happened...?"

Once again, all the Phantom cold do was stare at her in silence, contemplation dominating what could be seen of his face as he studied her, before he allowed himself a brief, grim smile.

"A chance to get rid of Sumner with a ready-made excuse to do it, without any blame being attached to me?" he said, the smile broadening slightly as she nodded in confirmation of his summary. "It's tempting..."

"Do it," Phoebus said, looking earnestly at him. "You owe yourself this chance; take Sumner out of the equation, and the path to you becoming the true defender of Atlantis will be assured."

In response to her statement, the Phantom cocked his weapon and smiled at her.

"Give me a chance to take Sumner's weapons from him before we kill him, and this could work," he said to her. "The expedition are pretty good when it comes to forensics work; if we don't kill him with his weapon, the story won't fit and Elizabeth might be able to work out that we shot him with intent rather than out of a lack of choice."

"Of course," Phoebus said, smiling slightly at she turned to walk off with her new ally, already savouring the feel of Elizabeth's desolation as the image of her city's dedicated protector was shattered at this sight of his true corruption.

It was like it had been with Thalen's people, really; they'd set out trying to 'prove' that they could do better if they ran things themselves, and in the end all that they'd accomplished was proving that they were incapable of doing anything other than plagiarising the greatness of her people and passing it off as their own.

For all of Weir's efforts to convince himself that the Phantom was 'better' than what he appeared to be, at heart he was nothing more than a monster who used fine words to try and conceal what he really was...

Putting those thoughts to the back of her mind- the last thing she wanted was anything that gave the Phantom reason to suspect that she had something else in mind for him apart from what she had previously claimed-, Phoebus smiled briefly at her new 'ally' before she activated her radio.

"Weir to Sumner," she said as she walked along the corridor, the Phantom just behind her; given the already-existent tension between the two leaders- coupled with the psychological impact it might have on anyone in the city listening into their conversation-, it seemed slightly apt for her to use the names of their hosts rather than their own at this point. "I'm assuming you can hear me?"

"Yeah, I can hear you," Thalen replied with his usual casual tone (He could never bother to show much emotion in any situation; his inability to really acknowledge the threat she posed was something that had always frustrated her), "but if we keep using these radios, it'll only help them find us."

"We don't don't have much time, Thalen," Phoebus replied. "The imprinting is temporary and these people are going to try to stop us."

"We've got all the time in the world, and there's only one or two of them I'm really worried about," Thalen responded dismissively.

"We both want a shot at the same thing," Phoebus continued.

"You mean each other," Thalen replied, prompting a brief amused laugh from Phoebus; Thalen always had possessed an amusing knack for stating the obvious.

"And neither one of us will get that chance if you keep running," she countered, exchanging a brief glance with the Phantom to make sure he was keeping their current goal in mind; now that he'd committed himself to helping her, making sure she completed her mission was the only thing she wanted him to be thinking about right now.

"You're the one that likes to run," Thalen retorted automatically. "My ship ran out of fuel before I could even get a clean shot."

"That was my plan," Phoebus replied simply.

"You didn't have a plan; you just wanted me dead," Thalen said in response.

"Still do," Phoebus said, allowing herself a brief smile at the thought before she forced her expression back to normal as the Phantom looked over at her; her chances of convincing him to help her would be better if he thought that she fought out of necessity rather than letting him be aware of the sheer satisfaction she felt doing her job. "Once I see that look of defeat on your face for the last time, it's all over."

"Are you referring to the look on my face when you rammed my fighter, making sure neither one of us would win?" Thalen asked in his annoyingly casual manner. "That was hatred, not defeat, Phoebus."

"Is that any way to talk to your wife?" Phoebus asked with a slight smirk, only to be met with silence. "Thalen?"

After a brief silence, she decided that it wasn't important; there really wasn't anything more she had to say to him, after all.

"Run all you like," she said. "The moment I find you, you die."

"Were you actually married?" the Phantom suddenly asked from behind her, prompting Phoebus to look back at her current 'partner' as they continued to walk through the city.

"To Thalen?" Phoebus replied, nodding in confirmation. "At one point, yes, before we went our separate ways due to ideological differences; he saw things one way, and I saw them another."

She didn't elaborate, but the Phantom's lack of interest in asking for more information confirmed her opinion of him; he might act like he wanted to be independent, but in the end everyone wanted someone else to be in charge of them.

And that is why Thalen's going to lose, Phoebus vowed to herself. He doesn't have anyone to give him orders now...

As she and the Phantom approached one of Atlantis's many interior balconies, she slowed her progress for a moment, taking stock of her surroundings; unlike the narrow corridors, these areas of the city held far more potential for an ambush than what they'd been exploring previously, and she couldn't afford carelessness, particularly when the already-low lighting in the area suddenly dimmed even further.

Thalen, Phoebus mused grimly; most likely her 'dear husband' was trying to make it harder for anyone to find them.

Still... if he thought that would make it harder to find him, he had another thing coming; Doctor Weir's memories made it easy for her to recall the location of the central power room, which was the only location where he could have gone if he was going to pull something like this off. Glancing over at the Phantom, Phoebus gave a slight questioning shrug- she had to make it look like she was thinking to herself; if she was being spied on, she didn't want to give her 'partner' a reason to turn on her to save his pathetic 'image' in the eyes of Doctor Weir's troops-, to which the Phantom simply jerked his head slightly to the side before running up to the edge of the balcony and jumping off.

As Phoebus ran towards the balcony herself, she briefly thought that she saw something moving out of the corner of her eye further down the balcony, but she was over the edge and on the lower level so quickly that she doubted anyone had time to even properly register her presence, never mind the Phantom's (The man was an arrogant reminder of the rebellious attitude that had destroyed her planet, but he was very good at what he did).

As they continued to hurry through the city, occasionally pausing to avoid any soldiers they encountered in their search, Phoebus spared a few moments when she wasn't planning Thalen's demise to wonder just how the Phantom had acquired these skills of his. His movements seemed somewhat rushed at times- it gave the impression that he'd developed his style of motion as a 'spur-of-the-moment' thing and never bothered to focus on minimising his energy output-, but his intense focus on the task at hand was definitely something that even she couldn't help but admire, particularly when she considered that he lacked her own personal investment in the current mission; if he was this focused when something he valued wasn't at stake...

She shook that thought off before it could progress further as they hurried up some stairs- narrowly avoiding another group of marines-, before they walked into a smaller room that was apparently used as a storage area.

"Wait," the Phantom suddenly said, reaching out to halt Phoebus before she could walk more than a few paces into the room.

"What?" she said, tuning to look at the other man with a pointed stare. "Why?"

"Because, if Thalen went to the central power room earlier- and has a good idea where you are-, this is one of the better areas for him to cross if he wants to find you," the Phantom clarified, his voice a low whisper as he spoke. "It's a quiet enough location with minimal sensors or living quarters in the immediate vicinity; Sumner may not know as much about Atlantis as I do, but I'm reasonably sure he knows this."

"And if you're wrong...?" Phoebus began, only to trail off as she heard footsteps from the other end of the room. Quickly moving into position alongside a nearby pile of boxes- even if it wasn't Thalen she should still be ready to strike-, Phoebus trained her gun in the direction of the approaching steps, barely even registering the Phantom's location as he moved off deeper into the room.

All that mattered now was finishing the mission...

As the muscular form of Ronon Dex came out from around the corner, Phoebus began to pull the trigger, only to be beaten to the punch when the red light of the Phantom's gun hit Ronon first, sending him falling to the ground before her bullets could make contact. Before Phoebus could take in what had just happened, Thalen stepped out from around the corner as well, his gun aimed in her direction, only for him to be taken down with another shot from the Phantom's gun.

For a moment, Phoebus smiled at how things had just gone- she'd won her peoples' long war and proven that the Phantom was nothing at heart but another animal-, but then she noticed the slight but significant slow rising and falling of Thalen's chest and realised what had happened.

"You didn't kill him?" she said, turning to look at the Phantom, only for her voice to trail off as she saw the masked man aiming his weapon at her.

"No," he said, staring at her with a cold intensity that would have almost made her afraid if she hadn't experienced the last few years of her life facing similar glares. "Unlike you, I don't allow a few issues with people's decisions to provoke me into killing an otherwise good man."

"What?" Phoebus said, looking at the Phantom incredulously. "You think he's 'good'? He'd see you locked up-!"

"We disagree with how I do things; it's an issue, but it's not exactly something worth killing him for," the Phantom interjected, still staring at her. "Anyway, that's not the relevant issue right now; what is relevant is that you're the last one standing in that war of yours, so congratulations for winning and you can get out of Doctor Weir's body now..."

"Winning?" Phoebus spat, staring incredulously at the Phantom as she continued to keep her gun trained on him; bullets might not do much if he possessed that 'personal shield' device that Doctor Weir's memories had informed her about, but the fact that he was reluctant to shoot at her body might be enough for her to gain the advantage if she could make him drop his guard for the necessary moments. "As long as Thalen still lives, this is not over; I will not allow anything of him to survive-!"

"What difference does it make, Phoebus?" the Phantom countered, glaring angrily at her. "Your war ended centuries ago; I doubt anyone in this galaxy knows who won it! There is no point to this-!"

"I will not go knowing that anything from Thalen still lives!" Phoebus practically spat at the Phantom. "As long as even the memory of him remains, he may outlive me; I will not let this war end in a stalemate!"

"And what was so great about this war, anyway?" the Phantom retorted, his grip on his weapon tightening. "You spent your life fighting, and for what? Victory for a race that died off years ago?"

"All I have to look forward to is excruciating pain before I cease to exist in this body; if I can achieve victory for my people-" Phoebus continued.

"It changes nothing!" the Phantom yelled.

"And what do you consider the purpose of your fight against the Wraith?" Phoebus retorted. "You seek their destruction as surely as I seek Thalen's-!"

"I seek their deaths to save innocent people from being fed on by them; that is not the same thing as this!" the Phantom yelled in response. "Who won or lost this war doesn't matter-!"

"It matters to me!" Phoebus yelled, pulling the trigger and firing the weapon as she ran towards the Phantom, the bullets impacting harmlessly against his shield as he raised his weapon to counter her attack, only for her to have him pinned to the ground before he could fire, smirking at him as she felt his body betraying itself at the close proximity to her borrowed flesh.

"Well well well..." she said, smirking slightly as she looked at the man below her. "I take it I'm doing something right, am I?"

"You're not her-" the Phantom spat, only to cut himself off as he realised what he was saying.

"I'm not Doctor Elizabeth Weir?" Phoebus finished for him, still smiling at the man below her; it had been a while since she'd tried seduction to get what she wanted, but her victim's obvious attraction to her host was definitely helping to compensate for that particular shortcoming. "Maybe not, but think of it this way; I'm your only chance to get what you've wanted since the moment you saw her."

"I don't-" the Phantom protested, even as Phoebus placed her hands on either side of his face, giving her lips a brief, seductive lick with her tongue.

"Oh, you know you do... John," Phoebus said, smirking at him as she felt the force field fade away- evidently the Phantom's subconscious desire for her host was overpowering his attempt at nobility- as she placed her right hand on his unmasked left cheek. "You know you've wanted this for ages; do you think that Doctor Weir hasn't noticed? You think that she hasn't been thinking about this?"

"She hasn't-!" the Phantom growled, staring back at her, anger clear in his eyes even with the slight hint of guilt in them that suggested to her that the man below her was enjoying his current position more than he wanted to.

"Oh, she is..." Phoebus said, smirking as she carefully slid a couple of fingers underneath the mask...

"Oh my God!" she yelled, sitting back in shock as her fingers came in contact with something hard and smooth that felt almost exactly like the few occasions during a battlefield medical crisis when she'd witnessed someone with a fractured arm where the bone stuck out of the skin; it felt like there was bone underneath that mask-

"You lose," the Phantom said suddenly.

Phoebus only realised that she'd relaxed her grip on her temporary prisoner long enough for him to get a new grip on weapon in the split-second between him shooting her with his gun and her falling to the ground, knowing that she could never again regain consciousness in this body or this life.


Damn... John thought to himself, shivering from a chill that had nothing to do with the temperature as he looked at Elizabeth's unconscious form, Sumner and Ronon lying a short distance away from her, one hand automatically adjusting his loosened mask so that it rested comfortably on his face once again. That was too close...

He knew that he should have thrown her off him as soon as she'd tried to pin him down, but even with the knowledge that it hadn't been her in control at the time, the feel of Elizabeth's body so close to his own... her smell... her hair... her hands...

He'd almost let his desire for what couldn't be take control of him, and come far too close to give Phoebus the chance to use him; he couldn't allow that to happen again.

Dammit, he'd already accepted that Elizabeth Weir didn't- couldn't- feel that way about him; how could he allow someone to use her body and try and exploit his desires like that? If she'd managed to pull it off, he'd have not only lost whatever trust he'd gained in Elizabeth's eyes over the past couple of years, but he would have lost every last bit of the self-respect he'd managed to hold on from the days before he'd become the Phantom.

Doing... that... with Elizabeth's body when she wasn't in control at the time...

That would have been crossing way too many lines for him.

Elizabeth and Atlantis might be safe now, but after what he'd almost done- and after what she'd felt; the feel of her fingers (Even if she hadn't been the one in control of them at the time) on what remained of his cheek had been a terrifying thrill, but it would attract too many questions-, he was definitely staying out of her way until he had to; maybe if he avoided direct contact with her for a while, she'd lose interest in asking about what Phoebus had felt under his mask...

It was a long shot, but he was going to give it a shot; anything was better than putting himself in a position where he would have to give Elizabeth such a clear look at what he'd become...
End Notes:
Well, there you have it; the first teaser of what's actually under John's mask, and confirmation that it's not just there to make him look good yet intimidating.

Coming up next chapter, the introduction of a villain from the series who will have a VERY significant personal impact on John himself...
This story archived at http://www.sheppardweir.com/fanfics/viewstory.php?sid=1597