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: Another jump forward, this one exploring Rod's time on Atlantis in 'McKay and Mrs Millar'; all details of our McKay's reunion with his sister and her trip to Atlantis so far are pretty much the same as they were, minus Sheppard slightly flirting with her for obvious reasons

Mystery of the Phantom

Among all of the unusual experiences she'd had since coming to Atlantis, witnessing Doctor Rodney McKay interacting with a man who both was and wasn't him had to be one of the weirdest.

It was actually rather interesting to see how McKay could have turned out under other circumstances, of course- Rod was clearly still as intelligent as McKay, but he just had a different manner of interacting with the rest of the expedition-, but the rest of Elizabeth was wondering how they'd cope with Rod in the long term. Putting aside her vague recollections of some kind of side-effect caused if two versions of the same person were in the same universe as each other for too long- it had been a long time since she'd read that report and she'd never expected this kind of situation anyway-, she wasn't sure how McKay would feel about giving orders to himself, even if Rod seemed like he'd be perfectly comfortable not being the superior in the situation.

Actually, she had to admit that Rod appeared to be far more comfortable working with them then she would have expected. He'd been rather surprised to see Sumner when he'd arrived- apparently Sumner had been killed by the Wraith during their first encounter with them in Rod's timeline-, but Sumner had dismissed it as an irrelevant item of news and was focusing more on questioning Rod about his past in case his history included something that they hadn't encountered yet.

"So… you're on the Athosian High Council in your world?" Sumner said, looking at him curiously as he, Rod and Elizabeth sat in her office discussing his world. "How did that happen?"

"Helped them reclaim their homeworld after the initial Wraith attack a year or two back; things just… fell into place from there," Rod said with a smile, before something seemed to occur to him, the other scientist looking curiously at the gateroom outside the window for a moment before he looked over at Elizabeth and Sumner. "That reminds me; where's Colonel Sheppard?"

"Colonel who?" Sumner asked.

"Colonel John Sheppard," Rod clarified, looking at Sumner in surprise. "You know, genius military officer who makes this me look humble, possesses an Ancient gene so powerful that he makes everyone else look like they're just trying to play the piano while he's completing Scherbert's last symphony?"

"I… don't think we have a Colonel Sheppard," Elizabeth said, looking at Rod in confusion.

"Uh… Major Sheppard ringing any bells?" Rod asked, looking over at Sumner. "I mean, if you're still alive, maybe he never got promoted to that level…"

"We have no John Sheppard affiliated with the expedition to the best of my knowledge, regardless of his rank or the level of his ability to control Ancient technology," Sumner said, looking firmly at Rod. "Is there a particular reason you're bringing him up?"

"Just… surprised he's not here, that's all; guy might have had an ego that would make your me look humble, but he earned it," Rod said, shrugging awkwardly at Sumner's stare in his direction. "Member of my Atlantis's chapter of MENSA, leader of Atlantis's military, natural understanding of most Ancient technology…"

As Rod continued to speak, Elizabeth's mind started to drift as she contemplated what she'd just been told.

Could it be?

John wasn't exactly an uncommon name, and it could be that he'd just chosen that name because he'd heard enough of the expedition talking about Earth to know that it was a common one…

But, on the other hand, if Rod's reality had most of the same personnel with the addition of a lieutenant colonel with that name and skill with Ancient technology, was it possible that the reason for his absence from this reality and the Phantom's presence on the city were the same?

She'd probably only be able to look into that when she was back on Earth for her next debriefing, but it was something to consider…


Shit, John thought to himself from his position in the maintenance tunnel off the commissary, noting the contemplative expression on Elizabeth's face after Rod's latest question.

It might not be particularly meaningful to anyone else- they'd assume that she was just curious about this person who would have been part of the expedition in another lifetime-, but he knew that Elizabeth was already putting together the pieces of a puzzle that nobody else even knew about.

Of all the ways he'd imagined Elizabeth somehow learning his surname, the idea that she'd hear it from someone from an alternate reality where he was an official member of her staff had never been one of them…

OK, in a weird way, it was comforting to hear that he may have come to Atlantis even if he'd had a normal life, but considering how he'd apparently turned out in that reality, he felt like his arrival under these circumstances had been for the best; his other self sounded like a dick at best.

If that was what he would have become if he hadn't come to Atlantis, he was glad that he'd come here; everything he'd endured was worth it if he was someone people could respect, rather than someone so goddamn self-assured he made McKay look humble.

In the end, however, the fact remained that Elizabeth wasn't stupid; with the information that she'd heard today, coupled with everything else she'd learned about him over the past year, it wouldn't take her too long to work out who he really was.

He just… he wasn't ready

Why couldn't the universe cut him a break?


AN 2: Short, but we're approaching the big moment; next chapter goes to "The Return"…