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Author's Chapter Notes: AN: Alternating between Earth, as Elizabeth carried out her research into her former city's masked protector, and Atlantis, as the aforementioned protector has a 'chat' with its new residents…

Sitting in her apartment, Elizabeth sighed as she finished typing up her latest sentence, once again feeling the pointlessness of everything.

She'd been trying to distract herself from the pointlessness of her life by looking over a few new treaties for the President, but she'd been unable to really concentrate on anything that didn't relate to the SGC or Atlantis- which she was still being ordered to remain away from-, leaving her stuck for any immediate activity…

It was strange; Atlantis took up so much of her time that she wasn't sure she'd done anything for leisurely purposes for years- discounting her meetings with John, which were mostly for work purposes more often than not-, but now that she had that time to relax, all she wanted was to get back to work.

She might have been a diplomat rather than a governor, but she'd grown so used to working in Atlantis that it felt wrong to be back on Earth; no matter what job she was offered, nothing could match the satisfaction she'd felt when she was in command of Atlantis, and even treaty negotiations seemed so small after negotiating alliances with other worlds against an enemy that would devour them all if given the chance…

She barely even had any kind of life right now outside of her half-hearted attempt at writing a set of memoirs that would have been classified beyond most levels that she could conceive of if she'd tried to get them published. She'd had relatively few friends before going to Atlantis considering the demands of her job, and of those she'd made in the city itself, Teyla and Ronon had remained in Pegasus, Carson and Rodney were busy with their new jobs at the SGC and Area 51 respectively, and Sumner…

Well, she knew that he was working at the SGC, but they'd barely had anything more than a professional relationship back on Atlantis, and he seemed perfectly content to leave it at that now that they no longer worked in the same city; she didn't actually mind one way or the other, but it felt slightly insulting to realise that someone she'd spent over two years working in close proximity to had no real interest in continuing the discussion.

Finally, with nothing else to keep her occupied but repetitive trains of thought, Elizabeth turned her attention to focus on the question that had dominated so much of her spare time in Atlantis; the true identity of the Phantom.

It had been a strange way to find a clue, but Rod's unintentionally-provided information had helped her crack the most obvious problem in that search. John Sheppard still wasn't an uncommon name, but focusing on John Sheppards old enough to match the Phantom's physical capabilities, coupled with any records of those John Sheppards mysteriously disappearing, had allowed her to narrow down the suspect list significantly.

After a few more hours of independent research, she felt that she had finally identified the John Sheppard she was looking for. With other candidates dismissed on the grounds of age, a continued presence on Earth- she wasn't going to consider time travel until she was sure all other options were exhausted-, and other factors allowing her to discount the other possible John Sheppards, her search had finally led her to various newspaper articles about the disappearance of John Sheppard, the fifteen-year-old son of utilities mogul Patrick Sheppard, over two decades ago during a family holiday in Britain.

From what the article revealed, Patrick and John had argued during their first week on vacation in Glastonbury and John had left the hotel in a huff, claiming that he was going for a walk in the area. His mother had reported seeing him enter the woods near their hotel after the fight- she'd thought that it was best to give him time to cool off on his own, and the hotel was fairly easy to find your way back to-, but he had subsequently dropped off the metaphorical map and never been seen again; his father had tried to arrange various searches in that area after John had been missing for a day, with search efforts expanding as time went on, but interest in the case had eventually died down after a few months with no breakthroughs and no sign that anyone would be stepping forward to claim responsibility.

According to some of the information they'd revealed in subsequent interviews, John had been interested in joining the Air Force as a child, which added further weight to the idea that he was the Phantom. An interest in the Air Force would give John the right psychology to become the Phantom- his mother had stated in her interviews that John was always interested in protecting others when speculating why he might have gone missing, which translated into an obvious 'hero complex'-, particularly with the skills he'd demonstrated in using the gateships during those occasions when he'd taken one from Atlantis's various hangers…

The discovery at least explained where John had come from, and the holiday taking place in England suggested some possibilities- considering what the SGC had recently learned about Merlin being an Ancient, it was possible that John had stumbled across some kind of Ancient teleportation device that had sent him to Atlantis-, but that still left her with more than a few questions.

For one thing, how had John learned anything about how to operate Atlantis? He wasn't stupid, but nothing she'd read about John Sheppard's past indicated a strong interest in ancient languages; he should have been incapable of even reading the city's operating instructions, never mind everything else he'd learned from the city's archives over the years.

On top of that, other questions included why he hadn't just decided to return to Earth once he'd discovered its address in the database, why he had decided to start going around in a mask and cloak rather than a less theatrical outfit… why he was so interested in her…

No matter what other theoretical explanations she came up with for what had happened to John, none of them accounted for his continually-expressed interest in her; what was it about her that inspired that kind of interest?

His explanation had sounded good at the time she asked him that question, but it didn't help her understand the obvious depth of his interest in her; even if he was from Earth, what had prompted him to try and talk to her, risking his safety by 'targeting' someone at the top rather than making contact with someone lower in the expedition's command structure and less likely to attract attention…

Even when she was fairly sure she knew who he was, all she found herself with was more and more questions; what was it about the Phantom that made everything so complicated?

She just… she almost didn't want to think about that particular issue; thinking about the Phantom… like that… made things feel more difficult than she was prepared to admit…

Crouched in the maintenance tunnel outside Elizabeth's office- and it was Elizabeth's office; the fact that someone else was using it right now was just a temporary inconvenience that John was certain would be resolved eventually-, John felt like growling in rage as he saw Commander Helia sitting casually behind the desk that should belong to the woman who had given so much to preserve this city.

He'd stood by for a few weeks to give her and her crew the chance to come to their own conclusions and do the right thing, but so far their only concession had been to allow General O'Neill and Richard Woolsey to remain in the city as Tau'ri 'observers', and what he was seeing gave no impression that they were interested in doing anything for the rest of Pegasus; they weren't even expressing the slightest interest in helping anyone cope with the Wraith's presence despite the fact that the Wraith were only even there because the Ancients had been screwing with things that shouldn't be messed with…

With General O'Neill and Mr Woolsey in another part of the city at the moment, and the rest of the Ancients working on making Atlantis habitable on a larger scale- they seemed to prefer to spread out where the expedition had concentrated their accommodation on the central tower-, along with the current 'night shift' consisting solely of Helia sitting in her office, this was the best time to take action. Exiting the maintenance tunnel, John landed casually on his feet, closing up the tunnel behind him before he coughed to attract Helia's attention.

"What-?" Helia said, looking up from the computer that she had been studying to find herself staring at a man in a long black cloak and silver mask. "Who are you?"

"You may have heard of me," John said, looking solemnly at her; her surprise had been slight, but it was enough for him to confirm that she didn't know how he'd arrived here, which would hopefully increase the impact of his current message. "I am the man known in this galaxy as the Phantom of the Ancestors."

"Excuse me?" Helia said, her eyes widening at the additional venom placed on that final word. "You have been claiming-"

"I was given that name by other sources; I didn't set out to identify myself as something I wasn't at first, and I now have no interest in affiliating myself with your people directly after what you have done," John said, making his contempt clear as he looked at her; the fact that he wasn't officially 'designated' as an operative from Earth at least gave him the ability to tell this bitch what he really thought of her. "Parts of this galaxy have been waiting for your return for centuries to save them from the nightmare you released, and what's your response when you come back? Kick out the heirs to the kingdom and set up shop in a secure location that you feel comfortable in."

"This is our city-!" Helia began, standing up from behind the desk to glare at John.

"Because you built it; that only takes you so far, as far as I'm concerned," John said, his expression cold as he stared back at the Ancient captain. "You created the most incredible city this galaxy- maybe even several galaxies- have ever seen, and when you come back to find that someone else is using it, your automatic response is to kick them out?"

"Why should we not reclaim what is ours?" Helia asked.

"There's a difference between reclaiming what's yours and kicking people out because of a stupid sense of entitlement," John retorted.

"You want us to abandon this city to them?" Helia said, her gaze narrowing as she looked at the Phantom.

"I'll settle for you showing them the respect they deserve by letting them work here, but I'd be happy with you leaving as well," John replied in a dismissive manner; he really would have preferred them leaving, but he didn't want to give Helia any reason to be so scared of him (Assuming she'd admit to fear) that she turned violent to try and get rid of him.

"We created this city; what have they done apart from use what we have created?" Helia said, looking at him with that same arrogant edge that . "They have taken what we have conceived-"

"Because it was there; can you honestly say you wouldn't have done the same if some race older than you had created something that you managed to find?" John retorted. "Using what others have created shows sense, not laziness; they respect what came before and are willing to learn from it… and, quite frankly, they use it a lot better than you did."

"What?" Helia said, looking at her opponent in shock.

"You ran and bailed on this galaxy when the threat that you created was too much; you might have been justified in leaving, but when faced with a similar situation, Earth managed to come up with a means of continuing the fight and fending off the current Wraith assault," John said, still staring at her with a cold glare that clearly demonstrated the contempt he felt for her compared to her predecessor.

"What our peers did is of no concern right now; what matters is that we are here," Helia said, staring at the masked man. "I will not be ordered out of our city because you object to what we have done; we need time to adjust to this universe-"

"Which involves dismissing the people who saved your asses as useless?" John interrupted, the glare under his mask still as solid as the mask itself. "They helped you, and all you can do for them is tell them to get lost?"

"And what makes you think that they will simply be-?" Helia began.

"For the record, there's no point going to any of them about this," John interrupted, suddenly guessing where she might be going with her next statement. "I don't work for Earth, I do not take orders from them, and I am not officially affiliated with them; I just like them better than you."

"And I should accept this?" Helia asked, looking indignantly at him. "I should just… allow them back into our city-!"

"You should at least consider it," John said simply, looking coldly at her. "Keep in mind that they were under no obligation to let you kick them out- you don't exactly have the numbers to resist them if things turned ugly- and give thought to bringing them back into this city, because if you don't, I can make things very difficult for you…"

"And I should believe this?" Helia asked. "We created this city-"

"Which, the last time I checked, you've only inherited control of right now as the most senior ranking Ancient left alive; your knowledge of Atlantis prior to you getting lost out there is relatively limited," John pointed out with a slight smile. "I, on the other hand, have lived here for over twenty years and have spent that time learning all the ins and outs of this city; do you honestly think that you know more about this city as it is now than I do?"

He gave her a moment to think about his last statement, and then he turned around to face the door of her office-

"STOP!" Helia yelled, the sound of something being pulled out of something else giving John a clue to what she was about to do even before she fired, the Ancient pulse-weapon's blast dissipating harmlessly against his personal shield as he turned to look at her.

"Is that really what you've come to?" he asked, putting the right edge of scorn in his voice as he looked at her. "The most enlightened race in the universe, shooting at people because they made a few points you didn't want to hear?"

"I-" Helia began.

"Consider what I said, and I might have some respect for you," John said grimly. "As far as the future goes, I can promise you that, from this day onward, I will be the Phantom of Atlantis only; you have proven that the Ancestors are not worthy of any veneration or respect from anybody."

With that statement, John turned and ran for the office door, leaping over the walkway to land on the gateroom floor before he turned and ran for the inactive Stargate, diving through the window behind the Stargate to leap from the tower before Helia could catch him or call for assistance.

As he adjusted the cloak to glide to safety, heading for one of the lower buildings with a convenient hatch in the roof, the man known as the Phantom hoped that what he'd done wouldn't make matters worse for Earth; he'd publically declared his independence of them, and it wouldn't be hard for others to confirm that assessment, but it was still going to take a while to change the Ancients' minds…

But he would change their minds.

If nothing else, they would not discover the room where he had left Elizabeth's body before he was ready to show it to Elizabeth herself…

AN 2: Well, there you have it; further information about when John ended up in Atlantis has been disclosed, and the stage is set for the confrontations that will reveal the missing answers within the next few chapters…

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