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: To whom it may concern, I'll be focusing more on the Phantom rather than Elizabeth's team at this point in the story- what they'll be doing is fairly similar to what they were doing in canon, such as picking up Niam and returning to Atlantis, so the absence of Sheppard doesn't really have enough impact to make it interesting-, but that will shift when the time is right, I assure you…

Mystery of the Phantom

Crawling through the tunnel, John tried not to think about how close he'd come to being detected by the Asurans; he really didn't need to know how low on power his personal shield was. With him having to turn it on to deflect his life-signs every time an Asuran came too close to him- he wasn't clear on what the Asurans were capable of detecting on their own, so anything he could do to minimise the signals he was giving off would probably be a good move-, he was running out of power for what may be a meaningless precaution, and he didn't know how much longer it would take for him to get somewhere safe enough for him to take a break.

Safe

Damnit, he thought to himself in frustration. I spend over two decades keeping this city safe, and then the original owners come back and it falls apart after six weeks.

Atlantis was meant to be completely safe, he shouldn't have to worry about even parts of it being dangerous-

The sight of movement caused him to stop, but when he saw an older man in green combat BDUs who could only be General Jack O'Neill walking along the corridor, too stealthy and quiet to be an Asuran, John didn't need long to make his decision. Slipping out of the nearest access panel, he landed on the ground and took a couple of steps forward.

"General Jack O'Neill, I presume?" he said, smiling slightly at the other man as the general in question started in shock at the sound of his voice, aiming his gun at John with a speed that John had to admit was impressive in a man of any age.

"Who the…?" General O'Neill said, looking at him in confusion for a moment before inspiration dawned. "You're that Phantom guy, aren't you?"

"The Phantom of Atlantis, at your service, General O'Neill," John said, taking hold of the edge of his cloak with one hand to give his bow an extra flourish before he stood up and looked at the other man with a slight smile. "I assume you've heard of me?"

"A few things," O'Neill said, looking at him with a neutral expression. "You've had an… interesting life, if nothing else."

"It's given me some equally interesting skills," John replied. "And right now, General, you and Mr Woolsey are going to need those skills if you're going to survive this."

"No offence, but I don't think even you can get us out of this," O'Neill said, sighing as he looked back the way he'd come; the fact that he took his eyes off John at least suggested that he trusted the other man, but that was small comfort considering what they still had to deal with. "SGC's under standing orders to nuke Atlantis if it falls under control of a hostile force."

"Oh," John said, resisting the automatic urge to yell at Jack about that particular decision- it made sense on a practical level, even if he didn't like it- and turned his attention to the more immediate issues he could deal with. "So… what were you doing there?"

"Grabbing some food and conducting recon," Jack replied, briefly opening a picket to indicate a few energy bars before zipping it up again. "Stargate Operations is crawling with these guys, so we're not going to be able to get out that way…"

"In other words, we're stuck until Earth either blows us up or we find some other way out," John said, looking grimly around himself at the corridor they were currently standing in before he turned to look at Jack. "I might be able to get us to a gateship bay so that we can evacuate, but I want you to be clear that if there's any way for us to save Atlantis-"

"Place is your home; I'm not going to begrudge you if you think you can stop it blowing up," O'Neill said, before he looked more pointedly at the other man. "Just so long as you're clear that I'll stop you if I think what you're doing is going to endanger us or Earth."

"Understood," John said, before stepping back slightly and looking hopefully at O'Neill. "Well, your guy's still missing; lead on."

With O'Neill leading the way, the two men continued to walk along an increasingly-damaged corridor, the lights growing obviously dimmer the further they went, until the sound of a voice whispering anxiously reached their ears.

"And if I'm a Replicator?" O'Neill said as he walked up towards the source of the voice, revealing the suit-wearing form of Richard Woolsey, awkwardly holding a gun in a manner that made it clear he had no real idea what to do with it as he peered around a corner.

"Then I just gave away my position," Woolsey said, having the decency to look guilty about his mistake before his eyes fell on the figure behind the general. "What-?"

"Richard Woolsey, meet… the Phantom," O'Neill said, indicating the masked man with a brief wave of his hand as they walked into the battered corridor, various items of furniture overturned. "He's offered to help, we're not exactly in a position to say 'no', so here we are."

"I see," Woolsey said, clearly stuck for anything else to say as O'Neill tossed him an energy bar, at which point he decided to focus on more personal matters than the presence of a man the IOA didn't officially like. "Thank God, I'm starving…"

"Make it last," John said, looking pointedly at Woolsey. "We don't exactly have much in the way of options right now, and then there's all the Asurans hanging around here…"

"That's an understatement," O'Neill said grimly. "Stargate Ops is crawling with 'em; we're not getting out that way."

"Are they looking for us?" Woolsey asked.

"No way to be sure," John said grimly. "With the life-signs detectors out of action in these areas, it's possible that they don't know there's anyone here to look for, but we can't exactly afford to underestimate them."

"And then there's the bomb," O'Neill pointed out.

"Bomb?" Woolsey said, looking sharply over at the general. "What bomb?"

"Landry has standing orders to nuke the city if there's any sign of a foothold situation," O'Neill said, at least having the decency to look awkward about that information.

"What kind of a standing order is that?" Woolsey said, looking incredulously at the older man.

"His," John said, grimly indicating the general before he held up his hands defensively as Woolsey looked between them in shock. "I don't like it either, but I get where he's coming from; if Atlantis is really lost to enemy forces, too many people would suffer if nobody at least tried to destroy it."

"And you have no objection to the fact that we're in it?" Woolsey said.

"I'm going to do what I can to ensure that it doesn't come to that," John said, looking firmly at Woolsey for a moment before he sighed as he leaned against the wall. "I just need some time to think of a plan…"

"Didn't you mention a gateship bay-?" O'Neill began.

"Getting out of the city just keeps us alive; I'd prefer a plan that will let us save Atlantis at the same time," John pointed out.

"Well, unless you've got an army in your pockets, I don't think-" O'Neill began.

"Authentication code Alpha One Delta Sierra Niner," a familiar female voice suddenly said from O'Neill's pocket. "General O'Neill, Mr Woolsey, do you copy?"

"Doctor Weir?" O'Neill said, pulling his radio out of his pocket and turning it on, thankfully missing the smile on John's face as he heard the voice he'd been wanting to hear again for months. "Is that you?"

"Yes it is," Elizabeth's voice replied. "I'm sorry for being abrupt, but we need to know if you're anywhere near Stargate Operations."

"We're not," John said, before O'Neill could say anything; maybe the older man would consider it rude, but after he'd spent weeks not hearing Elizabeth's voice, he wanted to let her know that he was still alive.

"That's… good," Elizabeth said (Was it John's imagination, or did she sound more relaxed than she had earlier?). "We'll get back to you later, General; Weir out."

As the connection terminated, the three men exchanged brief glances before a loud explosion shook the corridor they were standing in. Hurrying over to a door that he knew led to a room with a convenient window- he might not have accessed much of the database, but he knew where things were well enough-, John reached the window in time to see a gateship flying away from the central tower as it burned brightly, parts of it damaged by what appeared to be a fairly substantial explosion, one of the side towers collapsing as smoke and flame burst through the upper levels.

"What was that?" Woolsey asked, walking into the room and looking out of the window in confusion, his eyes widening at the sight of the damaged tower. "Is Doctor Weir attacking the city?"

"She'd better be," O'Neill said, nodding in thoughtful approval.

"Why can't she get back to us for two hours?" Woolsey asked, frowning.

"I don't know," O'Neill said.

"No immediate ideas here either," John said, looking apologetically over at the other two men as they turned to look at him, before his eyes narrowed as he looked at them in an authoritative manner. "However, if we can focus on staying alive right now, that's the main thing; the Asurans are going to be busy dealing with the damage to the control tower, but they may have detected that radio communication before everything went down, so we should use this opportunity to get to a more secure location while they're distracted."

"What makes you so sure they'll be distracted?" Woolsey asked.

"They want Atlantis to get to Earth, Mr Woolsey," John said, looking firmly over at the other man. "That means they need the Stargate, which means they need the control room to be fully operational; do I need to spell the rest of it out?"

"Check," O'Neill said, nodding at him in understanding. "Lead on."

This might be their first meeting, but so far, John was definitely enjoying the chance to talk with General O'Neill; everything he saw of the man only further improved the assessment of him he'd formed based on Elizabeth's old stories…


"That sounded like another explosion," Woolsey said, as another loud noise- albeit significantly quieter than the previous one- reached their ears after a period of silence, the three of them only occasionally talking to limit the risk of being caught. They'd been walking through the damaged portions of Atlantis for a while, John wanting to keep them on the move while not wanting to go too far from their original location in case they accidentally encountered a working scanner, but that was the first sign of any additional activity in the rest of the city.

"Yes," O'Neill said, nodding thoughtfully at Woolsey. "Yes it did."

"What does that mean?" Woolsey asked, looking urgently at the other two.

"Something exploded," O'Neill said, in the same calm voice.

"But is it our team attacking the Replicators, or the Replicators attacking them?" Woolsey asked, still sounding obviously flustered at this turn of events.

"We'll probably find out sooner or later," John said, attempting to sound nonchalant about it; he was as curious to learn the answers as anyone, but was trying to focus on what he could control rather than what he couldn't answer at this time.

"How did they even get here?" Woolsey said after a moment's pause. "Through the gate?"

"We've been right next to you since this started, Woolsey; how the hell are we meant to know those answers if you don't?" John pointed out, as O'Neill closed his eyes in frustration at the other man's questions.

"Look," Woolsey said, putting the gun down and practically tearing his tie off in frustration, "I told you I wasn't good at this-"

"They'll be back soon," John said firmly; the man might not be much use, but the last thing he needed was for oneo f the people he was trying to keep alive to have a breakdown. "We just need to stay on the go and out of danger until they get back to us…"

The man in the mask tried not to think too much about the implications of the explosions they kept on hearing taking place outside in other parts of Atlantis; he doubted that Elizabeth and her team would be so casual about attacking the city, which suggested that the Asurans were the ones firing weapons right now, but that still didn't give him much hope about their ability to evade for long.

He hated to be pessimistic, but he had to face the facts; if Elizabeth was on this team, it was unlikely to be an SGC-sanctioned operation, which meant that it was unlikely they had any fully-trained pilots on board their gateship, which meant that they'd be relying on luck and whatever natural skill their current pilot had to get to safety…

As further explosions rocked the city, he could only keep walking and hope that Elizabeth and her team would survive this mess…

"They're overdue," Woolsey said.

"Life doesn't exactly operate on a schedule, Mr Woolsey," John said, turning around to glare at the other man. "If you don't like unpredictability, I apologise, but we can't always accommodate your need for exact detail; this is the real world, and stuff happens in the real world that doesn't always happen on a timetable."

It was abrupt, but he wasn't going to treat this man with kid gloves no matter what the long-term consequences might be regarding his presence in Atlantis; their priority right now was staying alive, and that was what he was going to make sure they focused on.

"Hello?" Elizabeth's voice said over the radio at last. "General O'Neill? Phantom? Are you there?"

"We're both here, as is Woolsey," O'Neill said, pulling his radio out of his pocket as the other two men gathered around him. "Doctor Weir, can I ask what took you so long?"

"We had to pick something up in space; getting back was… more complicated than we'd anticipated," Elizabeth replied.

"And you're currently… where?" O'Neill asked.

"Heading for an underwater gateship bay," Elizabeth replied, prompting a slight smile from John; he was fairly sure he knew which one she'd be heading towards, considering that he had 'introduced' them to an underwater bay during that incident when he'd been tracking the hives…

"Neat," O'Neill said, before he continued. "And talking of interesting news, may I express my… surprise that Landry would send you on a mission like this?"

"Well, sir," Elizabeth said- to her credit, her tone was as casual as it always was, despite the news she was disclosing-, "General Landry didn't sanction this mission."

"So," O'Neill said, looking at John with a foreboding expression, "am I to assume you are not surrounded by heavily-armed S.G. teams and young strapping marines?"

"You've got myself, Ronon, Teyla, Doctor McKay, and Doctor Beckett," Elizabeth replied.

"Oh, Doctor Beckett!" O'Neill said. "Well, I'm comforted-!"

"Any help in this situation is appreciated, El- Doctor Weir," John said, hoping that nobody else noticed his slip-up; he was so used to talking to Elizabeth in private he'd almost forgotten that they weren't alone this time.

"We do have a plan, General," Elizabeth said, McKay's voice heard in the background saying something about a lock. "We'll fill you in on as soon as we're sure it's safe."

"Yeah, I'm sure you do," O'Neill said. "But just so you know, Doctor Weir, in the event-"

"She won't," John said before he could stop himself.

"Excuse me?" O'Neill said, looking critically at him.

"She won't fail," John repeated, committing himself to his current course of action as he looked at the general; as with Woolsey, making a good impression might be important, but he also wanted to ensure that everyone present knew him for what he was. "I've seen Doctor Weir in action as leader of this city, General; she might make questionable decisions, but she wouldn't take risks without a plan."

"Well," O'Neill said, looking at the now-silent radio in his hands- he must have turned it off when he turned to talk to John- before he sighed and shrugged, "looks like we're in her hands now anyway."

"And why do you have such faith in her?" Woolsey asked, looking curiously at the masked man. "As I understand it, you've been an independent operative in this galaxy for years-"

"Things change," John said pointedly, as he looked at Woolsey; regardless of the situation they were in or how Woolsey would react, that was one thing he wasn't going to reveal to anyone else until he'd had the chance to tell Elizabeth about it. "Maybe I'll answer that question once we get through this."

He just hoped that his attempt at projecting confidence was successful; regardless of what Elizabeth had planned, they weren't exactly faced with brilliant odds right now…