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As he crouched in a convenient maintenance tunnel near the centre of the city, his ears alert for the radio transmissions that he'd arranged to be rerouted via his mask if certain key words were heard- he may not know much about creating computer programming, but you didn't spend around two decades in a city like this without learning a few neat tricks-, John had to wonder if the current analysis was turning up anything about the hives that he himself hadn't picked up through trial and error. He might have learned over the years that each hive tended to have a better ability to cope with particular kinds of damage than its fellows, but that didn't mean that there weren't some areas that could be attacked that would do particular damage to the rest of the hive rather than just areas where the hull was particularly weak in one ship compared to how it was in others...

He wondered if it was still normal for him to have concerns about the Wraith even after all they'd done so far to live up to their end of the original deal. They'd even allowed McKay and Ronon to take a look around the hive and let them return to Atlantis afterwards without any objections or any sign that they had any problem with what the two men had seen or done while on the hive; for any Wraith to allow a non-worshipper on a hive like that was a definite step in the right direction for this alliance.

Still, their look at the Hive's interior had certainly helped them come up with a neat way of dispersing the retrovirus throughout other hives without worrying about issues of explosive devices igniting the resulting gas. Based on what he'd overheard in his last trip to the conference room as Sumner and McKay spoke to the Queen, McKay had isolated a central chamber that removed the CO2 from the ship's atmosphere that would allow them to disperse the retrovirus throughout the ship so long as they could get a canister of the stuff in there in the first place.

It might not be a perfect plan- as the Wraith Queen had pointed out herself, the only way to get that canister into the chamber that they'd thought of so far was to use the expedition's Asgard transporters to send it there-, but it was a step in the right direction; anything that would limit the threat the Wraith could pose to others was a step in the right direction as far as he was concerned.

He just wished he could figure out what was bothering him about this whole situation; the Wraith hadn't done anything to merit him being really suspicious of them apart from the fact that they were Wraith- and he wasn't going to let that get to him after his previous 'debate' with Michael-, but there was definitely something about this whole thing that he didn't feel entirely comfortable with yet. He acknowledged that it was probably just his natural disinclination to trust the Wraith after everything they'd driven him to over the years in order to survive, but that experience had also given him a sixth sense for danger that he couldn't afford to overlook just because he found it frustrating.

God, he needed to get past this; how was Elizabeth ever meant to see him as anything more than a masked vigilante if his response to everything that happened was to wait and prepare for the moment when it would backfire on him-?

Then an alarm suddenly flared up in his ear, followed by one of the emergency systems he'd installed in his mask activating to display a stream of information in his left eye- the small computer he'd installed there could itch at times, but if he was going to 'pad' that section of the mask anyway to make it look natural he was going to install something that served some kind of purpose-, and he knew that his fears were justified.

"Fuck..." he muttered to himself, as he closed his right eye to better process what was being displayed in front of his left. "So much for that hope."

The Wraith might not have shown any sign of hostile intent so far, but sending them a computer program equipped with a virus that would delete everything they'd sent to Atlantis and send the hive a message containing certain items of data wasn't something he wanted to think much about. Acting as quickly as possible, he reached out with his mask's mental sensors and quickly shut down the computer network- the worm had still sent off something, but by taking the computers offline for the moment he should be able to prevent it getting everything that it had been designed to transmit until they could reboot the system and purge it of the virus- before he turned around and began to hurry towards the room where he'd set up his emergency transporter system (He might not be a McKay when it came to gadgets, but he'd come up with some interesting adaptations of existing technology in his spare time).

He hated leaving the city while Elizabeth was still on it, but if these events meant anything, it was clear that it was time for him to use one of his 'special projects', and just hope that he'd gotten the programming right (He'd done his best, but when you were working with theoretical programs that the Ancients hadn't even put into practise before they left Atlantis there was only so much you could do) or that he'd have time to make the necessary corrections if this plan didn't work out.

"What happened?" Elizabeth asked, looking at Zelenka as he sat at her desk, Teyla alongside him out of a lack of anywhere else for her to be at this time, evident shock and terror on his face at the news that he was relaying.

She still wasn't entirely clear on what had happened or why the computers were rebooting right now, but she had a strong feeling that she was about to learn the answer to both questions soon, and she was equally certain that neither of them were going to be entirely pleasant.

"We got hacked," Zelenka said, staring ahead of himself as he spoke, apparently trying to avoid addressing her directly out of fear at her possible reaction. "Within the hive ship's schematics was a worm-like computer virus."

"Your people went over the data," Elizabeth said, trying to trace where the Wraith's deception of them had begun as she walked around to take her seat.

"I know," Zelenka confirmed. "We thought it was clean, but this virus was entirely different."

"What did it do?" Elizabeth asked, taking up position behind her desk as she leant forward slightly while continuing to face the Czech scientist.

"It very selectively probed our systems without damaging them or exposing itself," Zelenka explained.

"I don't understand," Beckett said, voicing Elizabeth's own confusion from his position at the side of the room. "If you didn't find it and it didn't reveal itself..."

"Once the hive left Atlantis," Zelenka clarified in response to Beckett's question, "the worm began to destroy all of the data they had sent down.

"Then this was their plan all along," Teyla said, her grim tone and resigned expression suggesting that she was berating herself for allowing herself even the brief hope that they found a Wraith who wasn't the same as the others.

"What did they get?" Elizabeth asked, hoping that she would be about to hear some good news;

"Well," Zelenka said, smiling slightly as he spoke- the smile faded as he continued to relay the information, but at least it provided Elizabeth with confirmation that something had worked out in their favour-, "apparently whatever happened to the computers caused them to shut down mid-transmission- the worm was programmed to activate as it was erasing the information from our databanks-, but from what I was able to see before the computers deactivated, the worm was able to send the Aurora mission reports..."

"And what else?" Elizabeth asked, sitting down in her chair as she noted Zelenka's suddenly apprehensive expression.

"The location of most of the worlds on our database," Zelenka said grimly. "I can't be sure which ones got through before the computers were shut down, but-"

"Doctor Weir!" Chuck's voice suddenly said, the technician hurrying into her office with an expression of obvious confusion on his face. "We have a gateship lifting off from the... well, the underwater gateship bay!"

"The underwater one?" Elizabeth asked, turning back to look at the technician in confusion, her mind quickly going over what she remembered of the reports on the submerged gateship bay they'd located underneath Atlantis. "But I thought we hadn't been able to-"

"We haven't," Chuck said, looking urgently back at her. "That's why I thought you should know; whoever took the jumper took care not to let us know they were using it until it was actually some distance away from us, and now-"

"Atlantis, this is Jumper Alpha Omega One," a familiar voice suddenly said over the now-reactivated radio, sounding almost grimly jocular as it spoke.

"Jo- Phantom?" Elizabeth said, quickly reminding herself that she was in public as she activated her radio to respond to this sudden message. "What are you-?"

"I'm sorry about shutting down the city's computer network like that, but I had limited time available to me after I realised what the Wraith were up to; I had to move quickly if I was going to stop them getting everything they were after, and terminating Atlantis's ability to send that information before it was completed was all that I could think of," John's voice interrupted, his tone an abrupt professional one that he never used when the two of them were alone. "Given the contents of the downloaded files, I'm sure you can agree with me that our immediate priority right now should be to prepare for the worst and send Orion and Daedalus after the hive as soon as possible; I'll do what I can to catch up- following them shouldn't be too difficult; it's just issues like precisely where they'll stop that's the problem-, but considering that this thing's a prototype I won't be able to push it as quickly as I'd like-"

"Hold on; what are you talking about?" Elizabeth asked, trying to get a word in to be sure she understood what her mysterious masked friend was saying to her.

"The Wraith have acquired the information they need to make their hyperdrives inter-galactic from the Aurora files, and at least the hive you've been working with for the past few days- and maybe one or two more- are now on their way to Earth," John replied, his tone a simple one that left no room open for hesitation or doubt. "Get in touch with Daedalus and Orion and send them after the ship as soon as possible; I'll do what I can, but even if I catch up with the hives I'm definitely too small to do that much to them right now."

"But-" Elizabeth began, before the radio connection suddenly terminated, Chuck turning to look at her in surprise a few moments later.

"The gateship just... went into hyperspace," he said, his confusion clear as he spoke.

"Hyperspace?" Elizabeth repeated, before she turned to look at Zelenka inquiringly; she acknowledged that it was a stupid thing to focus on, but she couldn't do anything about whatever the Wraith had received in that last transmission. "Would that even be possible?"

"With the right modifications to the engine system, I suppose they could go into hyperspace, but we have no way of knowing what those modifications would be; analysing the possibility of adapting the gateships for hyperspace hasn't come up so far-" Zelenka began.

"Atlantis, this is Daedalus," Colonel Caldwell's voice suddenly said over the radio, the transmission cutting off Zelenka's explanation. "Our hive-ship turned on us- along with the hive we were planning to test the retrovirus on- and then they both jumped into hyperspace before we could do much damage to them in return."

Elizabeth's blood ran cold, all thoughts of what John might have done to that gateship forgotten.

She didn't need to be a diplomat to know that, in a situation like this, it was what wasn't said that mattered almost more than what was said.

"Where are Doctor McKay and Ronon Dex?" she asked.

"They were still on the hive-ship when it went into hyperspace," Sumner's voice said, answering Elizabeth's next question before she'd even asked it; at least he was still here, even if she would have preferred John to be at Atlantis if she'd had a choice between the two of them. "We're on our way back to Atlantis with injured, but-"

"We already know where they're going," Elizabeth said, her voice grim as she exchanged brief glances with Chuck and Zelenka before she continued, recognising from their lack of objection that they understood and agreed with what she was about to do. "They were apparently able to transfer a virus into our systems when they gave us the information on their ships earlier; this virus allowed them to download the information we acquired during the Aurora mission, which we believe they've used to upgrade their hyperdrives to inter-galactic, and we have reason to believe that they're on their way to Earth."

"Earth?" Sumner repeated, shock clear over the connection before he continued speaking again, this time in a more professional tone. "Have Major Lorne prepare Orion to pursue and engage those hives as soon as we get back; the crew are doing what they can here, but it's unlikely that Daedalus will be in any position to begin pursuit immediately after the damage we took here."

"Understood," Elizabeth said in response. "I'll see you when you get back."

She didn't need to look at the other people in the control room as she terminated the connection to know that they were thinking the same thing as her; in this kind of situation, Daedalus's condition almost didn't matter.

As powerful as Orion was, it was still only one ship in an ambiguous state of repair- they had most of the systems up and running, but they had no way of really knowing how many crew were needed for it to operate at its peak- up against two Wraith vessels at full strength; nobody could be blamed for her wanting to ensure that Orion wasn't alone in its upcoming fight, particularly not with the current stakes facing them.

After she received the news that Daedalus had landed and reapirs had already begun on the damaged ship, Elizabeth wished that she could think of any kind of alternative course of action beyond the one that she was committed to at the moment; the idea of ordering people to what would probably be their deaths just to be sure was something she'd never wanted to resort to...

But, in the end, she also knew that she didn't have a choice; even if she'd received this command because some politicians wanted to 'play nice' with each other, John had been right when he'd told her that she wouldn't have kept this job if the right people didn't think she could still do it.

She might not be a military commander, but she was the leader of the colony that Earth had established on Atlantis, and she was going to fulfil that responsibility, no matter how distasteful she might find it.

"Colonel Caldwell, Colonel Sumner," Elizabeth said, looking over at the Daedalus and Atlantis military commanders as they walked up the rear stairs into the control room. "What's the status of the repairs?"

"Ongoing," Caldwell said, nodding grimly in response to her question, clearly deeply affected by recent events. "We lost a few key personnel in the attack."

Elizabeth wished that her primary emotion at that news wasn't relief that so far nobody she knew well had died; as a leader, she naturally felt responsible for every death that took place in Pegasus as a result of her decisions, but that didn't mean that she wasn't allowed to grieve for some deaths more than others.

"I'm sorry," she said, hoping that this apology would be enough as she turned to lead the way into her office, Caldwell, Sumner and Teyla close behind her as Zelenka joined them.

"I wish we had the time to mourn our losses, but the fact is that we don't," she said, walking into her office and taking up position behind her desk, grateful for Teyla's presence alongside her as she spoke; even if they weren't as close as she might like, she still considered the Athosian a close friend, and she needed that kind of reassurance at a time like this. "I just briefed General Landry. We're to check in in an hour and advise him of our response to this."

"I can have Orion ready to go in an hour or so- according to McKay's last report the last bits of programming had been written, and new power regulators and all other necessary systems have been installed-, but Daedalus won't be able to muster up much of a response-" Sumner began.

"I want you to redeploy both ships immediately," Elizabeth interjected before she could give herself any time to question the decision that she had just made.

She wasn't sure if it should be seen as a good thing or a bad thing that she thought of John when she gave that order; she was trying to act the way he would act in a situation like this, but whether it would have any effect was another matter.

"Excuse me?" Caldwell said, eliminating Elizabeth's hope that she could do this the easy way. "Both ships? You want me to send Daedalus out as well?"

"So long as they're still in striking distance, we have to at least try," Elizabeth said, keeping her tone solemn and level; raising her voice would encourage arguments, but she'd learned long ago that staying focused while speaking had a better chance of accomplishing her goal through sheer intensity of will.

"You know we can't intercept them in hyperspace," Caldwell said, a slightly incredulous tone in his voice at what he was being asked to do.

"Doctor Zelenka?" Elizabeth said, looking over at the Czech scientist to answer that particular question.

"Well," Zelenka began, "obviously they've upgraded their FTL drives using the information they were able to steal from our database- the Aurora mission reports-"

"Obviously," Sumner interjected, glaring briefly at the scientist, clearly hoping he'd get to the point (Not that Elizabeth could blame him; when Zelenka had first mentioned a means of tracking the Wraith, she'd been as eager for him to explain what he meant as anyone, even if she was slightly ashamed to admit that she'd been grateful for the news that she would be able to help John).

"However," Zelenka continued, as though he'd been about to move on to this topic on his own, "the ships are organic in nature; they will need to make brief pauses to recover from the effects of hyperspace radiation."

"Where and when?" Elizabeth asked, even as she mentally noted that this explained John's comment about knowing where they were going to stop; he must have some idea about what kind of stresses Wraith ships could endure from previous encounters with them (She momentarily wondered why he hadn't mentioned it, but dismissed that thought quickly enough; it wasn't like that kind of information would have ever been useful to them before now, so there would have been no reason for John to bring it up).

"Uh, yeah," Zelenka said, slightly shaking his head as he went over the possibility in his mind before he shrugged slightly. "It will take some time to calculate."

"Go," Elizabeth said, nodding grimly at the scientist, Zelenka simply nodding in confirmation before he turned around and walked out of the room (Elizabeth supposed that they should be grateful that the Wraith were heading to Earth; at least they were likely to simply follow Daedalus's usual route to and from the Milky Way galaxy- something about those 'Langara points' that McKay had told her about when they'd first discovered that satellite affecting the gravity in space meant that there were only a certain number of routes you could take to reach certain locations-, thus limiting the areas where they might decide to stop).

"Look, Doctor Weir," Caldwell said, looking back at her as Zelenka headed off to his lab, "I want to go after these bastards as much as you do, but the Daedalus is in no position to fight right now. Our shields are severely depleted and several decks are inaccessible; even if we could catch up with them, I don't know how long we'd last."

"Which is why I'm committing the Orion as well," Elizabeth began.

"Then why even bother with Daedalus?" Caldwell asked, still staring intently at her. "From what Marshall's told me, Orion's in excellent shape-"

"It's still not been tested in combat; regardless of the quality of the repairs that the Taranians and the Phantom have performed on it before we got a chance to work on it ourselves, I don't want us relying exclusively on a single ship when faced with stakes like this," Elizabeth interjected, staring grimly at Sumner and Caldwell, relieved to see Sumner nodding slightly at her assessment of the situation; he might not be happy with her decision, but at least he could appreciate why she had made it. "You've got some time until Doctor Zelenka can finish his calculations to deal with the worst of the damage right now; anything else you should be able to handle on-route."

"And if we can't?" Sumner asked

"Currently," she said, walking out from behind the desk to look more directly at the two colonels, her face betraying no sign of whatever personal reasons she might have for ordering them on this particular mission, "Stargate Command has no vessels capable of engaging the hive ships before they reach Earth. They cannot be allowed to get that far, Colonel."

For a moment, Caldwell simply stared at her, swallowing as he briefly looked away, exchanging brief glances with his Atlantis counterpart before he stared back at her.

"You're aware that there's a good chance this won't end well," he said at last.

"I am," Elizabeth replied, wondering as she spoke why the silver face of a masked man with some unspecified injury underneath that mask was the first thing that came to mind when he mentioned that; she was actually ordering Caldwell and Sumner to mount what could be considered a suicide mission, she should be worried about them...

"There's still repairs that need to be made," Caldwell said after another contemplative pause, glancing briefly over at Sumner. "Can I-?"

"Everything we can spare is at your disposal," Sumner confirmed.

"Do what you have to do," Elizabeth said, offering her own support for the two men as Caldwell and Sumner walked away, leaving Elizabeth to exchange grim glances with Teyla as she processed what had just happened.

She might have Sumner's support regarding her recent decision- or at least she didn't have his opposition; where Sumner was concerned the two amounted to basically the same thing in her experience-, but that didn't mean she was happy about it; she hadn't even realised how much she'd come to depend on John's faith until he wasn't here to give it to her.

It wasn't that she couldn't make decisions without him- their argument over Michael proved that-, but she would have just felt happier if he'd been there to talk to; the simplicity of the faith he'd always had in her always helped her feel... better about herself, somehow.

Right now, however, all that she could do was wait and hope that, wherever John was, he knew what he was doing; if Caldwell and Sumner couldn't get their only two available ships ready in time, the man who'd defended the Pegasus Galaxy for the last decade or so could be Earth's last hope.

As much as she believed in John- to a point where even she was surprised at the extent of the faith she had in him-, there was only so much one gateship could do against two Hives...

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