He was out of bed in a second, and had the lights on before another three had passed. It took several more before his eyes adjusted to the sudden brightness.

Elizabeth was curled into a ball on her side, hands clamped over her head and her eyes screwed shut. And she was still screaming, unearthly shrieks that didn't even sound human.

After calling her name several times and getting no response, John scrambled to find his headset. "Medical emergency in Dr. Weir's quarters!" he barked, then yanked on his sweatpants before trying to get Elizabeth's attention once more.

He doubted it had anything to do with his efforts but she had stopped screaming by the time the medical team arrived. She was still curled in on herself and hadn't opened her eyes, but her cries had faded to whimpers that left him feeling helpless.

"What happened?" someone asked over the roar of blood in his ears, and John shook his head.

"I don't know. We were asleep and the next thing I know she's screaming, like...." He faltered; he had no idea what could prompt a sound like that. "She hasn't said anything. I'm not sure she even knows we're here."

Another quiet whimper caught his attention and John slipped between the people working on Elizabeth. He took her hand, careful of the equipment that was already attached to her, and rubbed his thumb over her knuckles. Maybe she'd know he was there.

"Hurts."

The word was barely more than a breath, almost inaudible against the noise of the medical team. "What hurts, Elizabeth?" he asked, bringing her hand to his chest.

"Head," she whispered. "Too many voices. So many...."

She trailed off and John thought she might have fallen asleep; at least, he hoped it was only sleep.

The med team loaded Elizabeth onto a stretcher and John looked around fleetingly for his t-shirt before remembering that Elizabeth had claimed it to sleep in a few hours earlier.

Bare-chested and acknowledging that there would be no escaping the rumour mill anyway – and that at the moment, he couldn't care less – John followed the swiftly moving group towards the infirmary.

**

"Has there been any word?"

John blinked tiredly at Teyla. "She's stable, whatever that means." He nodded a greeting to Ronon, who threw him a t-shirt before flopping into a nearby chair. "They're running a bunch of tests." For all the good that seemed to do, John reflected bitterly before forcing the thought away.

"We will wait with you."

"You don't have to—" His protest died at the gentle touch of Teyla's hand on his forearm. "Right. Okay." She started to pull away but he caught her fingers with his own before she withdrew completely, squeezing his thanks. Then he settled back in the chair, letting his head thunk against the wall behind him as his eyes slipped closed.

He didn't know how long he drifted before quiet footsteps and Keller's voice had him snapping awake. "Colonel Sheppard?"

He stood, looking at her silently.

She cleared her throat. "Dr. Weir is asking to see you."

John merely nodded as he pushed his way past the doctor, hearing Teyla ask after Elizabeth as he made his way to her bedside. God, he'd already spent too much time here. She didn't deserve this.

Her eyes were closed when he approached and he paused, suddenly unsure. But then she looked at him, brightening at the sight of him, and all his uncertainty disappeared.

"How're you doing?" He took her hand, using the other to brush her hair off her face before leaning down to kiss her forehead.

"They're coming, John." He pulled back a little to study her face; she was pale but alert, her expression somewhere between fearful and determined. "The Asurans. They've found us, and they're coming."

"How do you know?" He wasn't sure he wanted to know the answer.

She lifted the hand he wasn't holding and touched the side of her head. "I can hear them."

**

John strode into the briefing room and started talking before he'd even sat down. "Here's where we are," he started, and the little bit of chatter in the room died immediately. "For those of you who might not know, Dr. Weir was admitted to the infirmary at about 0400 with a severe migraine due in part to 'voices'. At 0500 she informed me that the voices she heard were those of the Asurans, who have pinpointed our location and are not only in pursuit, but gaining on us. Tests confirm the presence of nanites in Dr. Weir's brain. I don't pretend to know what's going on, but apparently it's plausible that she is, somehow, 'hearing' them."

To his left, McKay straightened. "Well you see—"

"Not now." John cut him off with a curt wave, looking around. Gathered around him were his team and Lorne's, everyone watching him with similar expressions of solemnity. "Best guess is we have a day, maybe two, before they reach us. We can't outrun them and with our depleted ZPM power we wouldn't withstand a tactical assault for more than a few hours." He paused for a second to let that sink in. Then he leaned forward. "We need options."

**

Their meeting was interrupted three hours later by Chuck, who sounded wary. "Colonel Sheppard, sir?"

John stepped away from where two Marines were arguing the merits of using cloaked puddle jumpers to deliver bombs to the Asuran ship. He touched his earpiece. "Go ahead." Chuck had been instructed not to disturb him except for emergencies, so this couldn't be good.

"Dr. Keller is looking for you, sir. Dr. Weir is missing."

John's hands clenched. "What do you mean, missing?"

"She left the infirmary and no one knows where she's gone. She's not answering her radio."

John swore under his breath; with those nanites in her head, Elizabeth was potentially a security risk. He should have posted a guard by her bed. Shit.

"Lock down the city," he instructed, catching Teyla and Ronon's eyes and jerking his head toward the door. "Order off-duty and non-essential personnel to their quarters and have everyone else check in. Compare the locations of confirmed personnel with lifesigns readings and let me know of any discrepancies. Sheppard out." He shifted his attention to Ronon and Teyla. "Elizabeth's missing. There's no way of knowing if she's still... her." His teammates nodded and moved for the exit without a word. John breathed in. "Be careful," he said softly, and he wasn't talking entirely about their own safety.

**

A half-hour of fruitless searching was interrupted by Chuck. "Colonel Sheppard? We think she might be in a lab near the west pier."

John frowned, not sure what to make of that. It was something of a relief to finally have an idea where she might be, but he couldn't imagine why she would be in an abandoned lab.

With the transporter, it only took him five minutes to reach the lab almost halfway across the city. He paused at the door only long enough to draw his weapon and then entered without waiting for backup.

She was standing with her back to him, looking like she was working on something though he couldn't say what, since it was blocked by her body. "Elizabeth?"

She glanced over her shoulder. "John." Her inflection seemed a bit off but she turned back to whatever she was doing without saying anything else. Maybe he'd imagined it.

John readjusted his grip on his weapon and licked his lips. "Elizabeth, I need you to step away from the bench."

She kept working. "I can't. I have to finish."

John closed his eyes briefly. "Finish what?"

She hesitated. "I'm not sure. I just know that I have to complete it now."

"Eliz—"

"There's no time!" She spun to face him, her expression equal parts determination, desperation, and fear. "Please, John. Let me finish."

"I can't." He cut off the protest he could see coming. "You don't even know what you're building. You've got nanites in your head and you're hearing voices. I can't just let you keep working on something that could blow up the city for all you know."

She went rigid for a moment and then all of a sudden slumped. "You're right," she murmured. She set the tool in her hand carefully on the bench and took several halting steps in his direction. John activated his radio as he moved to meet her halfway. "Teyla, Ronon, I've got Elizabeth." He reached out to touch her arm, surprised to find her shaking. After a glance at the machine she'd been building he added, "Find McKay and get him to the lab in the west pier." Shifting his attention back to the woman in front of him he asked, "You okay?"

She made a face at him. "Stop asking me that."

"Stop doing things that make me ask." They grinned at each other but the moment of levity quickly passed. "Why are you here?"

Elizabeth shook her head, stepping away. They both looked at the mostly built machine sitting on the bench. She sighed. "I don't know. I was sitting in the infirmary waiting to hear the test results when I got this... urge. A compulsion. I needed to come here. I needed to build that machine. I don't know what it is or what it does but I know exactly what I need to do to create it. It's right here. Step by step." She touched her temple.

John didn't know what to say or do in response to that. He started pacing around the lab, frustrated at all the things out of his control lately.

He heard McKay before he saw him, complaining that he had more important things to deal with than an abandoned Ancient lab. "Over there," John said the instant Rodney came into sight, waving a hand in the direction of the bench. "We need to know what that thing is and if it poses a threat."

Rodney gaped at him for a second. "This lab was inventoried last year. What could possibly warrant bringing me down here when I could be instrumental in coming up with a plan to defeat the Asurans?"

"Would you just do it already?" John asked irritably, exchanging a look with Ronon, who had escorted McKay.

Ronon smirked as Rodney grumbled his way over to the bench. Off to the side, leaning against the wall with her arms folded over her stomach, Elizabeth watched without a word.

John waited impatiently as McKay poked around and muttered to himself. He found some instruments on the other side of the lab and took them back to Elizabeth's machine to take readings, or so John presumed. Then McKay jerked upright, dropped his instrument, and spun around; John prepared to hear that they had a bomb on the verge of exploding. That wasn't quite what McKay had to share, however.

"It's a ZPM," he said, sounding awed. "It's not quite functional and it's not of typical Ancient design but the underlying principles appear to be the same. Where did it come from?"

John jerked his thumb at Elizabeth. "She built it," he said wearily, somehow unsurprised that a woman who didn't understand Rodney's technobabble any better than he did had built a ZPM from scratch in just a few hours.

McKay rounded on Elizabeth, looking like he was about to have a stroke. "You? You built this? But—" He stared at her, the ZPM, then Elizabeth again. "But how?"

She looked exhausted. "I was hoping maybe you could tell me."

**

"We have a plan."

John raised an eyebrow when Rodney didn't continue. "Well?" he prodded, impatient. They didn’t exactly have time to waste.

Rodney seemed to be in a grandstanding mood. "What are the Asurans flying?"

John frowned. "Is this a trick question?" At Rodney's expression he sighed and said, "A ship?"

"But what kind of ship?"

"…One that looks like Atlantis?" He took a shot in the dark, not knowing what Rodney was getting at.

Apparently, he got it right because McKay snapped his fingers and pointed at him, a clear sign of excitement. "Exactly!"

John had had enough. "Get to the point, McKay."

Rodney sulked for a bit but then quickly began explaining his idea. "The Asurans built their ship in Atlantis' image, but it's not an Ancient design. We think it's likely that their ship was built using nanotechnology – essentially, it's composed of inert Replicator 'blocks'."

"How does this help us?"

"The composition of the blocks should match the composition of the nanites that make up the Asurans themselves, which means that the city should be vulnerable to the same weapon that deconstructs the Asurans to their base elements. If we can focus a large enough beam on their ship, it should disintegrate into trillions of tiny, useless pieces."

John looked to Zelenka. "You agree with this?" He'd learned early on that Rodney tended to have way too much faith in his "brilliant" ideas, whereas Radek was often overly pessimistic. The truth usually lay somewhere between the two men's opinions.

Zelenka's response surprised him. "It should work. The problem lies in constructing a directional beam large enough and powerful enough to deconstruct the entire ship."

"But," Rodney continued, "between my knowledge of Atlantis' systems and Elizabeth's freaky new ability to navigate the computer mainframe, we should be able to modify the beam that we used when we saved General O'Neill and Woolsey."

When they came right down to it, John thought, they didn't really have a choice. "Do it."

**

He was reading through the latest reports of Atlantis' repairs when a knock at the door drew his attention. He looked up to find Elizabeth hovering at the entrance to her own office and waved her in. "Hey. Why'd you knock?"

She shrugged, sitting in one of the chairs she had for visitors. "You looked busy. I didn't want to bother you."

He heaved a melodramatic sigh as he spun the laptop around so she could see the screen. "Just wading through reports. How long 'til Keller returns you to duty so I don't have to do this anymore?"

The smile he'd managed to get from her at his complaint disappeared, leaving her looking drawn and pale. In her lap, her fingers were twisting together, a sure sign of her anxiety. "That's sort of why I'm here."

John turned the laptop back around and lowered the lid, pushing it aside. "What is it?"

She was still coiling her fingers into knots. "I've been thinking about the Asurans and how they were able to find us." She drew a breath, avoiding his gaze. "I think it's my fault."

John shook his head, not following her reasoning. "How is it your fault?"

She closed her eyes and lowered her head. "I think they can sense me the same way I can sense them. I can't prove it, but I know it's true. I can feel it." One hand touched her chest lightly, above her heart.

John stood so abruptly that his chair rolled back and crashed into the wall behind him. The sudden need to move was overwhelming and he began to pace the length of the office, running through the ramifications of this new information in his head. This could be very, very bad.

"Can they read your thoughts?" he asked eventually, trying to determine just how much trouble Atlantis was in.

"I don't know. I don't think so, but I can't be sure."

Her voice was quiet, almost faint. John paused to look at her and realized she had folded in on herself, practically huddled in the chair. Questions and fervent pacing weren't what she needed from him right now, he berated himself. Slowing, he dropped into the chair next to Elizabeth and reached across the space separating them to touch her knee. "I'm sorry."

She shook her head quickly. "'S'okay."

"No, I mean—" God, this whole situation was so fucked up and it was all because of him. "I'm sorry for this. All of this. It's my fault."

"John, it's not—"

"It is! All of it. If I'd listened to you instead of Ellis, if I'd gotten the city's shields up just a few seconds sooner, if I'd headed for Earth instead of picking a random direction...." He studied her face, reaching to brush a lock of hair from her cheek. "I'm the one who authorized using the nanites." She knew that, of course, but they'd never discussed it.

Elizabeth took his hand and John squeezed it so hard, he had to be hurting her. "It's not your fault." She sounded so certain and he wanted so desperately to believe her. "When you agreed to Ellis' plan you were doing what you thought was right, what you felt would protect us and Earth. You did what you could to keep Atlantis safe and to get the away from danger." She ran her thumb over the back of his hand. "And I can hardly blame you for choosing to try the nanites. I wouldn't be here right now if it weren't for you."

In his mind he could still see her lying so still and pale in the infirmary, could hear Keller telling him Elizabeth's injuries were too severe and that there was no chance of her ever waking, and he wondered for the millionth time if he'd been too selfish in the decision he'd made. She was here and whole and her, but she was also doing things without knowing how or why and hearing voices and in pain. He'd never stop blaming himself for that, he knew.

"Hey." Elizabeth squeezed his hand and he looked up at her, deciding he had no right to feel sorry for himself when sitting next to her. "You've done everything you could to keep everyone safe, not just the past few weeks but the past three years. Atlantis never would have made it this far without you, John. Never think for a second that I've ever regretted asking you to come."

John wished severely that they were anywhere except the glass-walled office because at that moment, all he wanted to do was kiss her senseless and there was no way she'd let him do that with a potential audience just across the walkway. He settled for a grossly inadequate and embarrassingly tremulous "Thank you," wondering how he'd managed to find complete trust from this woman three galaxies away from the life he'd known.

After an awkward silence John cleared his throat and changed the subject. "So, McKay and Zelenka think they’ve got a plan figured out," he began. Their hands separated and he sat back, trying to clear his head. "They think we can modify the jumpers to emit a directional beam; by surrounding the Asuran vessel and having all the jumpers fire simultaneously, we should be able to destroy their ship."

"How long until the jumpers are ready?" She followed his lead, letting their conversation turn back to work. He wondered if she knew what that meant to him.

"They've already started the modifications. Rodney says they should be ready early tomorrow."

She nodded. "I'm going up with you."

"Elizabeth—"

"I'm going, John. I have to be there."

Damn stubborn woman. "Fine. But you're staying back with Rodney."

She tilted her head in acknowledgement, then yawned so widely he thought he heard her jaw pop. "How long has it been since you last slept?"

One eyebrow arched. "Not as long as it's been for you."

She had a point, he conceded. When he did the math, he figured he'd been up for nearly thirty hours. Before that, he'd only gotten a few hours of sleep before his very long day had begun with the sound of Elizabeth's screams. "Now that you mention it –" he stood, offering Elizabeth his hand to pull her to her feet "—it has been a pretty long day."

"Off to bed, then?" she asked with an impish smile, the one with the dimples.

Prospective audience or not, he risked resting his hand against the small of her back as they left the office. She let him. "Well, that's one idea. But you know, I'm not really all that tired."

"Is that right." John could have sworn there was a little extra swing to her hips as they headed for the living quarters. "Well, I'm sure we can find a way to fix that."

**

At 0700 the next morning, John set his puddle jumper in position and triple checked his controls. Satisfied that everything was ready and there was nothing more he could do until the Asurans arrived, he hit the radio switch. "McKay? How's it look?"

There was no answer for several seconds and the usual nervous anticipation he experienced before missions ratcheted up a few notches. "McKay?"

The answer, when it came, was not exactly reassuring. "Something's not right."

"Care to be a little more specific?"

"I don't know. Something's off about the sensor readings."

"Are they still coming?"

"They're definitely headed here. But there's something...." He trailed off for a second and then added, "Be careful, Colonel."

"Always am," he said flippantly. The conversation ended with the familiar blue flash of a ship exiting hyperspace.

Except it wasn't a ship, at least, not the single city-ship they'd all been expecting. Instead, a smaller vessel shot into view, followed by another and another and another until John lost count. "McKay! What the hell is going on?!"

Rodney sounded panicked. "I don't know! The Asurans must have re-structured their city into dozens of smaller ships."

More quietly, he could hear Elizabeth. "There are hundreds of them."

McKay had apparently forgotten he was on the radio. "They'll be killed."

"Thanks for the vote of confidence, McKay!" Then someone fired the first shot and there was no more time for conversation.

As he always did during battle, John became singularly focused on his target. His sight narrowed to the information his HUD showed him, his mind clear and empty but for the lightning-quick equations needed to lock on to the enemy and fire. Nothing existed except for him and his prey.

It could have been minutes or hours later – time held no relevance when he was in this state of mind – that the world outside the space battle was abruptly brought back into sharp focus by Ronon's voice. "There are intruders in the 'gate room."

"In the infirmary as well." Teyla.

"I'm getting reports of Asurans in the mess hall, living quarters, and the east pier." Chuck.

Shit. John took a quick recon of their situation, weighing the threat of the Asuran ships against the threat of the Replicators in Atlantis. With the number of civilians in the city, there wasn't much of a choice. Hopefully Elizabeth's ZPM would hold off the fleet long enough for them to deal with the invaders.

An Asuran ship appeared out of nowhere and John rolled his jumper one hundred and eighty degrees to starboard, firing off a shot that hit the other vessel dead center, blasting it into a shower of harmless silver bits. He hit the radio. "This is Jumper One. All pilots, fall back to Atlantis. Repeat, fall back to Atlantis."

Acknowledgements trickled in but John ignored them, concentrating on ducking and weaving his way through ships and weapons' fire. He managed to destroy two more Asuran vessels before reaching the jumper bay, but there were still too many of them.

The rear hatch of the puddle jumper hadn't even completely lowered before John exited, ARG in hand. He shared a quick look with Elizabeth and Rodney, who'd landed ahead of him. "Control room." They both nodded.

Halfway there they met up with Teyla and Ronon; she looked calm, he looked angry. "Dr. Zelenka requests Dr. McKay's assistance in the lab. He believes he can adjust the beam to fire in a burst rather than directionally." Teyla didn't look like she really understood Zelenka's explanation, but that didn't matter.

McKay looked equally excited and terrified. "You can't expect me to go to the lab by myself when there are intruders! Do you have any idea how screwed you would all be if one of those things stuck its hand in my head and read my mind? I know more about this city than anyone!"

Except Elizabeth, John thought, but he didn't have time to worry about that just then. "Teyla will get you there. Call me as soon as you know something." He shifted his attention to Ronon, already tuning out McKay's protests. "You're with us." Ronon merely nodded.

The three of them made their way down to the control room, managing to kill a few Asurans along the way. The sounds of ARGs and whatever weapons the Asurans used was almost constant now and not too far off, John heard someone scream.

There was a sudden boom, echoed by the shaking of the city, violent enough to throw John into the wall. Chuck's voice filtered through the rumbling before John could demand a report. "There's been an explosion in the engine room! Shields are down to less than a third of full strength!"

"McKay!" John shouted over the headset. "When the hell will that weapon be ready?!"

"We can't do it! That kind of focused power burst would overload the ZPM and destroy Atlantis!"

They were officially out of options. They were outnumbered and overpowered and though not a single member of the Atlantis expedition would surrender without a fight, it was only a matter of time. John couldn't see a way out of this.

The whine and roar of weapons surrounded them, closer and louder than ever, but he could still hear Elizabeth as clearly as if they were chatting over coffee in the mess hall in the middle of a sleepless night. "I have to leave Atlantis."

He froze. "You can't."

"The Asurans are here because of me. They found Atlantis because of me. If I stay, you'll never be safe from them."

"You can't." His voice cracked.

"I don't have a choice." She sounded confident, decisive, but he could see the tears in her eyes. "When I leave, you'll have a chance. Right now I'm a bigger threat to them than you are. They'll come after me and leave Atlantis alone." She dropped to a near-whisper but he could still hear every word she said. He almost wished he couldn't. "You have to let me go, John." She held his gaze until nearby weapons' fire caused a shower of sparks overhead. He ducked instinctively, covering his face for a second. By the time he straightened again Elizabeth was halfway up the stairs.

"Elizabeth!" Beside him, Ronon tensed, then twisted and took out an Asuran with a single shot. John hardly noticed. "Elizabeth!"

She didn't so much as pause.

Too late, John chased her up the stairs; by the time he reached the control room she had used her newfound knowledge of the city's systems to raise a shield none of them had known even existed, blocking the control room and the 'gate from his reach. Already she was moving down the main staircase, toward the active Stargate.

John swore, racing back down the stairs he'd just come up to approach the 'gate room from the side, where the shield brought him up short. "Elizabeth!"

She slowed, then stopped just a few steps from the 'gate's water-like surface. He saw her take a breath before she twisted to face him across the empty space.

He couldn't hear her – or maybe she never spoke aloud – but he understood her anyway.

"Me too," he whispered back, catching her sad smile before she turned and walked through the shimmering horizon. The 'gate and the shield protecting it both shut down. Not long after that, the sounds of fighting died down as the Asurans beamed out of the city, abandoning Atlantis and her inhabitants for more dangerous prey.

Alone in the middle of it all, John stood stock still, eyes still fixed on the empty space in front of the Stargate. Then he sighed and turned to start picking up the pieces of his city.

"Me too."