Standing in the control room of Atlantis, Jack smiled in relief as the last of the team passed the 'anti-Replicator' checks; taking blood tests might be a basic way to determine if someone was a Replicator or not, but it got the job done well enough.

They might have managed to present a convincing enough argument for the lack of Replicators in the city to get Colonel Caldwell not to try and blow them up with a nuke the second they dropped Atlantis's shield, but the SGC still had to worry about the possibility of Replicators trying to infiltrate them with convincing duplicates, which meant that they needed to be tested in a controlled situation before they were allowed anywhere else.

"That's everything," the leader of the medical team said, nodding at Jack from inside his environmental suit, needles of blood in their hands. "We'll get back to you once the tests are done and the city's been cleared."

"Sounds good," Jack said, nodding in understanding at the men before they stepped back and were beamed back up to the Daedalus, leaving him to turn and look at the rest of the group. "OK, so, while we're waiting for that, anyone got anything we need to do?"

"How about talking about this?" Elizabeth's voice said, prompting the group to turn around take in the sight of Doctor Elizabeth Weir walking into the gate room, the masked and robed form of the Phantom behind her.

"You… are still here?" Teyla aid, her immediate apprehension at the sight of the masked man fading as she restrained her initial reaction, noting the warning glances she was receiving from the rest of the team.

"I am," the masked man said, nodding in response at the Athosian woman before looking over at Ronon, who was looking tensely at him even if he wasn't actually reaching for his reclaimed gun. "I take it we won't have a repeat of that… incident… earlier?"

"We… had a little talk about that," McKay said, looking awkwardly at him for a moment as the masked man turned to look at him. "I mean, the face was a shock, but Doctor Beckett shared a few theories about… well, about where you come from…"

"Such as?" the Phantom said, looking curiously at the scientist.

"Well, let me put it this way," Jack said, looking inquiringly at the masked man. "Do we call you the Phantom, or John?"

For a moment, the man in the silver mask seemed surprised at what he had just heard, but then his eyes widened briefly before he nodded in careful understanding.

"It was Rod, wasn't it?" he said, looking over at the Scottish doctor. "He mentioned my name, and then…"

"Pretty much," Doctor Beckett said, smiling awkwardly at him before he looked at Elizabeth. "Actually, how did you-?"

"If you've found out about it, John's fine," the masked man interjected, giving the doctor a brief but firm stare before he looked back at Jack. "So… now that you know my name, what are you going to do now?"

"That's something to think about, really," Jack said, looking thoughtfully at the man in the mask before his attention turned to Elizabeth. "Doctor Weir, considering how you used his name before any of us did, would I be correct in thinking that you've got a few things to tell us about our masked avenger here?"

"A few," Elizabeth said, nodding in agreement at the general's statement before she looked around at the rest of the expedition members present. "If we could all… adjourn to the conference room?"

"Daedalus is running some scans to confirm a lack of other life-forms in the city at the moment, as well as running our bloodwork, so until they're done, we can chat to our hearts' content," Jack said, smiling reassuringly at her. "Lead on."

Even after all the other things he'd experienced in his time in the SGC, talking to a real-life masked vigilante was something he hadn't experienced before, but he had a feeling he was going to enjoy it.

---

"So… you really are from Earth?" McKay said, staring incredulously at the man he'd spent the last three years thinking of as 'the Phantom'. "You're actually called John Sheppard?"

"And I learned how to operate the city because of advice and instructions I received from an alternate version of Doctor Weir from a timeline where you all drowned; why are you having so much trouble processing this?" John asked, looking in frustration at McKay. "I know it's a weird situation all around, but I can assure you that it happened; do you really think I'd know that much about Star Wars if I didn't come from Earth originally?"

"But… seriously, that thing Zelenka found in that lab is a teleporter?" McKay said incredulously (Elizabeth had been surprised to be reminded of the lab with the burned-out equipment that Zelenka had discovered in their first year in the city; she'd thought it interesting at the time, but never imagined they'd seriously learn the answer to it). "How come we never saw more things like that?"

"Because the Stargate was better-built and generally safer to use; the teleporter's only advantage was that it was a bit more subtle, as far as I can tell," John said, shrugging as he looked at McKay. "After all, the one on Earth seemed to have been abandoned for a long time, and we can't exactly know what the one at this end went through, but considering its condition I'm betting it wasn't really expected to be in use for long."

"Getting back on topic, you're seriously telling us that you've been so insistent on working with Doctor Weir when you had to work with us before now because you met some… other version of her who got sent back in time when she first came here and set things up to save Atlantis this time around?" Jack said, looking at John in contemplative admiration (He had a feeling there was a little more to that part of the story than John was telling them, but if it wasn't going to be dangerous, he wasn't going to press the guy about it).

"Yes," John said, looking back at Jack with a neutral expression that would have given Teal'c a run for his money. "Do you have a problem with that?"

"Just… lot to put up with for someone you only met once," Jack said with a shrug. "She must have made quite an impression…"

"She gave her life to save this city," John said, smiling slightly back at Jack. "I had to do something to justify that kind of effort, right?"

"You really saw your own body?" Ronon said, looking curiously over at Elizabeth.

"Well, it's the body of a possible me whose timeline doesn't exist any more, but… you're essentially right, yes," Elizabeth said, nodding in confirmation at Ronon.

"Actually, that's the part I'm having… trouble with," Woolsey said, looking pointedly at the Phantom. "Why did you keep her body frozen all these years?"

"As a reminder of my vow to her and until I could ask Doctor Weir here what she wanted done with her body," John replied, shrugging slightly as everyone else at the table looked curiously at him. "I knew that she was coming back to Atlantis eventually, and… well, I hadn't actually discussed what I should do with her once she was dead- we had so little time already talking about that just seemed more morbid-, so I thought I'd be safe enough putting her on ice until I could ask the younger her for an opinion."

"Oh," Elizabeth said.

"Anyway," Jack said, looking at the masked man curiously, "now that the cat's out of the bag, what's your next move? Go back to Earth?"

"Actually," John said, looking at him with a slight smile, "all things considered, I thought I'd remain here."

"You did?" Woolsey said.

"I've already offered him a position as head of the military division," Elizabeth added, smiling in satisfaction at the stunned expression on the IOA representative's face.

"You- what?" Woolsey said, looking incredulously at her. "You offered command of this city's military assets-?"

"To a man who has continually risked his life for us and developed a detailed knowledge and understanding of our enemy's abilities and resources after fighting them for over two decades," Elizabeth interrupted, looking firmly at Woolsey before she looked over at Jack. "General O'Neill, I am aware that this is highly unorthodox, but considering his own experience with both this city and the Wraith, as well as the precedent you yourself set by recommending Teal'c for his position on SG-1 in the early days of the program… would you be willing to consider my recommendation?"

Recognising that the current topic did not permit his usual humour, Jack sat back and looked thoughtfully at the man in the mask sitting alongside Doctor Weir for a moment, turning over the request in his mind.

Even if it would require more than a few favours to be called in and offered, he could certainly see how the man he was looking at would be an asset to the city if what he'd heard matched what he was capable of. If nothing else, Teal'c still had no official rank back at the SGC and yet he had unofficial authority over most of the military staff in the place due to his experience with the Jaffa, and they did have the precedent of Teyla being in temporary charge of Atlantis after contact with Earth had been established even if she'd been sharing authority with a couple of Earth residents…

"Well," Jack said, looking over at Woolsey with a contemplative smile after giving the topic a moment's thought, "considering that he just saved our asses out there, I think we can see about pulling a few strings for him to get his dream job, right?"

"This is highly unorthodox; he doesn't even have any official training-" Woolsey began.

"But," Jack interjected, looking firmly at the IOA representative, wanting to be sure the other man understood the point he was about to make, "considering that he's got a reputation of kicking Wraith ass for almost two decades with a score-card of five hive-ships and various smaller vessels to his name, without any help or back-up, I think we can assume that he's pretty good at what he does."

"And," McKay said, looking at Jack with a slight smile, "he's got my vote, if that counts for anything."

"And mine," Carson said, nodding in agreement.

"Ronon and I will… also… vote for him," Teyla said, looking awkwardly at the masked Phantom sitting across from her, clearly still uncomfortable with the memory of what was under that mask despite Elizabeth's explanation about it (Not that Jack could blame her; a lifetime of thinking that people who looked like that were nothing but psychos created instincts that couldn't be ignored that easily).

"There we go," Jack said, looking at Woolsey with a smile. "That's three of this city's resident senior staff and two Pegasus natives voting for the man in the mask to take charge; majority rules in action, right?"

"Well…" Woolsey said, shrugging awkwardly as he looked around the table before he sighed and looked back at John. "I'll speak in your favour, but you will still have to undergo an evaluation before we classify you as fit for duty, and we still have to discuss how Colonel Sumner will feel about this."

Judging by the sceptical expressions on the faces of the Atlantis senior staff, Jack had a feeling that nobody else here was going to be that bothered about what Colonel Sumner thought of things- not that he could blame them; the guy was a good soldier but he'd just never seemed to really take the time to connect with anyone under his command-; the only question was how Sumner himself would react to the news that Doctor Weir had decided to replace him…

The sound of a radio message reminded Jack that they had other things to worry about before they could even get to that particular stage of the proceedings; for one thing, the Daedalus had to be informed that there were a couple of other people that needed to be tested before the city could be declared Replicator-free.

---

Caldwell hadn't been exactly happy when he'd learned that Elizabeth and John had shown up while his ship was otherwise occupied, as it required another round of tests to be carried out- fortunately, since the previous round of tests had come back positive and there had been no interruption in their life signs while they were talking, there had been no need to re-test the rest of the people in the room-, but once those tests were over, General O'Neill and Elizabeth had re-dialled Earth and quickly made contact with the SGC. After General O'Neill had provided the SGC with his report on recent events and confirmed that everyone in the city was human and unharmed, it had been left to Elizabeth to step forward and make the more crucial announcement.

What she was about to reveal would be a hard sell, but Elizabeth was going to give it everything she had; after all that he had done for them, John deserved nothing more than her best.

"Hello, General Landry," she said as she sat down in front of the monitor, smiling politely at the general whose orders she had so recently defied.

"Doctor Weir," General Landry said, looking back at her with an expression of long-suffering patience that was only slightly spoiled by the glare in his eyes. "I received Colonel Caldwell's message, but I had to see it for myself; you really re-took Atlantis?"

"We did," Elizabeth said, nodding at the general and smiling in response, before the sudden appearance of Colonel Sumner from the side of the screen distracted her from what she had been about to say as she turned her attention to him. "Colonel, I-"

"Doctor Weir," Sumner said, looking solemnly at the screen, "in the presence of General Landry and General O'Neill, I wish to inform you that, while I am gratified to see that you survived and that Atlantis remains under our control, I must tender my resignation as the military commander of Atlantis; I cannot continue to serve under someone who shows such disregard for the chain of command."

"Understood," Elizabeth said, nodding in acceptance at Sumner before Jack could say anything himself; she hadn't been expecting that news, but it certainly fit Sumner's focus on the rules above all else.

It was a slightly tragic example of their lack of a personal relationship that Elizabeth wasn't that bothered about Sumner's decision to resign his role in Atlantis, but even if he hadn't done so, she had a feeling she would have asked him to step down after recent events; his announcement just made it easier for her to say what she was about to say anyway (She.

"While the IOA have accepted General O'Neill's request for leniency towards the rest of your department heads for their role in the recovery of Atlantis," General Landry said, looking apologetically at her as Sumner walked off to the side, his business apparently concluded to his satisfaction, "Colonel Sumner's decision does mean that you're going to require a new military leader. I'm going over the files on potential candidates for promotion within Atlantis itself, but I also have-"

"Actually," Elizabeth said, smiling slightly at the screen- it would be best to cut that particular line of conversation off before it went too far in case her suggestion looked too much like a protest-, "I already have a candidate in mind for the new military commander; I've spoken with General O'Neill about it, and he's agreed that, considering my candidate's unique background, he is eminently qualified for the task."

"And who is this man?" General Landry asked, looking inquiringly at her.

"Right here," John said as he stepped forward, moving into full view of the screen, his cloak slung back over his shoulders and his manner more relaxed than she had ever seen him display in public.

"General Landry," Elizabeth said with a smile as she took in the older man's stunned expression, placing an affectionate hand on John's shoulder, "I would like to introduce you to John Sheppard, the Phantom of Atlantis, and my chosen candidate for command of Atlantis's military division."

"And, for what it's worth," Jack put in before Landry could say anything to that revelation, "Richard Woolsey and I have spent some time with Mr Sheppard, and we have complete confidence in him; guy saved our lives and helped us take out those Replicators with no thought for his own safety."

"You are… I'm sorry, you're endorsing the Phantom- a known vigilante and independent operative- as head of the military division of our first major outer-galaxy base?" Landry said, looking incredulously between Elizabeth and Jack. "I understand that he's been helpful-"

"He's from Earth, Hank," Jack said.

"Excuse me?" Landry said, looking at Jack in surprise.

"His name is John Sheppard," Elizabeth said, taking up the explanation herself. "He apparently activated an Ancient teleportation device back in the nineteen-eighties that sent him to Atlantis, and… well, it's a long story involving time travel that it would be easier to explain in person, but the end result is that he's spent two decades learning all about this city based on the same starting point that we had when we first arrived, has years of experience at fighting the Wraith, and his loyalty to Earth and us is beyond reproach."

"I… see," Landry said, looking thoughtfully at John for a moment before he nodded in resolution. "Very well, then; I'll expect the three of you to be back on Earth as soon as possible."

"All of us?" Elizabeth repeated in surprise. "General, I'm needed-"

"It's going to take time to bring everyone from the old expedition back together, Doctor Weir; I think the city can afford to be without you for a few more days," Landry said, looking firmly at her. "Considering the trouble that we've had regarding the Phantom situation for the last couple of years, Doctor Weir, I think you can understand my reluctance to just… hand over the keys to the kingdom without more information about this latest bit of news."

Elizabeth privately hated the unspoken implication that the IOA were only going to even consider her request because John was from Earth- he could do the job and he was dedicated to the protection of Atlantis; the fact that he'd been born there shouldn't be a factor in whether or not he could do the job-, but she didn't have the time to protest about something like that now.

At the moment, the IOA's fundamental 'Earth first' mentality was going to work in her favour, so she'd do what she could to use it; she'd work on the wider implications later.