Hope you enjoy my own spin on it.
He'd come up with this plan to keep Elizabeth out of harm's way, and now the only way to put it into action required him to take her into the lion's den and hope that the Asurans didn't notice them until it was too late.
On the bright side, he'd left Lorne and Teyla in charge of Atlantis, and he was confident that each of them would obey the orders he'd provided; if they weren't back in twelve hours, take Atlantis on to a randomly-chosen new planet to ensure that the Asurans couldn't track them again, contact Stargate Command, and work things out from there. He'd even given Teyla the address chevrons for his ZPM stockpile in case the worst happened, and he'd been comforted by her simple acceptance of his advice. He still caught Ronon looking at him as though the ex-Runner was just waiting for the moment when he'd snap, but the Athosian leader at least seemed to have reached a point when she was willing to listen to him.
He was glad that he didn't have to shoulder all the responsibility all the time any more, but at the same time, having so many other people actively depending on him to keep them alive made him strangely uncomfortable. Protecting people as a distant concept was one thing, but taking others out into battle and having to trust that they wouldn't end up dead because he made a mistake…
Still, his concerns aside, he'd been grateful to have McKay check over the hyperdrive for the jumper before they'd left; McKay might not have been able to make the thing himself, but he had enough experience with Ancient technology to be sure whether or not something would work, and he'd given the hyperdrive generator a pass despite the push John had given it during his confrontation with Michael and escape last year. There were some concerns about the power supply, but John had faith that they could use McKay's tentative plan to steal a ZPM to deal with that shortcoming if it became an issue, which meant that right now the only concern as getting in close enough to find a control node without the Asurans detecting them.
The hyperdrive flight had been fairly silent, but John had appreciated the lack of banter for once; he might wish that the team were more comfortable around him, but at the moment, his priority was making sure he had every plan possible for getting all four of them in and out of Asuras alive…
Finally, the jumper emerged from hyperspace over the Asuran homeworld, John quickly cloaking the ship as they advanced into orbit.
"How's things?" he glanced back at McKay.
"Well, it would appear that our concerns about the power supply issue were correct; if we want to get out of this, the optional plan of retrieving another ZedPM just became key."
"So do we do that before or after we upload that code?" Ronon asked.
"Mmm… before," McKay decided. "They've got enough ZedPMs down there that they might not miss one if I can find the right spot to set us down, but once we upload something to the main core they'll know we're there and this becomes trickier."
"Right," John said, looking around the jumper as he began to descend towards the planet. "OK, McKay, see what you can do from here."
"On it," McKay nodded, turning on his laptop and looking thoughtfully between the computer and Elizabeth. "First things first, I need to initialise the link…"
"Should I do anything?" Elizabeth asked.
"Just sit there," McKay smiled. "It's completely wireless; let me know if anything pops into your mind."
"What do you mean?" Elizabeth asked, John trying to contain his anxiety at the idea of what they were doing by focusing on their descent. "Will I just sort of sense something, or is it more of a… Oh my God."
"What?" John glanced back at her, Elizabeth now staring ahead of herself with a distant expression that seemed alien on her face.
"I did it!" McKay grinned. "I mean, she did it… look, we have to move fast. Even though Elizabeth's nanites are only in lurking mode, it won't take long for the Replicators to figure out another player has joined the game."
"In and out," John nodded. "Get us to a ZPM, find a command module, and then we're out of here; not the hardest plan we've ever had. You doing OK, Elizabeth?"
"It's strange… I can see the entire city directly in front of me," Elizabeth said, just as John passed through the planet's cloud cover to take up position above the Asuran city. "I mean, every corridor, every single room… that way."
Following her cue, John turned the jumper to fly towards the indicated area, weaving around the towers as the cloak remained active.
"There's a ZPM in the fourth quadrant, top level," Elizabeth explained. "Easy access; there's hardly anyone around."
"And from here to a command module where we could upload the code?" John asked, as he moved to settle the ship in position on the roof of one of the buildings.
"Well, I'll need some time to work out where the attack command actually is in their base code, and I'd like to make sure there isn't another option other than direct upload, but I should have it by the time you get the ZedPM now that I know what I'm looking for," McKay clarified.
"OK," John nodded, checking his weapon and making sure his mask was settled on his face. "Ronon, let's get that ZPM; McKay, you and Elizabeth need to find that command code, and you can guide us through the radio."
"Twenty minutes to the left behind the jumper, there's an access door," Elizabeth said, as John and Ronon grabbed their weapons. "Down one flight of stairs you'll enter Auxiliary Corridor Seven; it's clear."
With that instruction, John hurried out of the jumper, Ronon behind him, adjusting the inbuilt radio in his mask to match the jumper radio's frequency. Each of them were carrying their traditional weapons and the newly-designed Anti-Replicator Guns, although Ronon also had a case for the ZPM. With Elizabeth's whispered instructions as they advanced along the corridors, it didn't take long for them to reach the ZPM that they were after, particularly when Elizabeth could confirm immediately that they had been undetected by any passing Asurans rather than have them waste time worrying if they'd been seen or not.
John wasn't naïve enough to think that Elizabeth having active nanites in her wasn't going to have problems later, but if McKay could just turn them on, he had to believe that they could be turned off as well…
"It should be directly in front of you," Elizabeth reported, just as John saw a small room with a green screen at the end.
"Yep," John smiled, as he saw the familiar slot of a ZPM holder below the console. "I see it."
Leading the way into the small room, Ronon took up a position at the door as John headed for the ZPM console. "Won't someone notice when we pull the plug on this thing?"
"Probably, but they've got dozens of ZedPMs and this one doesn't appear to be running anything important," McKay replied. "Let's just hope that they don't notice until we're long gone."
"Risky, but workable…" John mused, placing his hands on the console and issuing the mental command to release the ZPM, carefully disconnecting the module and passing it on to Ronon. "You get this thing back to the jumper; I'll try and find the computer core."
"You're splitting up?" Elizabeth asked.
"No offence, but I'm the better one qualified to hack Ancient-style computers on short notice, even if I'll just be following McKay's instructions," John noted over the radio. "How are we doing on that front, anyway?"
"Well, I've managed to find the part of the Replicators' base code that controls the command code that will make them attack the Wraith- just one code among a billion lines, but like I thought it's clear enough once I know what I'm after- but like I thought, we need to input it directly into a physical data core," McKay explained. "I can use Elizabeth's access to keep them occupied, but if I uploaded the program through her, it wouldn't take effect until the next data merge uploads the code to the entire network, and then they'll know we're here and try to assimilate her."
"So I can turn it on?" John asked.
"If you can get to the node… maybe, yes," McKay nodded.
"And I take it it's some way to go between here and the central node?"
"City centre, several levels down."
"And coming back after we've left here isn't really practical because we'll have every Replicator ready for us once they work out what just happened and prepared to block our access," John groaned. "Can you do anything about it there?"
"Not really, and I'd prefer to be closer to the node to limit the risk of signal lag as we're trying to upload the program even if I could," McKay replied. "Once we get there, could probably keep the Replicators away from us by doing what we did in Atlantis and turning the jumper's shield into an anti-Replicator field, but that's only going to keep them out for so long, especially when they'd know we'll be there…"
"Everything that increases your chances," John said firmly. "Get that field working and then stay in the jumper; Ronon will take the ZPM back to you and you can join me at the central node while I see if we can do anything about it there."
"Hold on; shouldn't you-"
"Aren't you forgetting I came in full Phantom gear for this one?" John cut in with a slight smile. "I've been training myself to get around Atlantis for years, and this place is based on Atlantis itself; I can get there outside the city without any of their sensors detecting me, and you can get to the same building and pick me up once we're done."
"John, this is crazy-!"
"It works," John said firmly, as he headed for the nearest window. "Let me know if anything picks me up, and meet me at the top of the node building; we've only got one shot, so let's make this count."
"…All right," Elizabeth said at last, after a brief moment of conferring at the other end of the line. "We'll meet you there; good luck."
"Same to you," John replied, before he turned around and headed for a room with the nearest window. Taking out his grapple, he made sure that there were no sign of Asurans in the visible rooms outside the tower- he hadn't read anything to suggest that these guys had particularly heightened vision, but it was best to be sure- before he leapt from the window, cape spreading out behind him as he hurtled through the air above the Asuran city-ship. He couldn't configure the shield device to a cloak like they had for the jumper and city shields, but if he could stick close to the buildings, he might be able to get close to the central node building without them seeing him.
In a funny way, he actually enjoyed this part of the job. He'd taken a few practise swings around Atlantis at night once it had risen up from the ocean floor, in parts of the city where he knew that nobody was assigned to work at that point, but it was almost relaxing to do this during the day in a city where he knew nobody had reason to be looking for him.
It probably wasn't something he could do on a regular basis, considering that it was essentially a frivolous bit of exercise that was still extremely complicated to perform correctly, but he was going to enjoy the moment while he could. Swinging from one building to the next, getting gradually lower as he went along and had to latch on to a lower level as support, he soon found himself crouching near the building that held Atlantis's central node back home, and should hold the same thing here if his luck held out. He was a few levels below his target, but glancing up revealed no sign that the jumper had arrived and activated its new anti-Replicator field yet, which meant he could focus on getting in without worrying about whether anyone had noticed them arriving.
As good as Ronon was, the Replicators were going to notice someone entering the city from above, but John was willing to bet they weren't imaginative enough to think that someone would have tried to access the central node this way…
He could get up the wall and into the building easily enough, but he didn't know where the node was…
"John?" Elizabeth's voice called out in his earpiece.
"Elizabeth?" John replied, keeping his voice low just in case. "Where are you?"
"Just taking up position at the top of the tower you're on," Elizabeth replied. Glancing up, John saw a strange blue glow surround the top of the tower and advance downwards; the Replicators would probably detect that, but if they were quick, it wouldn't matter. "McKay's adjusted the shield to an anti-Replicator frequency and extended it down to the central node; if you can get inside and get to that level, you can input the code and then get up to the jumper."
"I still say I can go down there-" McKay tried to cut in.
"And I told you, Rodney, you need to stay here to keep an eye on me in case they infiltrate my nanites," Elizabeth countered before she continued talking to John. "McKay's working on a program that can be input to the node via his tablet if you can't activate the code yourself; Ronon will bring it down if you need it."
"Understood," John nodded, refusing to let himself think about what Elizabeth had just suggested; she would not have to be turned off because she wasn't going to 'flip out' on them, the nanites were just a small part of her right now... "What level am I going for?"
"The ninth level down."
"So, just need to get up a few and I'm in," John smiled, adjusting his position to climb the wall towards the nearest window. "See you soon."
God, I hope that works.
He had faith that the shield would keep the Replicators out, but he knew from the SGC files that they could still adapt to this kind of weapon if they were hit with it often enough and managed to send the data to other Replicators; the question was how long it would take for that to become a problem…
"Just hurry it up," McKay said anxiously. "If you can get into the room and find the right computer, that might cut down on how long we need to be here, but we'll still be cutting it close…"
"Well, you know what they say," John smiled, as he finally reached a suitable window and smashed through it with his sword. "If being the hero was easy, everyone would do it."
"Hey, who said- actually, never mind, I can work with that," McKay said as John climbed into the window. "OK, all Replicators immediately around you are out, so just go through the door down the corridor and you're at the node; Ronon can be with you in a few moments if you need it."
"And the code's ready to upload?" John asked.
"I already set up a basic block storage transport protocol to upload the attack command directly from this table to the core; plug it in and it automatically configures and uploads the command."
"Seems simple enough, particularly with Elizabeth keeping us up-to-date on their movements," John smiled as he went down the corridor. "I'll set things up; see you soon."
In a few moments, he reached the appropriate door, and walked in to find himself standing in a tall room, containing only an Ancient console covered with control crystals in front of a turquoise glass 'table' with a turquoise and orange top that resembled a half-oval made of glass panels with some kind of stylised ZPM on each panel, a central circle of pale blue panels at the top.
"I'm in," he said, looking up at the node thoughtfully before he studied the console. "OK, this is…"
"You need help?"
"I need help," John confirmed grimly. "I can see an access port and a few familiar crystals, but this is… well, it's a lot more advanced than anything we had back in Atlantis."
"OK, tricky, but if there's an access port, this can still work," McKay confirmed. "The interface might look more advanced, but based on what I've seem, their coding program hasn't changed much since the Ancients created them; Ronon can get the tablet down to you, then all you have to do is plug it in and let it run."
"Huh," John smiled. "Who'd have thought it; we turn these assholes back into an asset just with a few clicks…"
A minute or two later, Ronon came into the room, an ARG in one hand and a computer tablet in the other, passing the tablet to John while he drew his more familiar gun and turned his attention back to the door.
"Got it," John said, taking the tablet and turning back to the console. "And you're sure they won't find this and reset it before it's uploaded?"
"Like I said, we're uploading this command amid a mass of spam and junk; they'll just think I was trying to infect them with a virus or spam the system to delay them while we got away," McKay answered. "Just plug it in, get back up here, and we're away."
"Right," John said, nodding as he connected the cable to the node and sat back.
"Well what?" John asked. "I just plugged it in-"
"And I'm not getting any response up here; are you sure you plugged it into the right slot?"
"There's only one slot here, Doctor McKay," John confirmed as he glanced over the console, trying to ignore the sinking feeling in his gut at this turn.
"John," Elizabeth's voice cut in once again. "They're coming, and there's hundreds of them."
"Check," John said, gaze fixed on the tablet. "I doubt this is going to be an 'On/Off' equivalent problem; can you give me something else I can do about this right now?"
"OK… assuming that the issue is that the core isn't recognising the tablet, we're going to need to implement adjustments to the negotiation protocol to exploit parallelism at the device interface…"
"Which means?" John asked. "Keep in mind I don't know a thing about this kind of computer programming from your perspective…"
"We have another problem," Elizabeth added. "The Replicators are deliberately sacrificing themselves to the field."
"Why would they do that?" Ronon asked, his guns still trained anxiously on the door.
"Because the more they attack the field, the quicker they can figure out how to override it," Elizabeth answered, horror clear in her voice. "Ronon, adjust your ARG frequency by a few degrees…"
As Ronon reset his weapon, John tried to take in all of McKay's instructions as he worked on the tablet to rewrite the scientist's program, adapting something called the root directory to carry out a different function and going on from there. John briefly cursed his limited experience with Earth computers, but put that aside to focus on getting the job done while obeying McKay's orders; there wasn't time to keep track of what he was being asked to do for future, but if he could just get this done soon…
"You have to get them out of there now," Elizabeth suddenly cut in.
"We're not done-" McKay began.
"There's no more time!" Elizabeth said urgently. "The Replicators have breached the shield!"
"What?" John said, stopping in his work to pay more attention to this conversation. "You mean that field isn't working any more?"
"Yes," McKay said apologetically. "Look, we're going to need to move quicker; you have to make changes to the negotiation protocol to allow for direct data placement so we can allow for resynchronisation of the packet boundaries within the data stream-"
"McKay, I don't need to know how what you're telling me will help; just help me get this done!" John yelled, as Ronon tensed himself for action by the door.
"Oberoth is heading to the control room," Elizabeth put in. "He knows it's us."
"How far is he?" the scientist asked. "Can they make a run for it?"
"No!" Elizabeth said urgently. "Replicators are approaching from every direction-"
"Is the window an option?" John cut in, before he glanced at Ronon. "Actually, scratch that; no way could I get us both up there before something caught up with us."
"Better one than-" Ronon began.
"Leave no man behind is one of the first rules of the Stargate Program, Ronon," John cut the Satedean off firmly. "I'm not leaving you to get executed by a bunch of robots, so don't even ask me to-"
"Elizabeth, what are you doing?" McKay suddenly called out. "You can't go out there! Elizabeth!"
"McKay…" John said, his blood running cold at the implications of those last words. "What just happened?"
"Elizabeth just left the jumper."
If John's blood had been cold earlier, he felt like he'd been dunked in the Antarctic after that news.
Elizabeth Weir was out and about in the heart of enemy territory, contaminated by alien technology, and he could do nothing to help her…
"What do I do here?" he asked, making his choice.
"What?" McKay asked. "Elizabeth just ran out and she said that-"
"We don't have time to worry about that right now; we're only going to get one shot at this, so we have to keep trying to finish the mission," John said firmly. "Elizabeth already managed to act against those nanites before, and Doctor Jackson managed to take control of the Milky Way Replicators all by himself for a few moments-"
"He had access to Ancient knowledge at the time; that's not the same-!"
"If we don't finish this now, we're all definitely dead; we don't know where Elizabeth is or what she's doing, so we have to focus on what we can control and hope that this works and she's as strong as we think she is!" John countered. "Either help me finish this code or give up; what's it going to be?"
To McKay's credit, he didn't take long to make his decision as he continued to relay his original instructions, but as much as the argument had made sense, John still hated thinking about what he'd just done.
He'd promised himself long ago that he'd do everything in his power to protect Elizabeth Weir, and now he was leaving her in danger so that he could finish this…
The next few moments were a blur in John's memory, automatically tapping the relevant commands into the tablet while wondering if the next sound he would hear from Elizabeth would be her delivering an ultimatum from Oberoth, either as a forced hostage or a reprogrammed slave…
"OK," he said at last, finishing the last rewrite and plugging the tablet in. "We're back online; anything at your end?"
"Yes!" McKay said after a moment's pause. "Yes, it's working!"
John only just managed to exchange a relieved smile with Ronon before the door opened and eight Asurans entered the room. Ronon had already backed up and raised his weapons to open fire when John and he realised simultaneously that none of their would-be attackers were actually doing anything, but had simply frozen in place as soon as they walked through the door.
"Uh… McKay?" John asked, turning his attention back to his radio. "Did the command code get uploaded already?"
"No… I don't know what just happened…" McKay said, pausing for a moment. "Unless… if Elizabeth was able to link directly into the Replicator collective, she might have been able to issue a command… which would mean that the chances of her being taken over just increased exponentially…"
"Unless we shut the nanites down and get her out of here," John finished firmly, as Ronon moved among the Replicators and removed their weapons. "How long have we got?"
"Well, shutting them down should be as simple as hitting her with an ARG on the old frequency, considering that she doesn't need them for anything more than maintaining the link, but as to getting out… I can't be sure, but obviously we should assume less time rather than more."
"Check," John said, glancing back at the tablet. "How's the upload?"
"Just a few more seconds…" McKay said, prompting another few moments of anxious silence before the scientist spoke again. "Done; take that tablet, find Elizabeth, and get out."
"Done and done," John said, grabbing the tablet and running from the room. "Where's Elizabeth?"
"I can't track or communicate with her since she blocked my access to the nanites, but assuming that she was moving to intercept Oberoth, she can't be too far from your position."
"Gotcha," John said, mind already racing over the likely paths Elizabeth could have taken; this area wasn't a clear copy of Atlantis, but assuming Ancient architecture followed a logical pattern, but if he remembered the tower structure correctly from what he'd seen before entering that window, there was one of those strange excess bridge things a level or two up…
He wasn't going to think about McKay's warnings about the Replicators unfreezing at any moment; he still had a trick or two he could call on if they started moving again, and with the retuned ARGs, he and Ronon could hold them off for a few more moments if they absolutely had to.
When they rounded a corner and found Elizabeth standing in front of Oberoth, the 'old man' on his knees with his hand around her wrist, straining against some unclear force as he glared at the diplomat, John felt like he was going to scream; he was meant to stop Elizabeth from facing this kind of danger.
"Elizabeth," he began, raising his ARG in preparation.
"Get to the Jumper," Elizabeth responded.
"You're coming with us," John said firmly. Beside him, Ronon fired his ARG at Oberoth, only for the blast to have no effect on the 'lead' Replicator (John could only pray that this just meant that the bastard had only adapted to that frequency; the last thing they needed was Oberoth to become unstoppable).
"I can't keep them frozen much longer!" Elizabeth countered.
"We are not leaving you behind," John said, shifting his weapon to point at Elizabeth as he adjusted the frequency of the gun before sliding it under his cloak; this was going to be risky, but he had to hope that the unexpected would pay off…
"If you don't leave right now, none of us will get out of here, so go," Elizabeth said firmly, turning her head slightly to face him. "THAT'S AN ORDER!"
"And that's the one order I would never obey," John said, before he fired his ARG and struck her in the back. Stunned by his defiance as much as the attack, Elizabeth fell backwards, John only just managing to stop her hitting the ground as he slid forward, grabbing her in one arm as he glared up at Oberoth.
"Think fast," he smiled behind the mask, before kicking upwards to strike Oberoth in the chest, his opponent's smirk faltering when he realised that his chest was literally disintegrating around where John had come into contact with it. This victory assured, John slid back along the ground, pushing himself against the floor and using his cape as a slide, before he got back to his feet, turned around, and began to run back towards the jumper on the top of the building, Elizabeth now held in both arms while Ronon ran backwards alongside them to keep an eye on the situation behind them.
Maybe what he'd done had been stupid, reckless, and several kinds of dangerous, but if it meant keeping Elizabeth safe, John would do it all over again.
He'd probably just destroyed her faith in him by doing something this stupid, but at least she'd be alive to disapprove of it…
AN 2: And there you have it; my variation on how the Phantom of Atlantis saves Doctor Elizabeth Weir from her canonical fate (And for anyone wondering how he managed to hurt Oberoth by kicking him, I have an explanation for it; I just didn't want to give it away right now).
For those who prefer the personal developments, John will be saying those three little words you've been wanting him to tell Elizabeth in the next chapter or so, but I think you can appreciate that I didn't want to make this chapter too much longer when a moment like that deserves full attention