Chapter 3

By the time Teyla and Ronon arrived, John was seeing signs of consciousness returning to the figure lying on the floor before him.

"Elizabeth?" John's voice was surprisingly quiet and low. Elizabeth stirred slightly, and her eyes flickered open.

"John?" She blinked in confusion, then looked around at the rest of the faces surrounding her. "Rodney?" She was gaping at them in shock. "Wh – What's going on? Atlantis – is the city safe? Did you make it to the new planet –"

"Hey, take it easy, don't worry," John assured her, placing a hand on her shoulder. "The city is fine, we got to the new planet."

"After we landed and settled affairs with the IOA and Stargate Command, Colonel Sheppard insisted on coming back for you," Teyla said, her voice gentle.

Elizabeth squinted at them. "The IOA authorized this mission?" she asked, her voice incredulous. There was an uncomfortable silence as the team exchanged a few apprehensive glances with each other.

"Um, well, not exactly," Rodney mumbled, his expression nervous. "Sheppard here – he, uh – he kind of did this on his own." Elizabeth slowly turned to John, her expression suddenly serious.

"Colonel, explain yourself." Her voice was humorless. "What's going on?" There was a moment of silence before John relented.

"The IOA was taking too long to reach a decision, and they were never gonna approve of this mission in the first place. And Carter wasn't going to let us go because McKay was taking too long to come up with a plan –"

"Colonel Carter?" Elizabeth interrupted.

"Um, yeah, Sam's the new you," Rodney said after a brief moment of silence, his voice meek. "Atlantis' new leader, I mean."

Elizabeth turned back to John, and he saw that her expression was deadly serious. "Colonel, you're telling me that you went against orders from your military superior on an unauthorized mission that could potentially endanger Atlantis and everyone in it?"

"Well, I think that that's a bit of an overstatement, considering that the Replicators are fighting it out with the Wraith now and have no idea where we are in the galaxy –"

"No, John, you listen to me," Elizabeth interjected, looking squarely at John. "Did it ever occur to you that the IOA and Stargate Command probably had good reason not to sanction this mission? You are risking the safety of Atlantis and our people, and I am clearly compromised and a threat to the city."

"Look, I knew the risks, and I wasn't going to let them stop me –"

"John, it was a mistake for you to come back here. All of you." Elizabeth said, looking at John, then up behind him toward the rest of his team. "The Replicators have tampered with my nanites, and I am not safe to be around anymore."

"We'll take you back to Atlantis," John said, trying to keep his voice under control. "We'll put you in an isolation room, and Rodney will figure out how to program them so they can't control you or the other Replicators while still keeping you alive –"

"No, it's too dangerous." Elizabeth's eyes were wide with frustration and fear. "The Replicators can take control of me at any given moment, and I will not risk Atlantis and the lives of everyone in it!"

"We'll figure something out, we always do," John said in a low voice, his eyes narrowing. "You're coming with us, we're not leaving you behind. We already did it once, and we're not doing it again."

"No, John, I'm not going." Elizabeth stared at him directly in the face, her expression resolute. "This mission was reckless, and you know it. You and your team need to leave now." She suddenly stopped talking, and her expression changed as if she was seeing something that the others couldn't. "You need to go now," she repeated, her voice carrying a sense of urgency this time.

"Not without you," John insisted.

"You don't understand," Elizabeth said, turning back to him with a wide-eyed expression. "It's the Replicators. They've unfrozen."

"The Replicators are on the move," Rodney announced, reading the life-signs detector. "I'm picking up two life signs about fifty meters down the hallway, and they're headed straight toward us."

"Go," Elizabeth said, getting up. "I'll go distract them. They won't be expecting me." John suddenly reached out and grabbed her arm.

"We can take them," he said in a low voice, and Elizabeth looked up at him.

"Go," she repeated, this time more firmly. "More are coming. I'll find you and your team later." Without another word, she broke free of his grasp and ran out of the room.

"She's right," Rodney said, still looking at the detector. "Six more are coming from the other direction." John turned back to his teammates.

"We need a new plan," he said, frowning. "We need to freeze those Replicators again so we can get Elizabeth and get out of here."

"Well, there's no time for me to go through the Replicator base code now," Rodney protested. "And Elizabeth's gone, so I can't do it through her –"

"Figure it out," John cut Rodney off. "We're not leaving without –"

"I am sensing something," Teyla interrupted, and John saw her expression turn unsettled.

Suddenly, there were noises echoing in the distant hallway. John heard what sounded like snarling, and there was a voice giving out shouts and panicked yelling.

"Elizabeth," he breathed. He bolted out the door, sprinting down the empty hallway, approaching the corner from where he was hearing sounds of struggle. He turned the corner, and what he saw nearly stopped him from breathing. Instinctively, he pulled out his 9 mil and began firing, cursing himself for not having a P-90, knowing that his pistol wouldn't have much of an impact on the Wraith pinning Elizabeth against the wall, its feeding hand raised in position, ready to feast on its prey. The Wraith looked up, its face covered by an armored mask, and it released its hold on Elizabeth. Out of the corner of his eye, John saw her drop to the ground, gasping violently for air, and her eyes and face were laced with horror.

He felt himself being thrown off his feet and flung through the air. His body hit a wall, and he fell like a rag doll to the ground. He heard a sharp ringing in his head, and he wrestled to get up on all fours, seeing his pistol lying on the ground a few feet away from him. John reached for his weapon, only to have his hand nearly crushed by a Wraith looming over him.

"If it makes you feel any better, you probably would have gotten infected if you tried to feed on her," he rasped. The Wraith grabbed his shirt and forced him to his feet, and he tried to turn away from the pungent odor coming from underneath the Wraith's mask. He recoiled slightly as it raised its feeding arm – and suddenly, he heard a blast of energy, and the Wraith dropped to the ground. He looked up in time to see a second Wraith meet the same fate as the first, and he saw Ronon running toward him, swinging around his weapon, with Teyla and Rodney close on his heels.

"You all right?" Ronon asked, a little breathless.

"Yeah, I'm fine," John responded, breathing heavily, his head still ringing.

"John?" Elizabeth's horrified voice rang through the air, and he looked up to see her frightened eyes locked in the direction down the hallway. There were six Wraith, all wearing masks and armor and carrying stunners, marching down the hallway toward them.

"Run," he heard himself saying. He reached for his pistol and forced himself to his feet, and he went to pull Elizabeth up. "Run, go, go!" he shouted to his teammates. They all bolted down the hallway, dodging energy blasts from the Wraith stunners, and he heard Ronon covering their six with his weapon. Then he suddenly stopped, a group of Replicators heading in their direction. "Oh, crap."

"Wait," Rodney exclaimed, and John looked at him with an incredulous expression. "They shouldn't attack us," Rodney said, his eyes wide. John watched in disbelief as the Replicators passed by him and his team as if they were no more than wallpaper and proceeded to fight the group of Wraith not too far behind them.

"Let's go," he breathed, and he and his teammates continued running through the corridors. As they distanced themselves from their attackers, his heart beat as if it were racing against time, and his mind whirled upon realizing that their situation had just become a lot more complicated. Eventually, he stopped in a secluded hallway, and he heard his teammates' footsteps slow down behind him.

"Everyone all right?" John asked, breathing hard.

"Oh, yeah, just great," Rodney wheezed, "with me having high enough blood pressure as it is." He stopped for a moment, clearly out of breath. "The Wraith – they must have somehow managed to infiltrate the city," he stammered, "especially if the Replicators were frozen up in that space battle, then the Wraith could have destroyed them and…"

"Great," John replied, taking deep breaths. "So now, we have not one, but two bad guys in this city who seriously want to kick our asses. But at least the Replicators are programmed to go after the Wraith when they're around." He turned to look at Elizabeth, whose hair was disheveled, and she still appeared breathless.

"Elizabeth? You all right?" he asked, his expression concerned. Elizabeth turned to look at him, and he saw that her eyes and face were still in shock.

"Yeah. I'm fine, I just –" Elizabeth stammered, seeming to struggle to get words out. John looked at her fearful eyes, and he took her hand and squeezed it.

"You'll be ok," he said in a quiet voice. Elizabeth looked up at him, and after a moment, she gave a small nod.

"We need to head back to the Jumper," John said, turning to the rest of his teammates. "We don't know how many Wraith are in the city, and seeing as the Replicators are now on the loose, they're probably going to call for reinforcements."

"John, I –" Elizabeth began.

"You're coming with us," John cut Elizabeth off, his expression stern. "If you think that we're going to leave you here right now with the Wraith lurking around at every corner, you're sorely mistaken." Elizabeth looked as if she wanted to protest his words, but still clearly rattled from the trauma, she looked as if she couldn't bring herself to argue with him.

"All right," John said. "Let's get moving."

"I thought you had Replicator spidey sense to know exactly where each of them are, so how come you didn't know that it wasn't Replicators back in the hallway where we were just now?" Rodney was talking with Elizabeth as John led the team down the hallway.

"Like I said, the Replicators tampered with my nanites," Elizabeth explained, sounding calmer now. "I thought it was them who were coming, but I guess I was mistaken."

"Crap." Rodney stopped in his tracks, his eyes widening as he studied the life signs detector. "I'm reading multiple life signs coming from both directions," he said, jerking his thumb down the hallway in one direction and then pointing in the other.

"We need to split up," John said, trying to think of options. There was a small hallway adjacent to theirs just up ahead, and the team ducked into its shadows.

"Teyla, Rodney, Ronon, you go down that way." John motioned further down the corridor. "Elizabeth, you're with me. We'll meet at the hatch that we entered from and go from there." He watched as half his team hurried down the dim hallway, then turned to Elizabeth beside him.

"We'll take cover here until they pass." John motioned to a shrouded corner, and he and Elizabeth ducked into the shadows, cowering in the darkness. He held his breath as the sound of marching footsteps approached them from two directions, and nearly a dozen Replicators entered their hallway.

"They are around here, I am certain." John saw the black-haired Replicator again among those in the hallway, and he shrunk further into the shadows to avoid being noticed. He felt Elizabeth pressing close to him, and he sensed that she was trying to keep her breathing calm. "We will try this direction," the Replicator spoke again, and John watched as he led the others down the corridor. The sound of their marching faded, then disappeared into silence. He slowly emerged from his position.

"All right, let's keep moving," John said. "We got to meet the others." He turned around and glanced down at Elizabeth, and he saw that her expression was humorless.

"John, this is a bad idea," Elizabeth whispered. "I can't go back, not like this."

"Look, I told you, it'll be fine," John insisted.

"No, John, you can't know that." Elizabeth's expression was laced with trepidation. "As I was sitting here with you just now, I was trying very hard not to imagine what might have happened if they had suddenly tried to connect with and take control of me."

"The fact that they haven't taken control of you yet says something, I think," John replied, trying to sound less grim. "You said so yourself that you were able to exert control over your nanites and prevent them from communicating with the Replicators."

"That was before they tampered with them." Elizabeth looked down at her hands, her expression sober. "I don't know what they did to me." John looked down at her despondent expression, then knelt down beside her.

"Look," he began, feeling a bit uncomfortable. "You remember when I nearly turned into a bug?" He watched as Elizabeth looked up at him in surprise.

"Never thought that I'd hear you bring up the subject yourself," Elizabeth replied.

"Yeah, I know," John grimaced. "Not exactly one of my yearbook moments." Elizabeth gave a small smile. "But the point is, you didn't give up on me, not even when I was… you know. And I'm not about to give up on you now." He watched as Elizabeth turned to him, her expression changing slightly, and for a brief moment, he thought he saw gratitude in her eyes. But if there had been a flicker of hope, it was quickly extinguished as Elizabeth turned away again.

"This is different, John," she said, her expression remorse once more. "That time, it was your life that was in danger. If I go back, it will be the lives of everyone in Atlantis."

"Two men were killed trying to save my life," John argued. "I'm not about to live mine without doing the same for others. It's a principle, Elizabeth. We don't leave our people behind."

Elizabeth shook her head. "I'm sorry, John. It's too great of a risk to take." John felt a sense of frustration and impatience building up inside him.

"Look, we came all this way for you, and you're right, it was against orders," he said, his eyes narrowing. "But you should know by now that this is what I do, Elizabeth. You knew that before we came here. And I know that… you trusted me then."

Elizabeth turned to him, looking confused for a moment, then her eyes widened as if she suddenly realized something. "How did you –"

"Teyla found your letter. And I read it."

Elizabeth looked away, her expression somber. "You should know that I trusted you to do the right thing the last time you were on this planet," she said, her voice quiet. John looked away.

"I did what I had to do." He tried to suppress the emotion building in his throat. "But it wasn't the right thing."

Elizabeth looked at him, and her gaze was saddened. "John, when have we ever played by the rules of right and wrong in this galaxy?" she asked, her voice carrying a sense of helplessness. John looked into her eyes, and he couldn't respond. Then he heard radio static in his headset.

"Colonel Sheppard, this is Teyla."

He tapped his radio. "Teyla, what's your status?"

"Colonel, we were ambushed by the Wraith. They have taken Rodney."

John looked at Elizabeth, whose expression was now alarmed, and he cursed silently. "Copy that," he managed to say. "What's your position, Elizabeth and I will meet you there."

"Ronon and I are at the transporter nearest the hatch from which we came in."

"Copy that. Sheppard out." He turned off his radio, then looked down at Elizabeth, who was looking at him expectedly. He suddenly reached down and pulled her up.

"Come on, let's go." Without waiting for her to respond, he grabbed her hand and ran down the hallway, pulling her along beside him.

"We believe that the Wraith headed in that direction," Teyla said when John arrived with Elizabeth, motioning down the hallway.

"How many were there, and why didn't they take you and Ronon?" John asked, a little breathless.

"There were many, and I do not know," Teyla replied. "But they did not appear to want to feed on him, and they seemed particularly interested in Rodney because he did not appear to be military."

"Just great," John groused. "When I'm with a Wraith, I'm their food, but when McKay gets captured, he's somehow an asset." He exhaled sharply. "Ok, let's go see what these bastards want with our scientist of the week."

As he led his teammates down the endless corridors, nothing appeared on the life signs detector other than his and his teammates' dots. With every new corner they turned, John felt the pressure of time even more intensely, and he forced himself to suppress the apprehension building inside him.

"Maybe they took him aboard their ship," Ronon spoke up.

"Maybe," John replied in a low voice, half speaking to himself, "but we're not there yet." As he spoke those words, he looked down at his detector, and he saw that five dots had appeared on the edge of the screen. "This way," he said, taking off at a run, and he heard his teammates' pounding footsteps close behind him.

He heard muffled yelling behind a door at the end of a hallway. He signaled to Ronon to prep his weapon and nodded to Ronon and Teyla, then glanced behind him at Elizabeth, who was watching with fearful eyes. He gripped his pistol with one hand, and he threw the door open. Rodney was gagged and tied to a chair in the middle of the room, surrounded by four Wraith. These ones were not wearing armored masks.

"Let him go," John ordered, his pistol pointed at the Wraith.

One Wraith turned toward him, tilting his head as if questioning his statement.

"Or what?" it asked in a cold voice.

"Or we'll kill you," John replied, narrowing his eyes.

"Sheppard, I can take them," Ronon growled, his mouth curved as he aimed his own weapon.

"We will release Dr. McKay once he does exactly as we say," the Wraith said, his tone uncompromising.

"What do you want Rodney to do?" John demanded.

"To reprogram the Replicators' base code and remove the Wraith attack command code."

Dammit. "And why would he do that?" John gripped his weapon more tightly.

"If he does not, then you will not get off this planet alive," the Wraith threatened. "Our ship is still in orbit, and we have detonators planted in the city, and we intend to destroy it."

"Well, if you were gonna destroy the city and all the Replicators in it anyway, what difference does it make if we remove that attack command?" John asked.

"Don't play fool with us!" the Wraith accused, its tone sharp. "The Replicator ship that we destroyed above this planet was not the only one in existence, and the Replicators currently in this city comprise of only a fraction of their entire population. There are many more out there, and they will continue attacking our kind until the attack command code is removed from their base code."

"Well, you should know that that was kind of the point," John retorted. "We're glad that they're kicking your asses."

"Whether or not you agree to help, we will not leave this city intact," the Wraith repeated, its voice unyielding. "The difference is, however, that we may allow you and your people to leave with your lives."

"Might. Might allow us."

"It is your choice. However, you have no chance of leaving this planet if you do not help us." As those words came out of the Wraith's mouth, John heard the sound of marching footsteps coming from the hallway outside the door behind him, and his heart plummeted. But they didn't belong to whom he suspected, and he watched, his expression surprised, as a group of Replicators entered the room and began attacking the four Wraith. With the Wraith suddenly distracted, he hurried to Rodney to untie him.

"You know, I seriously thought that I was going to become their next meal," Rodney gasped as John removed the gag from his mouth.

"Relax, Rodney," John replied. "Apparently, they like you more than me. Now let's get out of here." He motioned to the rest of his teammates and hurried out of the room, leaving the Wraith and the Replicators fighting behind them.

The ground suddenly shook as the team ran down the hallway, and John stumbled as the surface beneath his feet became unsteady.

"Oh, no," Rodney breathed, his voice carrying the apprehension that it always did when something bad was about to happen. "This city's about to blow."

Before John could reply, he heard Elizabeth inhale sharply, and he turned to see the corridor behind them come crashing down, the infrastructure collapsing and smashing into the ground and sending a massive blast of energy through the ground in his direction.

"Run!" John shouted. "Get back to the Jumper!" He was racing against time, leading his teammates through the endless corridors as the city shook more violently with every step taken. At one point, he was nearly knocked off his feet as the ground lurched suddenly, and he coughed as plumes of dust arose from massive amounts of debris, clouding the air and obscuring his vision as he struggled to see through the destruction.

As he rounded a corner, he stopped abruptly when he saw a group of Replicators marching toward him. He turned around, and he widened his eyes as the same appeared behind him and his team. The air around him suddenly felt colder, and he raised his ARG, firing at the Replicators, hearing his teammates do the same around him. But the Replicators continued approaching them from both directions, and eventually they stopped crumbling to the ground. The face of the black-haired Replicator was among those in the sea of endless replicating robots.

One Replicator punched him in the face, and the ground seemed unstable as he felt his arms pinned behind his back and himself being forced to his knees. He looked around him, realizing that three of his teammates were in the exact same position, and they were all surrounded by dozens of Replicators.

"Shall we do this here or take them to the brig?" one Replicator asked.

"There is no point in detaining them there when they will not leave this city anyway," the black-haired Replicator replied, his voice void of emotion. "Do it now."

John expected one of the Replicators surrounding them to approach him as they approached the rest of his team. Then he noticed that Elizabeth was not detained, and she was walking toward him, her eyes cold and narrowing. In a flash of movement, she raised his arm, and he felt an excruciating pain as his vision flashed white.