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Author's Chapter Notes: AN: I apologise in advance that this chapter doesn't end this episode, but it felt like it would be too long if I included Atlantis taking off as well given my other plans for these events; hope you like the results anyway

"So," Elizabeth said, looking contemplatively at Major Lorne as he stood in front of her and John in her office, "you're sure the ships were destroyed?"

"Believe me, they couldn't have survived what Horizon sent out against them," Lorne said firmly. "That explosion was… well, it was big."

"And the Replicators couldn't have done something about it?" John asked. "They are pretty fast…"

"Colonel Ellis considered that," Lorne replied. "We had opened the bomb bay doors while still in hyperspace and dropped them at pretty much the moment we got out of it; they wouldn't have had time to react to a blast like that, and that's before I ran a closer check. Zelenka said something about it being hard to get an accurate yield calculation at this distance, but McKay seemed fairly sure we had done all the damage we needed."

"That's good to know," John said, before looking probingly at Lorne. "And… did Ellis have anything to say about us?"

"Actually, the colonel had a few things to say about Doctor Weir's abilities as a leader in a military situation like this, but he just seemed to want to get a general feel for my thoughts on the situation rather than actually objecting to you two," Lorne clarified. "When I told him that I was completely satisfied with the two of you as leaders, he decided that it wasn't worth pressing the issue at the time."

"Really?" John looked at his official second-in-command with a smile. "Thanks, Major."

"No problem," Lorne nodded back. "The SGC isn't exactly a conventional military outpost by any stretch of the imagination, and that's when we have immediate access to anything we need back on Earth. In my book, that means we need an unconventional leader to deal with the situation out here; if the IOA don't like it, they should give us an alternative that we can be sure would actually work, instead of just complaining about you."

"We appreciate the support, Major Lorne," Elizabeth nodded, just as Chuck hurried into the conference room.

"Doctor Weir?" he said, looking anxiously at the city's leader. "You're going to want to see this; we've got a contact, just came out of hyperspace."

With a quick glance at Elizabeth, John got up and hurried from the conference room to the control room, looking anxiously at the data on the screen.

"Is it broadcasting IFF?" Elizabeth asked.

"No, ma'am," Chuck confirmed.

"Too small to be anything Wraith, but get the shield up just to be sure," John put in.

"Done," Chuck nodded, triggering the relevant controls before turning back to the screen. "Whatever it is, it's taking up a geosynchronous orbit above the city."

"Can we get the Apollo to check it out?" John asked.

"Tell Colonel Ellis to get right on it," Elizabeth noted, glancing at Chuck as he tapped a few controls on a nearby laptop.

"Think it's them?" Ronon asked, as he and Teyla walked into the control area, a grim expression on the former Runner's face.

"I'm learning to expect the worst," John said simply, even as the screen indicated the Apollo taking off to take a closer look at the new arrival.

"Apollo to Atlantis," Colonel Ellis reported at last. "We have a visual on the object; it appears to be a satellite, but it has… well, there appears to be a Stargate in the centre of it."

"Hold on; it's a satellite and a Stargate?" John asked. "Are you saying someone built a satellite around a Stargate and fired it off to us?"

"Actually… since this Stargate only seems to have eight chevrons, I wouldn't be surprised if someone built it and the satellite at the same time…"

"Built a Stargate…" John said, looking thoughtfully over at McKay as the Canadian scientist hurried into the control room. "I'm getting a very bad feeling about this…"

"The Replicators?"

"It just activated," Ellis' voice said before John could reply to the scientist's query. John was about to ask for more details when there was a loud series of explosions at the other end of the radio connection before it cut out.

"What happened?" John asked, glancing anxiously at the technician.

"Apollo's still up there, but there's been a major energy surge from the satellite; it must have forced Apollo to back off," Chuck reported, his fingers flying over the board. "The satellite's turning around; it's firing… it looks like some kind of energy beam at the planet."

"Shield's up, right?" McKay asked.

"Yes-" Chuck began, just as the city shuddered when the beam made contact with the edge of the shield. As those in the control tower ran to see the source of that shudder, they took in the sight of a vast beam of red energy hurtling down from the sky, the city's shield rippling against the force being directed against it even as it held up to the barrage.

"It's a sustained beam," Chuck confirmed grimly.

"That is bad for a dozen different reasons," McKay noted grimly.

"It's protected by a shield," Ellis's voice called out over the radio. "Give me some options, McKay."

"The shield's taking its power from the beam," McKay

"Look, I registered a slight drop in output when you fired on it…"

"Could I get a nuke past its shield?"

"No, probably not," McKay said.

"I'll get down to the Chair and give it everything we've got," John said firmly, his gaze fixed on the beam. "Maybe that'll collapse the shield…"

"I said 'slight'," McKay said, before John could do more than turn towards the door of the control room. "As in point zero zero two percent."

"Ah," John noted.

"Not something we can rely on, then?" Lorne added.

"Quite frankly, I doubt any amount of firepower is gonna collapse it while that beam is active."

"So what do we do?" Ellis asked.

"We stand down and let me think, is what we do," McKay said as he headed for another console. "Just give me five minutes to get my bearings. I'll brief you."

"McKay, it's shooting at us," Ronon noted.

"Yes, and the shields are holding," McKay said firmly. "We've got plenty of time; just give me five minutes."

Exchanging anxious glances with Elizabeth, John noted that at least he wasn't the only one sceptical about that idea; if they were being attacked by something able to build Stargates, he had his doubts that even McKay could come up with a solution in five minutes.

For the moment, he was going to make sure that all of his own emergency measures for a direct attack on Atlantis were still available if he had to resort to them; the hyperspace-capable jumper had been kept in reserve in the underwater bays ever since he'd become the official military commander of the city, but there was nothing he could do about the power supply as they already had three ZPMs plugged into the city, and he couldn't be sure if Apollo had one of the ones he'd donated already or not…

"We're in trouble," McKay reported, as Ellis joined John and Elizabeth in Elizabeth's office once he'd been beamed through the shield.

"And it took you five minutes to work that out?" John asked.

"Look, the satellite is basically just a stripped-down ship," McKay explained. "There's a hyperdrive engine, a shield, and navigational systems. There's a small power source that was designed to take it to its intended target and power the shield until the Gate can be dialled. But once a wormhole has been established to whoever's on the dialling side, it fires a beam into their Stargate and it comes out on our side, allowing them to fire on us and to power the satellite."

"Clever," John noted.

"Yes; as long as they can keep the beam powered from home, the weapon remains operational. Oh, and one fun added side bonus is that because their Stargate is in such close proximity to our planet, we can't dial our Stargate. We're stuck."

"But can't we… hold on…" John began, pausing mid-sentence as one of the SG-1 mission reports he'd read back on Earth came to him. "Didn't Anubis once try something similar to this on Earth's Stargate? I read a file where he found some Ancient weapon that sent a massive amount of energy into the 'gate so that it couldn't shut down until it blew up and took everything else with it?"

"Are you saying that bypassed the whole 'thirty-eight minute' rule I heard about how long we can maintain a wormhole?" Ellis asked. "I thought that wasn't possible?"

"Oh, it's possible, believe me; I was in the SGC when Anubis mounted that attack and I couldn't figure out any way of stopping it," McKay confirmed grimly. "We had to dump the Stargate in space and make some complicated deal with Russia to get back our original Stargate… God, they were annoying…"

"How do you get the power for something like that?" John asked. "Last I checked, it takes a lot of energy to run the Stargate normally, and I think if the Ancients left that kind of thing lying around we'd have seen it before…"

"Considering that you'd need either a black hole or an unlimited number of ZedPMs to do something like this, we can safely assume this is new," McKay said grimly.

"Well, at least that confirms it's the Replicators," John noted. "Who else could do that and build a Stargate?"

"Hopefully," McKay noted. "It's either that or we've just discovered another super-powerful enemy, so here's hoping it's just them."

"If this is anything like a normal Stargate, could we contact the dialling planet?" Elizabeth asked.

"Well…" McKay paused in thought for a moment. "I'd need to boost the signal considerably to get through the interference, but, uh, yes."

"See what you can do," Elizabeth nodded at the scientist.

"You want to talk to them?" Ellis asked, looking incredulously at Elizabeth as McKay left the room. "It's a waste of energy-"

"And trying to destroy a shield we have no idea how to destroy isn't?" John interjected firmly. "You can keep running your tests if you like, but we've already established that our available weaponry can't do anything to that shield, so apart from sitting around and twiddling our thumbs until we come up with a better plan, talking is all we've got right now, so we might as well use it."

"Precisely," Elizabeth nodded gratefully at him before fixing Ellis with a firm stare. "And before you get started on a massive debate about who's right or who's wrong in this situation, at the end of the day I'm responsible for the well-being of this city, and you don't have the authority to tell me to stand down, so with all due respect, I think I'll place my call."

Ellis clearly didn't like that turn of events, but as Elizabeth walked out to the control room, all the colonel could do was look at John in frustration while John shrugged nonchalantly back at him.

It might be a petty act, but considering that this man had basically been asking around to find out if John and Elizabeth were considered bad leaders by their people, John felt entitled to enjoy the notion that the man had misread the situation that badly.

As he returned to the control room to wait for further developments, occasionally checking the power controls to be sure that the shield was still holding against the barrage that it was being subjected to, John was relieved when McKay reported a response to his transmission through the orbiting Stargate. As Elizabeth waited in front of the communication screen, John moved to join her, but Elizabeth was clearly startled at the sight of the old man who responded to the transmission.

"Oberoth?" she said, John taking a moment to recognise the name as the 'leader' of the Replicators when they'd assumed they were just another Ancient city.

"Doctor Weir," the apparent old man responded.

"I must say, I'm surprised to see you," Elizabeth said, quickly collecting herself.

"Each of us exists within the collective and can be replicated many times," Oberoth replied.

"Ah," John noted, before privately dismissing it; in this situation, it might actually be enjoyable to have more than one chance to kick that arrogant bastard's ass.

"You need to disable your weapon immediately," Elizabeth responded, bringing the conversation directly to the topic at hand.

"That is not possible."

"We had no choice but to attack you," Elizabeth said, returning to her diplomatic roots. "You're building warships. They need to be neutralised."

"And now, so do you."

"That assault was just the tip of the spear," Elizabeth continued. "We were hoping it would bring you to your senses. If you don't stop this aggression, we will be forced to launch an all-out attack."

"Really?" Oberoth asked. "Why have you waited?"

"Because we were hoping that we could talk to you people and work out something that we'd all find agreeable rather than just blow you all up," John noted.

"The annihilation of your people is not our goal," Elizabeth continued, shooting John a look that he wasn't sure how to interpret. "Ideally, we would like a peace to exist between us, but we will not stand idly by while you build ships and weapons that can be used to destroy us."

"Interesting," Oberoth said in his usual cool tone. "We feel the same way about you."

John wished that he had some way to wipe that condescending grin off the old man/Replicator's face, but considering that Atlantis and Earth had been planning to attack the Arusan homeworld anyway, he didn't exactly have a moral high ground to stand on.

"Perhaps I should remind you every time we've met in battle, our side has been clearly victorious," Elizabeth countered.

"Elizabeth," McKay cut in, "they're attempting to upload a virus on the comm bandwidth. I've been able to stop it for now but I'm not-"

"Shut it down," Elizabeth said, nodding at McKay to terminate the video link as the screen shifted to static. "Well, that went well."

"So," John asked, before McKay could voice his own frustration, "assuming that they can keep that beam going regardless of usual time limits, how long have we got until it penetrates the shield?"

"With our current ZPMs, assuming constant pressure… I'd give it a week at most," McKay said grimly.

"OK," John said, looking around the control room. "First priority is be ready to try the simple option in case this thing does shut down at the thirty-eight-minute mark; after that, I need options, like… shut this thing down at the source?"

"The Apollo isn't in any state to get into a battle right now-"

"I need options, not objections, Colonel," John said, turning to glare at Ellis. "We're in this mess because your superiors decided to start firing rather than wait; find me something we can actually do about this mess."

"Oh, now we're responsible for this?" Ellis countered, walking over to stand in front of John, the man once known as the Phantom suddenly wondering if Ellis would be this bold if he'd taken his make-up off to reveal his true face. "You know, you might have managed to pull some strings to get this job-"

"I got this 'job' because General O'Neill and the SGC agreed with the decision to trust my experience over my lack of official qualifications, Colonel," John countered. "If you have a problem with my decisions, put them to the IOA when you get back to Earth, but right now this is my outpost, my responsibility, and my enemy to beat, so stop trying to convince our team to turn on us and let me work out how the hell we're going to survive this mess, comprende?"

Maybe it wasn't professional, but that was the advantage of his position existing technically outside the conventional chain of command; he might not have an official rank, but in Atlantis, it had been made clear to the SGC that his word would be law, which meant that he had full authority to tell Ellis to get out of his face while he focused on saving the city he'd come to call home.

Looking at the anxious expression on Elizabeth's face, he just hoped that she wasn't going to start doubting her own role in the city if this kept up; the IOA might want her to act as a scapegoat for some of their worse decisions out here, and they may not have faith in her role as anything more than an administrator, but John would make it clear to anyone who would listen that he trusted Elizabeth above anyone else, and would cite these events as proof that her opinion had value in a crisis.

He just had to be careful he didn't let that out of the bag…

A few hours later, staring up at the red beam now coming down at Atlantis through several tons of water, John wondered if he should feel nostalgic at the moment.

He might not have always felt comfortable living alone in Atlantis when he'd arrived, but there had been something cool about the concept of living in a sunken city created by an ancient civilisation. He'd taken to watching the fish on a few occasions when he'd known that particular shoals were passing by the tower- it had reached a point where sometimes he could only be sure what time of year it was on the planet based on what was swimming near Atlantis- but at the moment he didn't have anything to distract him from the bigger problem, the beam churning the water between the surface and the shield to such an extent that he doubted anything was going to pass the city now.

Submerging the city to use the water as additional protection had seemed like a good idea at the time, but even with all three ZPMs powering the submersion system to make it as efficient as possible, and as much as the residents had tried to appreciate the moment, it didn't change the fact that they were in trouble. Even with everything they'd done, going underwater had only brought them another couple of days at most, and John didn't want to run out these ZPMs any more than he had to; he might have a secret surplus, but those things didn't grow on trees.

John had been working on a little plan of his own, but he couldn't see how it would work unless they could take the beam out of the picture; right now, the city was the Asurans' priority, and he doubted that it would be easy to make them stop that beam even if he could convince them to go after another target.

So far, however, all he'd managed to do was make a weak joke comparing his recon team to the Fantastic Four that Teyla and Ronon didn't get, and he was running out of patience; no matter how much time they had, he hated being stuck in one place when there was a threat to stop.

"John?" Elizabeth asked, as she walked out to join him on the balcony. "Are you all right?"

"Well as you'd expect," John shrugged, looking back at her with a brief smile. "Just feeling stuck, I suppose."

"Feels like the old days?"

"Worse," John mused, indicating the marine landscape before them. "Back when I was here on my own, it was kind of cool to see some of the fish swimming around- I even worked out the best towers to watch some of the more regular migrations- but now we've got nothing to look at thanks to that beam stirring up the water, I can't work out what to do about this, and I don't even have the option of gating somewhere more interesting to think."

"That… must be frustrating," Elizabeth noted, looking thoughtfully at him. "I mean, I knew Atlantis was your home before we came here, but I guess I never really thought about how you spent your time… when you weren't killing Wraith, anyway."

"It had its ups and downs," John noted. "You can only exercise and train so often before you start feeling like you're just wearing yourself out when you can't actually compare your results to anything else. Managed to trade for some paper and pen equivalents to try writing and drawing at times, but… well, the results were poor."

"Just like my reputation back on Earth?"

"You're still here-"

"And I'm starting to wonder if I'll be here much longer, given how far the IOA went over my head with the attack that started this mess in the first place."

"…You don't think that's my fault?"

"Excuse me?" Elizabeth looked at him in surprise.

"The IOA jumping over you like that, I mean," John clarified. "It's just… well, you pulled a lot of strings to get me an official role here, and that can't have made some of the IOA very happy; could I-?"

"Don't," Elizabeth cut in, looking firmly at him. "You earned your role on this expedition with every drop of blood and sweat you've given to keep this galaxy as safe as one man could; you may not have been an official part of this expedition at the beginning, but I will never regret making sure that you were allowed to stay here."

"…Thanks," John finally nodded, not trusting himself to say any more as he looked out at the sea once again.

God, I wish I could kiss her right now

"We have something!" McKay's voice suddenly yelled over the radio, cutting John's thoughts off before they could become any grimmer.

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