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Author's Chapter Notes: AN: For the record, I decided not to look at the events of 'Reunion', considering that the key details wouldn't be altered whether Sam or Elizabeth was in charge of Atlantis- apart from Elizabeth being maybe slightly more explicitly upset about having to reject Ronon's initial request for his old friends to come to the city, as she knew him better than Sam would have at that time- but I also felt that 'Doppelganger' had more obvious plot potential considering the psychological issues it would force John to confront

Looking out of her office at the gate room outside, Elizabeth was amazed at how smoothly things had gone after their latest close call. After relocating Atlantis, while the SGC were content for them to maintain contact with their allies in the Genii, the Athosians and the Taranians, among others, it had been widely agreed among the IOA that nobody could know of Atlantis's true location to ensure that the Asurans didn't discover it themselves. As a result, they were prohibited from making any direct visits to their old allies until the threat posed by the Asurans was over for good, resulting in a new policy where they would gate to a random uninhabited world before going on to make contact with their allies. Elizabeth wasn't entirely comfortable with that plan, and steps had already been taken to tell the Taranian leaders where they were considering the Taranian crew members on the Orion, but she had to agree with the idea in principle even if she didn't like the idea in practise.

Besides, she smiled to herself, reaching into her pocket to stroke the shield device John had given her so long ago, considering all the rules I'm bending right now, making sure the IOA know I'll play by their rules the rest of the time can't hurt.

She and John had each come to the unspoken agreement that they were didn't want to treat this relationship as though it was something to be ashamed of, but at the same time they hadn't gone out of their way to make it public knowledge to the rest of the city. Some people at the SGC and Homeworld Command might object to the secrecy of it if they knew, and some of the expedition staff might feel obliged to report her if they knew what was going on, but considering that she was essentially the governor of Earth's first offworld colony, so long as she and John didn't do anything that would compromise Atlantis's safety, she felt that she had enough leeway to defend the relationship when the time came. So far they hadn't gone any further than kisses and a few discreet dinner dates in their rooms, but Elizabeth and John were both in unspoken agreement that they'd take it further when the time came, and for the moment, they should just take things slow before they told anyone on Earth about their new relationship.

The recent situation where Ronon's old friends from Satedea had turned out to be Wraith followers had been an emotionally difficult experience for him, but in a dark way, Elizabeth was glad that things had worked out the way they had. As sad as she was about what had happened to Ronon, the knowledge that he was staying on John's team had been fairly reassuring, particularly for John's sake.

John was doing well as Atlantis's military leader, but the more time she spent with him, the more Elizabeth realised just how emotionally fragile he really was. He had become used to acting on his own for so long because he'd come to believe that anyone who saw his real face would treat him as a monster, and he couldn't ask anyone for help because he would have risked his reputation as a solo hero. Teyla and Ronon might still sometimes look at him as though he was about to snap, but in general they seemed to be willing to accept his presence, and McKay had never been that bothered about the mask or John's real face so long as he got the job done. Elizabeth was doing her best to lend him that kind of emotional support, but she'd been around enough soldiers even before taking charge of Atlantis to know that sometimes only other soldiers could understand everything they'd been through.

Still, after the emotional tension of their relocation to a new planet and the confrontation with Ronon's old friends, Elizabeth was privately grateful that John's last few missions had been fairly simply surveys. She appreciated that she couldn't stop him risking his life as the Phantom, and she had faith that he could take care of himself and others, but she could do her best to make it easier for him unless she was sure it was important that he put himself at risk.

Their latest planetary survey mission had been a fairly simple outing, McKay's curiosity about a possible energy signature just leading them to a series of strange crystal growths, even if the scientist seemed to believe that they could be harnessed as some kind of power source. John had taken a jolt from the crystal when he'd touched it, but he seemed to be fine despite the initial shock, even if he'd admitted to confusion about why he'd even touched the thing in the first place. She was still debating whether the crystals were worth sending a team back for a more detailed assessment, but she'd give McKay the chance to carry out his own assessment of the sample he'd brought back before she made any decisions on that issue herself.

"Hey," John smiled at her as he walked into her office, once again wearing his mask and most of his usual 'Phantom' outfit, even if he'd apparently left the cloak and sword in his quarters. "You OK?"

"Shouldn't I be asking you that question?" Elizabeth asked with a smile. "You were the one who got zapped on the last mission, remember?"

"But Beckett hasn't detected any sign of a problem, Teyla already double-checked that I'm good, and I ended up cheating McKay out of winning some pointless bet with Zelenka," John grinned nonchalantly. "You know, I really think I'm starting to enjoy the quiet ones; nice to get a break from risking my life all the time."

"Quiet?" Elizabeth said, smiling slightly at him even as she partially regretted what she was about to say. "Does that mean you'll have the time to deal with that report backlog of yours?"

"…Good point," John noted, nodding grimly as he looked at the woman he loved. "I suppose I should get that over with before the pile gets any bigger…"

For a moment, Elizabeth was tempted to give him a reassuring kiss, but forced the thought down; they might be sure that several other people knew about their relationship, but kissing in her office was still pushing the lines of privacy and discretion a bit too close for comfort.

"Teyla had a nightmare about Jo- the Phantom helping the Wraith kill her father?" Elizabeth asked, looking inquiringly at Doctor Heightmeyer as they sat in Elizabeth's office the following day.

"Trust me, under normal circumstances, I'd be keeping this between us, but…" the psychiatrist shrugged. "We all know that things with John aren't exactly normal."

"Because of his status as the Phantom?"

"And the way his face disrupted that 'ideal' for Teyla and Ronon, even if Ronon wouldn't admit he ever had anything like that," Heightmeyer nodded. "Consciously they might have come to accept that John isn't going to snap and rip them apart just because he feels like it, but it's possible that there's still… well, some residual issues that have been stirred up by recent events and a lifetime of belief."

"You think this was stirred up by the relocation? They both went through a far more significant upheaval when they joined us in the first place-"

"Which doesn't mean there couldn't be something there. Last time they legitimately didn't know what they were getting into; this time around, an argument could be made that they're more thrown by having what they've become familiar with be so changed."

"Possible, I suppose," Elizabeth nodded, even as she looked uncertainly at the psychiatrist. "So… what do we do about this?"

"I'm not sure if there's anything to do," Heightmeyer shrugged. "Teyla's admitted that she's actually having trouble even sleeping because of this dream, but she's also confirmed that she knows it isn't actually the Phantom in the dream, so there's no way to be sure what we're dealing with. Doctor Beckett's taken a look at Teyla and confirmed that the only problem is a lack of sleep, but from what he told me, that's just the symptom rather than the cause; aside from prescribing her some sleep medication, there's really nothing else he can do."

"Well… I suppose all I can do is hope it gets better soon," Elizabeth said, looking apologetically at her expedition's psychiatrist. "That's… thanks for bringing this to my attention."

"You're welcome," Heightmeyer nodded, smiling slightly at her. "For what it's worth, I believe that John's adapting well to his new role; he just… needs some time to get used to answering to other people."

"He's getting there, certainly," Elizabeth nodded, thankful that she wasn't the only person who could see that John was doing his best in an unusual situation.

She just wanted him to feel like he had somewhere to belong once again after everything he'd done for the city. He'd already spent over two years hiding here because the unconventional nature of his arrival meant that he was worried the more inflexible members of the expedition would have treated him as undeserving simply because he wasn't officially qualified. Teyla's nightmare was a concern, but John could hardly be held responsible for what someone else's subconscious thought of him, and he was doing everything he could to overcome those fears.

There has to be some way I can make this easier for him; it's just a question of what

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