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Summary: Following "The Return Part 1" - What would have happened if Caldwell decided not to take the command staff's word at face value, and instead chose to let standing orders stand? What would they have done to protect their home?

Updated: 23 Apr 2007; Published: 02 Dec 2006

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Story Notes:
Spoilers up to, and including "The Return Part 2" (SGA 03x11).


Note to the Reader: This is the story that started the Bridges Universe. Everything in that series branches from the events of this piece, but they are subdivided into various categories depending on main characters and/or pairings. This particular piece is in the "Gen" or primary arc. Other arcs include the Weir Arc and the Secondary Romances Arc (featuring Miko, Kate Heightmeyer, and others)



The re-taking of Atlantis was both easier and indescribably more difficult than Elizabeth had imagined it would be. Not that she'd spent days or weeks imagining it, because she hadn't. Well, not that she'd admit to. When they'd learned that not only had the Asurans taken over their home, but the SGC was prepared to destroy it without attempting a rescue? Those wistful dreams became frighteningly real.

She'd lived through a siege of the city; she'd lived through several, actually. But she'd never been the one attempting to seize control; she'd always been a defender, a champion of her city. The change in roles was disconcerting. She dealt with it the way she'd dealt with everything Earth had forced her to allow since the initial reconnection. She buried herself in the work of the moment, focused on details and ignored the big picture just as hard as she could. It was easier than she would have thought; to finally be doing work that meant something made her feel alive in a way she'd thought was lost to her. Even the certain death that loomed on the horizon couldn't dampen her spirits (it occurred to her in the still moments that it might not be normal to be so cavalier as she prepared for what might well be the end of her career, if not her life. She found that those moments were few and far between, however, and easy to ignore).

The moment they left the SGC in their stolen Jumper (was it really stolen if it didn't belong to the SGC in the first place? The Jumper wasn't even from Earth – it was from the 'Gateroom bay in Atlantis. It belonged to the Athosians as much as the Tau'ri. It was something to consider at a later time, if they lived long enough to worry about the inevitable legal charges), a line was crossed. It was a personal Rubicon, and the reference made her smile. They were hardly the triumphant heroes, and they certainly didn't hold enough sway to wave off charges of treason such as Julius Caesar had faced.

If things went badly, or even if they didn't, John was going to be the worst off (providing they survived. If they died, it was a moot point). Elizabeth had worked with the military for many years before she accepted a role at the SGC; she knew the military. They would want their pound of flesh, and John was the easiest target by far. Especially with his service record. The IOA could go after all of them, but only John was directly accountable to the Uniform Code. Stargate Command might be used to this kind of behavior, but that was from their prized team. She, Beckett, McKay, and Sheppard were hardly SG-1, and they weren't saving Earth. If the IOA went for blood (and there was no reason to think they wouldn't; even if they saved Woolsey, the IOA had been all too happy to be rid of the money-sink they viewed Atlantis to be. Potential weapons be damned; now that they knew Atlantis didn't possess Merlin's Weapon, their short-term perspective showed it to be more trouble than it was worth. They told her as much when they'd told her not to bother staying on-tap for further Atlantis negotiations), they were all screwed. Every time she closed her eyes while they sat at the midway station, she could see the lists of charges growing - Planetary Treason, Conspiracy (multiple counts), Theft of SGC Property, Destruction of SGC Property...

Should things go well - if O'Neill was still alive, and if Woolsey was alive, and if they won back the city – they might be hailed the liberating heroes. There were no guarantees.

When the Jumper landed at the new Athosian settlement, Elizabeth was surprised at how much comfort she drew from just the sight of Teyla and Ronon. When she'd returned to Earth – on both occasions that she'd been given time off – she'd tried to strengthen ties with her mother, the only biological family she had left. It had been something she'd resolved to do before the first siege, but it had been easier said than done. That first year, her mother had been out of town during her first week off, and then things with Simon had fallen apart and she'd been terrified that she'd lose her remaining tie to Earth so she'd left things as they were. When she'd lost her city, Elizabeth had returned to Earth quietly broken. She'd contacted her mother, hoping for support and understanding, but had found herself unable to see her mother without paranoia creeping up on her. How did she know it was really her mother? How did she know any of this was real?. She had no qualms about Ronon and Teyla. She was pleasantly surprised to find the feeling mutual; Teyla pulled her into a brief but fierce hug before they settled down to business.

* * *


20-odd hours later, Atlantis was theirs. It took three different plans and some unexpected help from O'Neill and Woolsey (who were alive! They might actually make it out of this mess with some hope for their futures!), but they'd managed to rig a city-wide burst by modifying an ARG to interface with the shield. It was another thirty hours until they'd gotten the scanners back online throughout the city, the shield operational, insured that the 'Gate would do what they wanted it to, and swept the high security regions of the city for any remaining replicators (they'd been at this too long to believe that they were all gone; they were never that lucky. They were just glad they weren't anywhere they could cause damage). Unfortunately, the clean sweep was the last of the good news.

The first problem was one they should have expected, but they'd been focusing on retaking the city, not the recovery. Within an hour of Rodney's magic ARG wave, they lost both Woolsey and O'Neill. It began with severe headaches, followed by unconsciousness. They'd gotten them down to the infirmary, but Carson had only been able to confirm their fears – both were suffering nanite-induced comas. They didn't even have a particle accelerator to try and EMP blast this time, or handy Wraith DNA to distract the nanites. With the Ancients all dead in the Asurans' idea of righteous vengeance, there was nothing they could do but make the two men comfortable and attempt to send them back to Earth.

Therein lay the second problem. There had been no initial hurry to contact Earth – they had another two days until the Daedalus arrived, and wanted the city secure before dialing out. Once they'd learned O'Neill was alive, they'd believed they were in the clear. Even if SGC wouldn't listen to them, O'Neill's word was law – it had been his order. When they did dial in to Earth, thirty hours after their departure from the SGC, they received a disturbing response. "I'm sorry, Doctor Weir. That authorization code has been suspended, and the IDC you are broadcasting is not acknowledged by the system."

A sick feeling began to grow in her stomach. "What do you mean suspended?"

"Following your defection and presumed contact with the replicators, your clearance may have been compromised. General Landry ordered that all identification codes relating to Colonel Sheppard, Doctor McKay, Doctor Beckett, and yourself be suspended indefinitely."

"I...see. I need to speak to General Landry; there are facts he is not aware of, which may impact his decision to lock out the Atlantis command staff."

"One moment, ma'am." He turned, conferring with someone out of sight, and a moment later the general stepped into view.

"Hello?"

"General Landry, hello. This is Doctor Weir, and as I was trying to explain to your sergeant, I need you to open the iris; we have two injured men here whom we cannot treat. General O'Neill and Richard Woolsey are currently suffering what we believe are nanite-induced comas. They can be successfully treated with an EMP, as is in the reports of my own experiences with nanites, but we don't have that capability here."

There was a long pause, and Landry appeared to be thinking the idea over. "I'm sorry, Doctor Weir." He shook his head. "We have no way of assuring your identity, and no way to send someone to Atlantis to verify your status. I will not risk the safety of this planet based upon your transmissions. My orders stand, as do General O'Neill's."

"But General –" The connection was terminated, and she pounded her fist into edge of the closest console. The clatter caused the rest of the team, who had been prepping the men for evacuation to Earth, to look up. She sighed, and stood so they could see her more easily. "They've locked us out."

Teyla cocked her head. "I do not understand."

It was Rodney who explained, while Elizabeth walked down the stairs to meet them. "They've deleted our authorization codes; they probably did it the moment we went through the 'Gate. They don't care that they could save General O'Neill's life. They think we're replicators, or that's what they'll say."

"So we are on our own?" The native woman looked to Elizabeth for confirmation, the disbelief visible on her face. Elizabeth placed a reassuring hand on Teyla's arm.

"We are. I'm sorry; I had hoped things would go differently." She sighed, and pushed a loose piece of hair behind her ear. "Somehow." She turned to look at the others. They were exhausted, injured, and now Earth had turned its back on them. "Let's get these two back to the infirmary and get some sleep. I need some time to think and I'm sure you would like some as well. We've got the command tower secured; let's stay up here for tonight. We'll figure out the rest in the morning." They scattered, then. Ronon and John helped Carson carry the general and Woolsey down to the infirmary, while Rodney and Teyla poked around at the lounges a few floors below the 'Gateroom. It looked like most of them were going to be sleeping in the old NCO Club, but at least it had the good couches (she was pretty sure of that, anyway. It might have been the O Club that had the good couches, but it all blended together in hindsight. It didn't matter to her anyway; she had intricate plans for the evening that involved the desk in her office).

* * *


Elizabeth woke up to find the sun beating down on her. She sat up, peering around for a minute and trying to remember how she'd ended up on her balcony. She'd been working at her desk (or trying to, at least), and she'd taken a break to get some fresh air. Then... Oh. That made sense. She must have been more tired than she'd thought (or, if she were honest, it might have been the lack of caffeine catching up with her, too. She hoped the Ancients had left the bean stores intact; she wasn't sure how long Rodney would be functional without some kind of a fix).

She stood, stretching slowly and moving to peer out over the ocean. God, she didn't want to lose this. She couldn't lose this. It wasn't hers to lose, and certainly wasn't Earth's to destroy. This city belonged to those the Ancients had left behind 10,000 years ago. The thoughts circled round and round, until John's voice brought her back to herself.

"Elizabeth, you up?"

She tapped her earpiece. "I'm here. And I think..." She cocked her head to the side, considering. "I think I've got an idea."

"Is that anything like a plan?" She could hear the smile in his voice, and was glad that he seemed to have gotten his equilibrium back. He'd been shaken when they'd gone their separate ways the night before; she could only assume that it had been from General Landry's abandonment of O'Neill. They both understood the numbers game that surrounded their own authorization lockdowns; they didn't like it, but there was a certain kind of logic to it. It was the refusal to even try to save the city that made her chest ache.

She tapped her earpiece and headed to the 'Gateroom. "I think it just might be. Get me whatever information you can scrounge on the Genii, the Athosians, anyone who we were on good terms with before the evacuation." She logged off, and then activated the device again. "Teyla, I need to see you in my office. I've got an idea..."

* * *


The Daedalus dropped out of hyperspace right on schedule (two days after the replicators had been driven out). Elizabeth was in the 'Gateroom, as ready as she could be. The days leading up to the vessel's arrival had been filled with frantic planning, deal-making, and a handful of promises she'd likely come to regret. Now she just had to hope it was enough, that it would work. Caldwell was the wild card in all of this; while she could hope for the best, there was no way of knowing what orders he was actually carrying.

"The Daedalus has dropped out of hyperspace, and is approaching the city." She was seated at the DHD console when Rodney's voice announced that the moment they had been waiting for had finally arrived. She stood, and crossed to face the video feed.

"Bring it up, Rodney." The screen flickered for a moment, and then resolved into the face of Colonel Caldwell.

"Daedalus, this is Dr. Elizabeth Weir requesting that you stand down."

Caldwell gaped for a moment before pulling himself back together. "Doctor Weir? How did you, wait – I need verification of your identity."

"Authorization code Alpha-Six-Charlie-Sierra-Nine. I assure you, colonel, I am Elizabeth Weir. The city is no longer under replicator control, though I have two wounded in need of immediate transport to your infirmary."

"Unfortunately, Doctor, I can't take just your word for that. Your authorization code is invalid; I have no choice but to assume that you and your command staff have been compromised."

"Colonel, you don't want to do this. The city has been reclaimed; there's no reason to go forward with the bombardment now. Why don't you land on the South Pier. We'll submit to whatever scans you require to verify our human status. Is that an acceptable compromise?"

Caldwell thought it over. "Why don't we bring you up instead? It's an awful lot of work to land the Daedalus just to deliver a medical crew."

She shook her head. "I bring down the shield, and my staff will be in holding cells before they can blink, am I right? We both know what the standing orders regarding planetary treason are. Can you promise me that my staff won't be taken into custody if they prove clean?" Caldwell shifted uncomfortably. "That's what I thought. This city is neutral ground, under the authority of the Alliance of Atlantis. The shield isn't coming down unless you're coming in for a landing. We'll be more than happy to submit to whatever medical scans you require, but they need to be done down here. We're not going anywhere until the SGC acknowledges that we're alive and uncompromised. The way I see it, Steven, you have two options. You can land, and send out a team to ascertain our status, or you can turn around and go home. Either way, I will not allow you to destroy this city."

"Elizabeth, this is nothing personal, but I have my orders. They were verified less than an hour ago; surely you've contacted the SGC since retaking the city?"

She nodded. "Yes, General Landry refused to allow us to send General O'Neill back to Earth for treatment."

"Then you know that the decision is not mine to make. What is this about an Alliance?"

"The Alliance of Atlantis, Colonel. A coalition formed to aid in the battle against the Wraith, governed by a board made up of the representative peoples."

"I am unfamiliar with any such organization, Doctor."

"It is a recent development, you might say."

"Regardless, my orders stand. We're not just talking about Atlantis here, Doctor. We're talking about the safety of Earth, and by extension the whole Milky Way galaxy." There was a whispered conference behind him, and he looked away from the screen. A moment later she heard a muffled curse, and glanced over to find John and Rodney looking entirely too pleased with themselves. She raised an eyebrow, but didn't have a chance to pursue the matter before Caldwell returned his attention to the conversation.

"That's an interesting trick you've got there. Am I to assume that Doctor McKay is not one of the injured?"

"Good guess. Since I obviously won't be beaming up, and you just as clearly won't be beaming any nasty little surprises down... I would be happy to grant you permission to land. That way I can give you a more complete explanation of this alliance in person. I would need assurances that there would be no attempts to re-take the city from Alliance control; provided that all members of the command staff receive a clean bill of health, of course."

Caldwell's expression grew resigned. "You have my word, Doctor Weir. You've bought yourself a medical exam."

"Just to clarify, when we say 'no attempts', what we really mean is that the replicators left... surprises lying around down here. Nano-viruses, disintegration beams, that kind of thing. It would be a shame if your crew were to run into any of those while poking about where they don't belong." She smiled good-naturedly as she delivered the warning, and John moved to stand next to her, arms crossed. He'd apparently been taking intimidation lessons from Ronon in the last few days.

Caldwell sputtered and went from resigned to livid in a heartbeat. "Colonel Sheppard, I knew that you had been locked out of the SGC systems, but I would have assumed you'd have better sense than this. I can't believe that you'd threaten the lives of men and women you've served with."

John shrugged. "We know how to turn the nano-viruses off; I'm not the one putting your crew in danger." His voice grew harder, quieter. "I'm also not the one who planned to nuke this city just because Landry believes the glass is half-empty. Maybe that makes me the bad guy here, but I know where my priorities are." He looked around at those scattered around the 'Gateroom floor and watching the conversation with interest. "We all do."

Caldwell sighed. "Dust off the pier, doctor. We'll land in 20 minutes." He shook his head ruefully before adding "I hope you know what you're doing." and disconnecting the transmission.

The discussion concluded, Elizabeth took a deep breath and uncrossed her arms to lean back against the console.

"Well, that was fun." She ignored John's sarcastic response, and turned to face those below her on the 'Gateroom floor. She felt a smile touch her lips as she recognized some of those in the crowd.

"I would like to take this opportunity to welcome all of you to Atlantis. I know that we've had our differences in the past, but I truly believe that we are stronger united than we are apart. We will one day defeat the Wraith, and we will do it together. Until that day, we will fight and die side by side. From this day forward, the City of the Ancestors will provide refuge to all those who participate in the Alliance - Genii, Athosian, and Earthborn alike."

There was silence, followed by a quiet round of applause. Thankfully, Teyla stepped forward as the applause died down and began directing the new city residents to the wing where they'd set up temporary housing. God, she hoped she was doing the right thing, but they needed warm bodies if they were going to lay legitimate claim to the city. The Genii had warm bodies to spare, and Ladon had offered to include his sister in the first batch of immigrants as a guarantee of cooperation. Elizabeth was cautiously optimistic; if Ladon was to be believed, the effects of the radiation were becoming more visible within the Genii population – there were many who were willing to trade their underground housing for a chance to live in the sunlight in Atlantis. Hell, she was reasonably sure that he'd been subtly offering his sister up for a political marriage for the sake of stability. It wasn't something she could condone, but the 'proposal' did have obvious advantages.

She nodded as John caught her eye, and watched him round up the Athosians who'd been pegged for the Daedalus 'welcoming committee'. Anyone familiar with a P-90 or who had serious military background was being drafted into a temporary security force until a more permanent solution could be arranged. Elizabeth was just glad that the Ancients hadn't found their stockpiles. She'd felt guilty leaving the inventory behind, but it had been a result of careful hoarding, and there simply hadn't been a way to fit an extra eight storage rooms of gear into the Daedalus without causing more questions than she was prepared to answer. Now, she wished they'd left even more behind.

The 'Gateroom empty for the moment, and with a good fifteen minutes until John headed up the initial meeting with the Daedalus, Elizabeth escaped to her office for a few minutes of peace. She sank down into the chair behind the desk, and buried her head in her hands. Her mind vacillated between two extremes. She couldn't let them destroy her city; she could not turn her back on the people here. But she could never go home after this; there was no going back. No going back.

Except that wasn't quite right, because she was home.

~ Finis ~