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Story Notes: 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 third part in my 'Phantom of Atlantis' trilogy (Reading the first two stories in the series is highly recommended to ensure that you understand what's going on); for those returning fans, this take place about a month after the conclusion of 'Mystery of the Phantom', and as currently planned will cover the remaining key storylines in 'Atlantis', with some obvious and significant differences…
Author's Chapter Notes: AN: Thanks are due to Elgin, who helped me refine a few details regarding the consequences of John's new role

Sitting in his room as he adjusted his new suit- his complicated status meant that 'dress blues' weren't an official requirement, but General O'Neill had convinced him of the need to have something smart to wear in case a formal occasion or two came up- John was amazed that his life had gone through so many changes so quickly over the last few months.

On some level, it seemed like only yesterday that he'd still been acting as the Phantom the same way he'd done for years, hiding in the shadows and secret passages of Atlantis as he kept a careful eye on the city's inhabitants, and now he was in charge of the city's military contingent and essentially the second-in-command of the whole place. He'd been back in Atlantis for over a month now since his training on Earth had concluded, but it felt strange to have an actual room to himself rather than whatever safe location he could find in some of the city's maintenance tunnels.

With his presence in the city now public, Elizabeth had convinced him to deactivate some of the security protocols he'd established around certain parts of the city, arguing that they weren't needed now that he was there to explain why he'd sealed them away in the first place. Most of the rooms' contents were a surprise even to him- he'd recognised that the objects within the locked areas were dangerous when he'd found them, but he hadn't thought about most of them for so long he'd almost forgotten about them- but with the expedition's scientists to confirm his own assessment, they'd managed to dig up a few interesting pieces of technology.

The Ancients' temporary residence in the city had also opened up far more doors than even he had ever been able to access; he might have had access to several ZPMs, but he'd always restricted himself to one at a time when he was alone in the city, but the Ancients had been able to access far more buildings during their brief return. He'd had to stop McKay accidentally activating a DNA resequencing device they'd found in one area before the scientist did something serious to himself, and it had been a bit difficult to convince some of the staff not to touch that bizarre social experiment thing- it apparently resembled some kind of computer game back on Earth; he'd had to make a quick change and then take a team to the planet it was looking at to prove his claims- but once the first couple of teething troubles were out of the way even the most doubtful had accepted that he knew what he was talking about.

He'd even ensured that those new areas would stay open by providing the city with additional ZPMs from his own storage unit, as well as sending a few more back to Earth for use in the Daedalus and other future ships, even if he'd taken care not to reveal just how many he had in his 'storehouse'; he wanted to keep some in reserve in case they were needed. He had also managed to neatly deflect attempts to convince him to reveal that information to the IOA and the rest of the Atlantis by claiming that he preferred to keep it quiet for reasons of security (The fact that the Wraith had already hacked the Atlantis database at least once made that far easier; he might have stopped the hack then, but it set a precedent that nobody wanted to risk repeating).

Of course, it wasn't as though there hadn't been some problems with his transition from his old role as mysterious vigilante to his new official status, but it was nothing for him to worry about. Most of the military personnel who disapproved of his presence had made their tastes clear by requesting to be transferred from Atlantis after the announcement was made, and while some of the science or medical team sometimes looked at him as though they were waiting for him to make some kind of mistake or expose his 'true intentions' (The memory of what General O'Neill had told him some people believed he'd been doing was hard to forget), in general everyone seemed willing to accept that he was only here to help, and the only thing that had changed since the old days was that he was officially allowed to do so. The new additions to his staff had also been generally welcoming. Captain Satterfield in particular had appreciated his insight into how the Wraith thought beyond a purely military perspective, and John admitted that he was coming to like her as well; her welcoming attitude made him feel like she was his younger sister in an odd way, appreciating his insight into life while still capable of handling herself.

Even without the larger problems, his appointment to the senior staff was currently somewhat problematic. Elizabeth had accepted him without hesitation, but Teyla and Ronon still looked at him as though they were waiting for the moment he'd revert to type and attack them; even if they accepted that he wasn't a traditional Wraithspawn, centuries of prejudice wasn't something that would be easily forgotten. McKay and Beckett were fairly neutral about his presence, accepting his new role even if they weren't completely comfortable with it, and Lorne and Satterfield were generally casual about it (He'd requested that they attend the meetings to provide him with the necessary military perspective and strategic intelligence he was still working on presenting, and so far they'd lived up to all his expectations).

Still, complicated personal dynamics aside, the Expedition's return to Pegasus had gone rather well. They maintained their tentative alliance with the Genii, the Athosians were willing to return to their previous roles working as local guides for recon teams, and their other major alliances had been easily re-established, particularly when their allies learned that the expedition was now officially working with the Phantom.

As far as the wider galaxy was concerned, nobody outside the expedition staff aside from a few trusted Athosians were aware that the Phantom and Atlantis's new military commander were the same person, but the knowledge that he was working with them officially was a definite boost to all relevant morale.

The Taranians had been particularly grateful to learn that contact between the Phantom and the city was now official, and their role in the daily operation of the Orion continued to be appreciated; Norena was essentially the ship's chief science officer, and Colonel Dixon had expressed nothing but satisfaction with her performance so far. With the recovery of the Tria's database, the Orion crew and the expedition had managed to uncover some interesting details that it would have taken far longer to find if they were searching through Atlantis's own records.

The ships' databases hadn't provided anything particularly interesting yet- as an example, there were some brief descriptions of how to recharge the ZPMs, but there was nothing to indicate how to create them in the first place or how to assemble the necessary recharging equipment- but they had been able to direct them to a few interesting gate addresses that they wouldn't have arrived at on their own for some time.

The current destination was a planet on the outskirts of the Pegasus Galaxy, which had helped to protect it from attracting the attention of the Wraith. Unlike the expedition's less pleasant contact with Halcyon the previous year- one planet where John freely admitted that the expedition had been far better qualified to help than he had been; his status as a legend made it difficult for the Phantom to encourage social change- this world, known to its inhabitants as Rhean, had managed to develop a far more positive culture, based less around military conquest and more about improving their own world. The Ancient database from the Tria had identified the world as the sight of a former Ancient research outpost that had fallen victim to some kind of accident during the Wraith war that had infected most of the population with an unspecified disease, but had noted that the radiation that caused the disease would have died down by now.

When John and his new team had visited the relevant gate address, they'd learned that the planet had acquired an indigenous population that had set up a colony in most of the abandoned Ancient buildings at some point after the radiation had died down, using some of the information in the planet's database to improve their environment and ensure their safety from the Wraith.

While Rhean was far enough away from the heart of the galaxy to avoid attracting the majority of the Wraith forces in Pegasus, the Rheans were still aware of the dangers out in the wider universe, and were using the outpost's available resources to try and improve their daily lives before they tried to look further afield. The outpost had little to offer compared to Atlantis's resources, but they'd already managed to uncover some interesting terraforming systems, and had even worked out how to activate the outpost's defensive shield- a weaker version of the Atlantis shield but still fairly durable- along with a cloaking system.

Of course, the Rheans' limited population- virtually the planet's entire population lived around the outpost itself- meant that their study of the outpost had been highly publicised, with the result that Atlantis's contact with them had swiftly become a major cause for celebration on the planet as well as for the expedition. As the official announcement of the new alliance with the Rheans was the first big event that Atlantis had experienced since John Sheppard had become its military commander, it meant that his presence was required at the treaty signings and the party that was being held in their honour in the aftermath (Elizabeth was going to do most of the work, but it was still up to John to be there to supervise everything).

It might not be a completely leisurely outing, but as he finished adjusting his suit and left his room to join his team at the Stargate, John had to admit that he was kind of looking forward to this; he hadn't been to a party since before he arrived in Pegasus…

And the fact that he was going to get a chance to dance with Elizabeth was not the main reason for his enjoyment; the dance was just a… welcome bonus.

He'd accepted that Elizabeth would only ever see him as a friend and colleague; why couldn't he get over it…?

Chapter End Notes: AN 2: Slow start, I know, but be patient; things will become more interesting after the next chapter…

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