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: As promised, we've gone straight to the events of "The Return"- nothing really changed much for the rest of Rod's time in Atlantis or during the events of "Phantoms", so I didn't bother rewriting them-, shortly after the expedition has been 'asked' to leave the city…
Mystery of the Phantom
Standing on her balcony for what may be the last time, Elizabeth almost couldn't believe it.
They were being kicked out?
She'd spent three years working with the members of this expedition, and now they were being ordered to pack up and go their separate ways just because someone else objected to their presence in Atlantis?
All right, so the Ancients were the original builders of Atlantis who'd just been recovered from centuries trapped in a weird form of diluted time perception that Elizabeth didn't fully understand, but after all the time they'd spent in the city, to be told that they should just get out even when the Ancients were only there because of their efforts…
She'd done everything she could, and it still wasn't good enough for them; the Ancients were acting as though they were still nothing more than ignorant savages who'd moved in to an ancient city and messed up the system. They might have made some mistakes, but they were still leaning everything they could about Atlantis, and some of those mistakes had been the result of the Ancients themselves not leaving clear instructions; it wasn't their fault that the Ancients had been too arrogant to make notes about how they'd failed…
Admittedly, they were still in control of the Orion, but that was mainly because it was back in the Milky Way galaxy at the moment undergoing some additional repairs- the SGC had expressed some hope that they'd be able to use the Antarctica research site to find ways to improve Orion's own drone reserves- and everyone concerned had agreed to keep quiet about it. Considering that ships were easier to manufacture than Atlantis, Elizabeth doubted that the Ancients would be as concerned about reclaiming Orion as well, particularly in its current damaged condition, but it was easier to retain a hold of it when it wasn't on Atlantis. All records of Orion's presence in Atlantis had been kept primarily on the expedition's own hard drives rather than Atlantis's own computers, and those were all going back to Earth with them, so by the time the Ancients found out about the ship, the SGC could probably claim that they'd recovered it as salvage in the Milky Way and leave it at that.
"I'm sorry," John's voice said from behind her.
"For what?" Elizabeth asked, smiling weakly at John as she turned around to look at him; she might resent the fact that she was losing Atlantis, but she'd never resent John for anything.
"That I can't do anything to keep you here," John said, looking sadly at her. "I can't exactly drive the Ancients out of Atlantis without compromising any possibility of an alliance with them, and I think we're both aware by now that I don't have any real influence over the Ancients themselves…"
"It's all right," Elizabeth said, smiling briefly at him; she still hadn't found the time to actually talk to him about Rod revealing his real name, but the fact that he was willing to even acknowledge that he wasn't an actual Ancient…
"I can't come with you."
"What?" Elizabeth said, looking at the masked man incredulously, her earlier thoughts pushed aside with this sudden admission. "You're staying here? But the Ancients-"
"They're never going to find me- Atlantis has been programmed not to register my lifesigns unless I want it to register that I'm there, and the Ancients are never going to be able to find that program unless I tell them where to look-, and I don't… well, I think we all know I don't belong on Earth," John said, shrugging slightly awkwardly as he looked at Elizabeth. "I'd like to think that I've been a lot of help to you over the last year or so, but we all know that Sumner's never going to accept me as an official part of the team. Even if his superiors did, there's only a few commanders back at Stargate Command I'd respect enough to take orders from, and I somehow doubt that they'll assign someone like me to a position where I'd be reporting to anyone on that list..."
"Easier for who?" Elizabeth asked, glaring at him.
"Wh- Elizabeth, we both know that the SGC isn't going to just welcome me to Earth-" John began.
"You're not even going to try," Elizabeth said, staring coldly at John, trying not to analyse just why she felt so strongly about his decision. "You've gone through so much for us, and you're just going to leave-"
"We both know that I'm still considered a rogue element back on Earth, Elizabeth," John said, his expression grim as he looked at her. "I know that there are some people who'd try to do the right thing for me as an individual, but with my knowledge of Ancient tech they'd be overwhelmed by the people who'd consider me an asset and nothing more; it's easier for everyone if I just stay here-"
"John Sheppard, don't you dare!" Elizabeth yelled, the words bursting from her before she could stop herself as he turned towards the edge of the balcony.
As soon as the words had passed her lips, Elizabeth wished that she could take them back- this wasn't the kind of situation where bringing up his name would be remotely comfortable for anyone-, but when John froze mid-motion, Elizabeth knew that she had no choice but to follow up on the topic she'd just introduced.
"That's your name, isn't it?" she said, looking at him, keeping her voice at a slow tone so that John wouldn't be provoked into leaving before she'd said her piece. "Your name's John Sheppard… and you were born on Earth."
For a moment, silence dominated the balcony, Elizabeth staring at John while John stood on the edge, each one waiting for the other to give in first, until John finally broke the silence with a sigh.
"It doesn't matter," he said at last, looking back at her.
"What are you talking about; of course it matters!" Elizabeth protested; she might not have meant to bring this up, but she wasn't going to ignore it now that it was out there, particularly when John had virtually confirmed her theory by his lack of denial. "You're from Earth, John; we can take you home-!"
"John Sheppard died over twenty years ago, Elizabeth," John said, turning around to look at her grimly. "There's only the Phantom now… and there is nothing that Earth has to offer right now that the Phantom would want."
As he looked back at her for a moment, Elizabeth had the sudden feeling that John was trying to tell her something, but she had no opportunity to analyse that feeling further before John turned and leapt off the balcony, vanishing into the depths of the city before she could think of anything else she could attempt to stop him.
"Great…" she said out loud, staring up at the sky that she would soon never see again.
Her last chance to get some personal answers from her city's mysterious guardian, and he'd gone and vanished on her, leaving her with nothing more than an ambiguous confirmation of his true name.
The only good thing about her going back to Earth now was that she'd have the chance to do some actual research on whoever John Sheppard had been before he became… what he was now; maybe if she could work out how the Phantom had actually ended up in Atlantis in the first place…
AN 2: Next up, we're back on Earth, as Elizabeth learns exactly who she's dealing with…