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: The last chapter of this story, as John assumes his new position in Atlantis; not my longest, but I felt that I stopped at an appropriate point regardless.

Mystery of the Phantom

As he walked through the wormhole and found himself back in Atlantis, John couldn't help but feel relieved at the sight of the city that he'd lived in for so many years.

Earth might have been where he was born and grew up, but Atlantis was where he'd experienced so much of his personal development; maybe it was disloyal to his home planet or something warped like that, but he didn't care. Even if he'd taken the first few steps towards reconciling with his family during his recent visit, there was still a long way to go before Earth felt anything close to a home the same way that Atlantis was to him.

As part of his new role as Atlantis's military commander, they'd recruited some outsiders to design some facial attachments that he could use as a disguise if he wanted to go around without looking like the Phantom. Plastic surgery might be impractical due to the scale of the facial damage, but some of the SGC's intelligence contacts had been able to provide John with a disguise kit that he could use to give himself the appearance of a normal face while on missions; he'd tested them back on Earth, and everything could go on and come off fairly easily, even if he felt more comfortable in his familiar mask. It wasn't a long-term solution to his facial damage as the fake skin would eventually wear away, and it would obviously be discovered if he was ever struck in the face, but since John wasn't planning on engaging Wraith in hand-to-hand combat as John Sheppard he should be fine (He'd fight them as the Phantom, but that was another matter).

As far as his old identity was concerned, John had retained his traditional garb as the Phantom, but would only actually wear it if he was going on a mission with the primary goal of engaging the Wraith in combat. When he was just going on a standard mission with his team- he'd chosen to basically replace Sumner's position in Atlantis Recon Team One; McKay, Teyla and Ronon had made a good unit so far and he appreciated their contrasting strengths- he'd wear a standard Atlantis uniform and the facial make-up, but when going around on Atlantis, he'd managed to reach a compromise where he went around in his standard mask and a simple black uniform without wearing his cloak and weapons. He still stood out a bit, but he wasn't as intimidating as he had been in his cloak and with his usual weapons; it was enough to make everyone feel slightly more at ease than they had been while allowing him to feel comfortable.

Thoughts of the training were forgotten as he saw Elizabeth standing in front of the Stargate, hands in front of her in a professional manner that was only slightly 'marred' by the warm smile on her face as she looked at him.

"Doctor Weir," he said, nodding at her in as formal a manner as he could manage (She was just glad to have an exceptional asset back in the city; there was nothing more to it than that).

"John Sheppard," Elizabeth said, smiling warmly back at him as she shook his hand. "It's good to see you again."

"Agreed," another familiar face said, stepping forward to shake John's hand as well. "Major Evan Lorne; I understand I have you to thank for my continued presence here?"

"Your record… made me pick you as the best candidate," John decided at last, hoping that he'd phrased that statement the right way; he didn't want to sound like he'd been keeping too obvious an eye on everyone.

"So," Elizabeth said, looking encouragingly at him, "now that you're here, maybe you should… announce yourself to the city?"

"Uh… sure thing," John said, nodding awkwardly at Elizabeth as he realised what she meant; public speaking was one area he'd never really covered as the Phantom, but if he was going to lead these people, he had to make sure they knew where he stood. Walking up the stairs and moving to the balcony overlooking the gate room from the control room, taking a moment to collect himself and make sure that his new make-up was reasonably straight, John stepped out onto the balcony and looked down at his new troops.

"Hello," he said, looking at the assembled military forces gathered before him, trying to appear friendly without appearing too casual. "I know most of you have only heard of me by reputation... and some of you haven't got a particularly high opinion of me from that… but whatever you might think of my past approach, know this right now; my priority is, always has been, and always will be, the safety of Atlantis and the continued existence of the Atlantis expedition. I might be new to having an official position while doing that, but I want to assure you all that I will do my utmost to be worthy of the responsibilities that I now possess, and live up to the faith that you have all entrusted me with. Atlantis is more than just the latest project of the Stargate program; it, and the Pegasus Galaxy, are now under our protection, and we will defend it for as long as we can."

For a moment, the expedition members simply stared at him in silence, but then a couple of them started to applaud, and that started the ball rolling for the rest of them to do the same, culminating in the entire room clapping as John stared out at them, a steadily-growing smile on his face.

He'd been thanked as the Phantom for so many things over the years- even if he'd never dared to stick around for too long in case someone tried to take his mask off- that it was surprisingly nice to be applauded for something he'd done as John.

The future might be a mystery, but he could at least be reasonably sure of a few things; he had the trust of some of the most respected members of the Stargate program, he'd received an extremely thorough crash-course in training from a group of living legends, and he was going to do everything in his power to protect Atlantis and the people who had adopted it as their home… particularly the woman who-

No.

He couldn't think of that.

He couldn't be what Elizabeth was looking for in a partner; she was a diplomat who always sought the peaceful solution and could see both sides of an argument, whereas his default reaction to every threat he'd encountered over the years was to hit it with whatever he had until it either let him go or couldn't hit back any more…

It didn't matter.

Even if Elizabeth could never see him… that way… she had accepted him as an official part of her life in Atlantis; he wasn't going to waste time wishing for what could never be after everything else that she had done for him.

He could never be her lover, but he was her friend and colleague; the second part alone was more than he could have realistically expected to achieve even a few months ago.

What mattered was that Elizabeth was free to make her own choices…

AN 2: Before anyone starts hating me for dragging out John and Elizabeth's relationship, think about it logically; while John has loved Elizabeth as an idea and a person since he came to Atlantis, Elizabeth has only even known he even existed for less than three years, has known very little about his background for all but the last few weeks, and hasn't really had the chance to talk with him about anything outside of the latest crisis whenever he's dropped in for a visit. They might start something, but they'd start it for all the wrong reasons if they got together now.

They will make progress towards a relationship before I'm too far into the third story in this series, I assure you; it just isn't the time to include that yet.

AN 3: If anyone wants to know, the third story of this series has already begun; check my profile for 'Clash of the Phantoms'…