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Author's Chapter Notes: AN: I had to make a short jump forward for this chapter, but it wasn't that much further than the one we experienced in the episode itself (Even with the Asgard helping Elizabeth and Woolsey return to Atlantis, they can't have been that much faster than the ZPM-enhanced Daedalus, and it still would have taken a few days for the Daedalus crew to get sufficient control of that Wraith ship to take it back to the city)

AN 2: Sorry about the delay in this chapter; real life and writer's block, you know

As she sat in her office in Atlantis, Elizabeth wished that she could bring herself to feel more relaxed now that she was back in her home (Even now, a part of her almost couldn't believe how comfortable she felt in this alien city after less than two years in Pegasus; she was in a city that defied almost everything she had come to expect, at threat from an army of life-sucking aliens. patrolled by a man in a mask whose real name may still be a mystery to her, and she still felt safe here?); the mere thought of Richard Woolsey's continued presence in the city made even the possibility of relaxation near-impossible.

Getting back to Atlantis hadn't actually been that difficult- they'd called in some favours from the Asgard to provide a ship that could take her and Woolsey back to the city in a few days-, and at least Orion and Daedalus had come through the recent battles relatively intact, but she had more than one problem facing her right now. Not only was there the obvious issue of Woolsey carrying out an evaluation for the IOA, but there was also the more personal problem of John's continued absence from the city; nobody had seen any sign of him since he had rescued Ronon and McKay from the Hive, even with the entire city on alert in case any other Hives or any kind of ship appeared anywhere within range of Atlantis's sensors.

Right now, she just wished that she could get past the varying degrees of fear facing her and get back to dealing with a crisis that she could actually deal with herself; maybe it was John's attitude rubbing off on her, but this current mess with the evaluation and the possibility of her losing her command of the city was frustrating her precisely because she had absolutely no way of resolving it quickly and efficiently other than just letting the situation play out however it would.

She supposed the thing that made it worse, of course, was the fact that two of the most senior members of the expedition- even if one of them was only peripherally affiliated with Atlantis on a semi-regular basis- couldn't be guaranteed to speak up in her favour. Caldwell had a certain respect for her abilities, but she wasn't entirely certain how much of that respect was due to her decision to keep Sumner on as the expedition's military commander rather than respect for her as a person, and Sumner himself, while loyal to the chain of command, still expressed the occasional doubt about her occasional dependence on the Phantom to help them out when the situation they were facing became particularly desperate (She was just grateful that he hadn't expressed any objection to their recent alliance with the Wraith; at least he recognised that they'd all been at fault rather than trying to absolve himself of blame by pinning it all on her).

She had tried to hold the city together in the face of the ever-increasing threat of the Wraith, and now, here she was, facing the possible end of her career in Atlantis, and the people whose opinion would really make an impact on the IOA probably wouldn't even care enough to support her.

She supposed that she should just be grateful that they'd managed to destroy both Hives without resorting to more desperate measures like, for example, trying to defeat the Wraith with the retrovirus; even if it had actually worked, it would have left them with far more problems as they tried to figure out a way to make the retrovirus's effects permanent before the human Wraith regressed back to their original natures like Michael had, to say nothing of how the IOA would have reacted to them having to deal with that kind of issue...

In the end, however, what was almost the most disturbing thing about her current situation was that she was regarding a man in a mask as a regular source of stability in this increasingly chaotic world.

As much as she might have laughed at the idea in the past- if she was honest with herself, in the past she would have found it disturbing to see any other person display this level of faith in someone under these circumstances-, it didn't change the facts; out of everyone she worked with in Atlantis, the man she relied on the most had never shown her his real face and she didn't even definitely know his real name.

Nevertheless, even if the IOA or Stargate Command weren't entirely comfortable with his presence, Elizabeth would always believe in John's loyalty to Atlantis; he had done and risked too much for their sakes for her to ever doubt him, no matter how much her superiors back on Earth might oppose his presence.

She just wished that she knew where he was now...

"Doctor Weir?" Chuck suddenly said, breaking into her train of thought as he stood anxiously at her door.

"What's wrong?" she asked, looking uncertainly at him; everything seemed fairly calm outside, so it probably wasn't an approaching Wraith vessel, but in an unknown location like Pegasus the list of things that could cause concern without being obviously dangerous were relatively high.

"We're receiving... well, we're receiving a rather strange signal on the long-range sensors," Chuck said, looking suddenly awkward as he looked at her. "It's basically just some kind of intense energy pulses from some distant part of the galaxy- we'd probably assume it's some kind of natural phenomenon if they weren't so regular and coming from subspace-, but... well, they seem to be an SOS."

"An SOS?" Elizabeth repeated, sitting up sharply before she got up from her desk and walked into the main control room, where McKay, Sumner and Caldwell were already staring at the main display screen, which currently showed a basic galactic map with what she could only describe as an intermittent beam coming from one corner of the map.

"What is it?" she asked, looking at her chief scientist.

"In basic terms, something's churning up subspace to send us a seemingly random signal across a great distance," McKay explained. "It's basically similar to old radio transmissions back on Earth; before we had the ability to send anything more sophisticated like actual speech, we just relied on basic signals like this one."

"That's actually one of the things that has us concerned," Sumner said as he turned to look at her, even if his tone made it clear that 'us' referred primarily to himself and Caldwell. "Considering recently events, we have to consider the possibility that the Wraith picked up details of how to use this code from the information they acquired during our brief alliance-"

"Oh, of course; they looked up a code that is so old as to be virtually obsolete, and then choose the most basic pattern in the book," McKay said, shaking his head in frustration. "I know I'm not a military genius, but I studied the information about what they stole, and they did not take anything to do with our ability to communicate; even if they did, anyone who knew Morse code without knowing the background information would try and use something more sophisticated because they'd think we'd be more likely to fall for it. The only people who'd send such a basic message would be people who came from here without knowing anything more than the basics, and they wouldn't send something like that unless they really had no other way to get in touch with us."

Elizabeth was just grateful that McKay didn't say anything about the possible identity of the sender; regardless of how much help he'd offered them in the past, the possibility that they were being contacted by the Phantom might make the colonel a bit more reluctant to take action...

"All right," she said, looking over at her senior staff. "What are our options?"

"Well, Orion's more advanced, but Daedalus is probably better for getting in and out undetected; I've been working on a way to modulate the shields to absorb Wraith scans so that it looks like we're not there, but the catch is that it'll leave us vulnerable to attack if we're spotted and can't switch in time-" McKay began.

"Then we'll just have to ensure we aren't spotted," Elizabeth said, looking firmly at McKay before she looked over at Sumner and Caldwell. "We'd better get moving; the sooner we can determine where that signal came from, the better."

"Understood," Sumner said, standing up as he and Caldwell headed for the door to the conference room.

"The rest of you..." Elizabeth began, turning to address the other three members of Sumner's team before she realised the pointlessness of it; as a professional soldier, Sumner had made it clear more than once that he wouldn't take his team with him in a situation where they weren't needed, and with the Daedalus crew available this was definitely one of those cases.

"...just do what you can here," she finished, shrugging slightly uncomfortably at them out of a lack of anything else to say or do.

"And... send a series of pulses back," she added, looking over at Chuck with a slight smile even as the rest of her staff left the room, grateful to remember that there was something she could do in this whole mess. "If there's someone sending that, we should let them know we're on our way."

They might not be able to receive or understand it- if someone was sending something like that, it seemed likely that their communication options were limited-, but she had to do something to let the person at the other end know that they weren't alone, particularly if it was who she thought it was...

"Ugh..." Ford muttered, shaking his head in frustration, his movement limited by the tendrils that continued to grow around his body.

"Well?" John asked, looking hopefully at the face of the still-mutating lieutenant, trying not to pay too much attention to the mass of tendrils that were still emerging from his body; if he didn't think too much about it, it was easier for him to deny the scale of what he was facing and focus more on what he could control.

"I'm..." Ford said, wincing slightly as he closed his eyes, a focused concentration clearly visible on his face, before he opened them and looked at the other man. "It's confusing, but I'm getting something back... three long pulses... a long and a short one... three long ones..."

"'On our way'," John said, smiling slightly as he looked at Ford. "It's the signal for 'On our way'."

"There's more-" Ford began.

"What you've given me is enough to know that's what the rest of the message would be," John said, smiling reassuringly at the younger man. "Just hold it together and stay calm, Ford; I'll just go and make sure that Michael's still locked down, and then we should be ready to move on when everyone gets here."

The hyperdrive-capable gateship might still need to be found- he doubted Michael had taken it too far from here, but it wasn't like he'd had the time to look and see what else Michael had done to it even if he couldn't fly the thing on his own when Ford was the first priority-, but if he had his way, they were all going to get out of here...

It was only when he walked out of the room where he'd been staying with Ford and saw Michael standing in the corridor with a drawn weapon that looked like a sharper version of the Wraith stun pistols that he realised that he'd spent too long with Ford; why the hell hadn't he tried to lock the damn door?

"Oh," he said, deciding to go with feigned nonchalance and hope for the best; given the Wraith's arrogance, acting like you weren't afraid of them was often the best way to get them to make mistakes. "You woke up."

"I did," Michael replied, glaring resolutely at John as he flexed his fingers in anticipation before he charged towards his opponent. John barely managed to shift into a combat stance that allowed him to throw Michael off to the side before the hybrid could grab him by the throat, leaving the hybrid pinned to the wall as the masked man stared at him.

"Damnit, Michael; would it kill you to stop acting like it's kill or be killed here?" John yelled, glaring in frustration at the hybrid. "Is it such a crime for people to want you to become something that doesn't feed on people?"

"When it involves destroying who I am now, yes," Michael practically spat at the Phantom, reaching up to grab John by the upper arms, gradually pulling the arms holding him down away from him. "You cannot simply cure what I am like a disease-"

"Your body can't cope on its own; I call that a disease-!" John protested, still straining against his opponent's grip.

"It is no more a disease than your need to eat to survive-" Michael began, glaring firmly at John as they continued to try and force the other to release their grip.

"Which doesn't involve taking what other sentient beings need to survive themselves; if you can't survive without others dying for you, I'd call that a problem!" John countered, before he rolled his eyes in frustration at the increasingly repetitive nature of the current debate and rammed his knee upwards between Michael's legs; as much as the moral debates would be interesting mental exercise in other circumstances, right now his priority was Ford. As Michael's grip instinctively lessened as he moved to clutch in pain at the part of himself that had just been hit, John shoved him away before lashing out with a spinning kick- an extravagant move, but he liked the effect it created when he did that with the cape- that struck Michael in the face, sending him flying backwards into the nearest wall.

"Can't we just talk about this?" John asked, glaring in frustration at Michael. "We are trying to help you here-!"

"And who is to say that this is not helping Lieutenant Ford, if we use your defence?" Michael asked, taking a small object from his belt and holding it up in front of himself. Before John could react, Michael pressed a control on the small device, and suddenly John heard a loud scream of agony from down the corridor where he had left Ford earlier, far more intense than the scream he'd heard earlier.

"NO!" John roared, firing a quick 'force-blast' at Michael- he wasn't sure what the technical term was, but it basically dialled down the gun's energy output so that it only generated a brief burst of energy that left you feeling like you'd been hit with a large beanbag; solid enough to knock you down, but not to the point that you'd break something in the process-, that sent Michael flying backwards, only for John's smile to turn into a frustrated glare when he realised that Michael had just fallen through a door. Even as John started to charge towards the door, Michael somehow managed to raise his head enough to glare at John and kick the door shut, a clicking sound emerging from the solid door that represented the universally-recognised sound of a lock clicking into place.

Cursing as he slammed his palm against the now-sealed door in front of him, John paused to shoot the lock- if he couldn't get Michael back to Atlantis for treatment willingly, and the guy was this willing to delay him getting picked up, the bastard could just stay here and get blown to smithereens- before hurrying back to check on Ford, praying that his worst fears for the younger man weren't about to be realised...

As he arrived back in the room where he'd originally left the lieutenant, however, John quickly realised that he was indeed dealing with the worst-case scenario. When he'd activated whatever that device had activated, Michael had either triggered some kind of implant or just activated something connected to the tendrils that John had missed in his earlier examination of Ford; judging by the faint steam coming off his body, Ford had just received a not-inconsiderable electric shock, with the result that his pathogen-infected body had automatically tried to respond to the pain in the manner that it was currently best suited for, thus causing the mutation he was currently undergoing to accelerate significantly in order to keep Ford's body in working order.

Whatever it was that Michael had activated, the result of it was that the lieutenant's mutation was now progressing at a far more rapid rate than it had been before he'd taken action, which meant that John's chances of getting the lieutenant back to Atlantis before the mutation had progressed to a point beyond any cure that they might be able to give him would reverse the process...

"It's... not... good... huh?" Ford said, his every word an obvious strain, as though he was not only having trouble speaking but was also having trouble remembering what word to use to convey what he wanted to say.

"No," John said, shaking his head grimly as he looked over Ford; tendrils actually seemed to be emerging from Ford's fingers as though they were extensions of his body now, rather than just something that was growing out of him. "Whatever Michael did to you just now, the pathogen was able to use your weakness to gain a better grip on your physiology- probably 'decided' to evolve into something that could better cope with what you were going through-; as far as I can tell, you're..."

He fell silent, trying to figure out the best way of saying this, but Ford beat him to it.

"In other words, I'm screwed, huh?" he said, looking grimly at John.

"Yeah," John said swallowing awkwardly as he looked at Ford, his eyes earnest behind his mask. "Trust me, if there was anything that I could do to help you, I'd do it, but the shock you received has accelerated the spread of the pathogen; even if you're mentally more in control of yourself than I'd expect, you're going to succumb to this thing before anyone can do anything..."

"Fine," Ford said, looking grimly at the other man. "Shoot me."

"What?" John said, his eyes widening in horror. "I can't-"

"Shoot me!" Ford said, glaring at the masked man. "If you can't stop this, kill me while I'm still able to think about it; I'm not going to become a fucking hive-ship!"

"I can't even guarantee you'll be able to die in this shape-" John began, trying to find a way around what he was being asked to do (The fact that the pathogen might heal anything he did certainly helped him in that regard; he couldn't predict what the consequences of a direct attack would be when Ford was in this kind of shape).

"Take my fucking head off, then; just don't let me die like that!" Ford said, raising an arm a few inches before giving up when the tendrils prevented him from moving it any further, terror obvious on his face. "I don't care what it takes; I can't lose myself to this!"

For a few moments, John could only stare at Ford in silence, his mind racing as he tried to figure out what he could do next even as he knew that nothing he had available would make any difference to the situation at hand, until he finally raised his gun with one hand and drew his sword with the other.

"Shot to the head should put you down, and then I cut it off before the pathogen can start to heal anything," he said; no matter how grisly it was, Ford deserved to hear what was about to happen to him. "Lieutenant Ford, believe me, if there was any way I could cure you-"

"I know..." Ford said, smiling slightly at him. "You're... the Phantom... right? You save people..."

"And I will save Atlantis," John said, nodding solemnly at the other man. "Until I don't have the life in me to do so, I will protect that city from whatever will threaten it in the future."

"Good..." Ford said, smiling briefly at the other man before he closed his eyes and laid his head back against the table.

Not giving himself time to hesitate, John fired the gun with one hand before he thrust his sword forward, turning away from the sight and only allowing himself to briefly register the sickening slight thump as something hit the floor.

With that bloody business done, he left the room, sealed the door behind him, and hurried down the corridor, pausing only just long enough to check each door he encountered until he found the one he was looking for; a large, open room with a ceiling that had clear signs of moving parts within it, along with the welcome sight of the hyperspace jumper in the middle of the room along with a couple of Wraith darts. John briefly noted that the darts appeared to have started to decay slightly- most likely they had been left here in this base when the Wraith had originally abandoned it for whatever reason they'd left it-, but pushed that thought aside as he entered the jumper, his attention focused on making sure that everything was where it should be. From what he could determine, a couple of crystals relating to the ship's databanks had been removed, but they didn't control anything vital and they would certainly get destroyed when the Atlantis expedition reached the base.

Settling down into the chair, John started the ship's engines, turned the force field up to its strongest setting, and tore out of the base, shattering the ceiling as he left; he wasn't going to stay in that place of death for any longer than he had to. After taking a moment to ensure that the base's power supply was still active- it wasn't that much power, but on a planet with no other forms of technology it wouldn't exactly be hard to find it-, John turned around and set a course back towards Atlantis, determined to leave the whole bloody mess behind him.

A few hours later, as Elizabeth stood on her balcony, she couldn't believe that she was actually still here.

The exact origin of the SOS was still a silent question-mark- she, at least, was fairly certain that she knew what had sent the original message, even if she'd been fully aware that she couldn't provide anything to support that theory-, but they'd at least been able to destroy the facility after the Orion had arrived there and sensors had confirmed that the only living things in the base were a Wraith and the anomalous life-readings that they'd learned signified the presence of Wraith ships; according to all reports, the attack on the base had been so thorough that nothing was left standing.

Add in the fact that Woolsey's report had favoured her remaining in command- even if he'd slightly bent the rules by claiming that she'd given orders to fire on the base immediately after the Orion dropped out of hyperspace when she'd actually requested that Sumner wait to confirm that there were no humans alive in the base before taking action-, and things were generally going rather well for them after their recent run of bad luck. The Wraith were down two hive-ships, Michael was gone, and Atlantis's location remained secret; all in all, on a galactic scale, things in Atlantis had never been better.

Almost never... Elizabeth thought to herself, allowing herself a momentary sigh as she stared out at the sea before her.

Even after everything else they'd accomplished, she didn't know what had happened to the Phantom... to John. Sumner and the others might not be that concerned about it- Teyla didn't seem to think that the Phantom was even capable of dying sometimes-, but the fact that she still hadn't heard from him since the last message he'd sent before leaving Atlantis was not encouraging...

"Hi, Elizabeth," the voice she'd been waiting to hear said from behind her.

"John!" Elizabeth said, not even bothering to suppress her grin as she turned to look at him, only for her smile to falter at the dejected expression on his face. "What... what's wrong?"

"Ford was there," John said, his expression grim under the mask as he looked at her. "Michael had captured him."

"Ford?" Elizabeth said, her eyes widening incredulously. "But-"

"I don't know how, but he was there; Michael had infected him with some kind of freaky Wraith pathogen and was working on mutating his body into something that... well, it wasn't human," John said, sighing as he walked over to lean against the railing, a defensive aspect to his posture that Elizabeth didn't need her long experience with body language to read. "I did what I could... but then Michael activated something that forced the infection to spread..."

He swallowed slightly, his jaw tightening as though trying to prepare himself for the worst, and then he looked back at her, clearly wanting her to understand what he was about to say. "I couldn't save him."

Elizabeth could tell that there was more John wanted to say about that particular topic, but she didn't give him the chance to say it; on impulse, without even thinking about it, she walked up to him and wrapped her arms around him, giving him as reassuring a hug as she could manage.

"You did everything you could, John," she said, smiling slightly as she felt him wrap his arms around her in response to her efforts. "If you could have saved Ford, I know you would have; don't beat yourself up because you failed."

It wasn't exactly the best therapy she could provide for him given his obvious grief at his failure to save the former lieutenant, but, in his current state, it was the best that she could do for him.

She knew so little about this man who'd dedicated his life to protecting the city that they'd come to call home long before any of them knew that it had any kind of existence beyond the ancient legends, but what she knew of him left her reassured that he could be trusted to do everything in his power to help them; that was all that anyone could rely on in a world so far outside anything they knew.

Even if she couldn't safely convince anyone else to have her level of faith in him, she could believe in him...

AN 3: Hopefully, I'll have the next chapter up sooner; the current plan is to include John's thoughts on seeing SG-1 during 'Pegasus Project', and then the next chapter will explore his thoughts on a very particular git...

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