Chapter 4

John opened his eyes, and he was sitting in Elizabeth's office in Atlantis. On her table sat sculptures from different cultures on Earth, the Athosian pot that he had given her several years earlier, and a framed photo of her dog. Behind him, he heard numerous technicians and scientists running their business like it was a normal, uneventful day in the city. In front of him, sitting in her chair and wearing a red t-shirt, was Elizabeth Weir.

"Not much has changed, has it?" Elizabeth asked, her voice relaxed.

"I wouldn't really say that," John replied, keeping his tone light. "If you ask me, I think Rodney's kept his ego on a leash recently." Elizabeth chuckled softly, then leaned back in her chair.

"And Colonel Carter?" she asked. "How is everyone getting along with her?"

"People like her," John responded. "Mostly. Ronon's still kinda on edge around her. But she's doing a good job."

"That's good," Elizabeth said, smiling softly. "Though I can't say that I agree with the IOA's decision to place Atlantis under a military commander. But then again, I suppose I should have known that it was coming." John avoided her gaze.

"Do you remember the day that you found out about all this?" Elizabeth asked. "About Atlantis? The Ancients? The SGC?" John suddenly wasn't in Elizabeth's office anymore, and he was sitting in a control chair, though this one appeared different from that in Atlantis, and the cold temperature of the room signaled to him that he was in McMurdo.

"Yeah, I remember," he replied. "Carson fired a drone and nearly killed me and O'Neill." Elizabeth was standing beside him, shaking her head ruefully.

"Carson was very much a cowardly lion in the beginning," she said, her expression contrite. "But he, like many others in the expedition, soon realized what he was really capable of."

"Things haven't been the same without him," John said, his words barely audible.

"No, I bet they haven't," Elizabeth replied, her voice quiet.

The scene changed again, and John was standing outside on the control room balcony. The sky was dark with foreboding storm clouds, and the waves were coming in as heavy rain pounded down on the city's shield. Lightening electrified the stormy sky, and thunder reverberated through the air.

"You saved my life that day." Elizabeth approached him and leaned against the railing. "And the city. I think it was that day that I realized whom I could count on to protect the city and its people, no matter what." John looked at her, unable to say anything.

"And later, you asked for vacation twenty years in advance." Elizabeth tapped the railing and walked away. "I wasn't surprised that you somehow managed to keep your sense of humor in even the most trying circumstances."

Then John was in a lab, and in the middle of the room were two life pods. They were both empty, though it seemed as if the ghosts of those who had been stored in them were still drifting around the room.

"What happened that day was a result of poor judgment on my part," Elizabeth said, shaking her head. "I think I allowed the idea of enduring love to overwhelm me in that moment."

"Well, who doesn't love the idea of love, especially in this galaxy?" John said, half speaking to himself. Elizabeth turned to him, her eyes questioning.

"John, where do you find love in this galaxy? In Atlantis?" she asked. John was silent for a long moment.

"I don't know. But you don't know it's there until… it is." His words were barely above a whisper. He turned around and found himself in the infirmary, where a clear isolation tent was set up. Nearby was a powered off scanner, and in a corner lay several discarded red hazmat suits.

"You can be reckless at times, John," Elizabeth said, turning to him. Her gaze was serious. "But I know that you never do anything without believing that it's worth the risk." She placed her hand on his arm. "I can't say that I regret you doing what you did that time."

Then the shadows lengthened, and John was standing in an abandoned hallway. The lights shone eerily, and a cold chill ran through his veins as he realized he wasn't in Atlantis.

"They captured me, John," Elizabeth said, standing next to him. "And I was prepared to accept my fate. You and your team escaped, and you saved the lives of everyone in Atlantis and instigated conflict between two of the most formidable enemies in this galaxy." She looked into his eyes, her gaze unwavering. "If there was a price to be paid, then I am glad that we paid it." John swallowed hard, unable to meet her gaze.

"Well, I'm not," he whispered.

"I know," Elizabeth said, her voice soft. "But the situation couldn't have turned out any other way." She squinted hard at him. "And you need to accept that."

His heart felt like it was being raked across hot coals. When he looked up again, Elizabeth was gone. He turned around, finding himself alone in the ominous hallways, in the company of only the ghosts of his past, haunted by whispers of a time already long gone.

There was a piercing ache in his head as John regained consciousness. He twitched his fingers and stirred slightly, and as he slowly opened his eyes, he noticed the dim blue lights in the cold room as slats of metal material reached up to the high ceiling in all four directions.

"Sheppard." He heard Rodney's alarmed voice, and he shifted his head slightly and saw his teammates.

"Are you all right?" Teyla asked, her expression concerned.

"Second time today that my head feels like it's been split in two." John slowly rose to a sitting position, his head still in a piercing pain, and he leaned against the wall. "Looks like the Replicators changed their mind and still threw us in the brig." He then looked around him, realizing that their weapons were missing. Then someone else.

"Where's Elizabeth?" he asked. There was a moment of uneasy silence as his teammates exchanged a few apprehensive glances with each other.

"We do not know," Teyla replied, her face downcast. "We assumed that the Replicators took her."

"Though they obviously didn't play any mind games with her," Rodney muttered, massaging his head. "I mean, she hasn't left this planet at all, so there's no point –"

"She probed my mind," John interrupted, his voice barely audible. He watched alarmed expressions appear on his teammates' faces, laced with apprehension and worry.

"John, if Elizabeth has been compromised to such an extent…" Teyla began. And John felt his heart rushing again with emotions that he couldn't deal with, that he didn't want to deal with. If only to survive, he couldn't face them.

The hallways were dark and dimly lit aboard the Wraith ship, and John fired his weapon at a Wraith. As he prepared to turn a corner, he stopped upon realizing that Ford wasn't following him. He turned around, not believing his ears when Ford insisted to him that he go on ahead.

"John. I'll catch up. Now go!" And the last that he saw of Ford was the Lieutenant bolting off alone, disappearing into the maze of the unforgiving Wraith ship. As the alarm blared overhead and John darted off to find Teyla and Ronon, the image of his Lieutenant burned in his mind. One year ago, the twenty-five-year-old Lieutenant had been cracking jokes and grinning, always dependable in combat, always loyal to his people. And now… one eye was filled with a complete blackness, and his expression was always agitated and unsettled, as if something sinister had swallowed him whole. He had been a normal boy whose life and future had been stolen from him because a drug had twisted his mind, and he couldn't escape its clutches. Hell, he was just a boy. For a while, John had held on to some semblance of hope, even when it was clear that the Lieutenant was no longer thinking straight, that he could bring his fellow soldier and friend back. But the past couldn't be undone, and painful emotions threatened to burst out of his heart as he realized that the Ford that he once knew would never come back.

"Why are we still here?" Ronon grunted. John looked at Ronon, who shrugged. "We should be dead. Why hasn't this place been blown up?"

There was an abrupt noise behind John. He turned to see the door open, and three Replicators, including the one with black hair, entered the ominously lighted room. The Replicators marched in synchrony as they approached, their movements sounding rehearsed, their eyes filled with darkness.

"The Wraith ship above the planet has been neutralized," the black-haired Replicator spoke, its tone emotionless. "And we have returned in greater numbers to assume back control of our city."

"Where's Elizabeth?" John demanded, stepping in close to the wall so he could see the full faces of the Replicators in between the metal slats.

"Dr. Weir has been taken to be returned to stasis," the Replicator responded. "For the moment, she has served her purpose."

"If you wanted her to probe my mind," John began, his voice low and menacing, "why didn't you do it earlier? Why delay the act?"

"It was necessary to wait until more of our kind returned from afar to defend our city," the Replicator replied. "Based on information already stored in our archives, we knew that Dr. Weir would not leave this city because she viewed herself as a threat, and you would not leave her behind if she did not appear to be of immediate danger to you and your people."

"It was a trap," John heard Rodney say aloud, his voice agitated. "They waited until they returned before they made her turn rogue on us."

"We found it impractical to act earlier and sacrifice a number of our kind before we could successfully detain you and your people. On the contrary, we knew that you would never harm her."

"Why didn't you just stick your hand into my head yourself?" John demanded, feeling his blood cold as he realized the truth behind the Replicator's statement. "Why did you have to go through her?" The Replicator appeared to tilt his head slightly.

"There is one matter that surprises even us, Colonel Sheppard," the Replicator replied in a toneless voice. "We did not command her to extract information from you. Dr. Weir acted with full autonomy." John felt as if his entire body was paralyzed.

"No."

"She was able to successfully obtain information regarding Atlantis' current location from you, Colonel Sheppard, and transfer it to the entire collective," the Replicator continued. "Thanks to newly gathered information from Dr. McKay as well, we are already in the process of figuring out how to remove the Wraith attack directive from our base code." The Replicator's voice was void of emotion. "Within the hour, our base code will be amended, and we will send our forces on course to Atlantis to destroy it."

"We're gonna get out of here," John said, his voice rising. "We're gonna get Elizabeth, and we're gonna get back to Atlantis and warn our people."

"Your words carry lost hope," the Replicator responded, his voice toneless.

"Maybe they do, but who would I be if I didn't try?" John retorted.

"The Dr. Weir whom you knew no longer exists." The Replicator's gaze bored into John's eyes. "Perhaps you simply need some convincing."

There was an ominous click that echoed in the room as the door opened again. A group of four Replicators marched in, two by two. In their middle was Elizabeth, her head held high, her face completely expressionless.

"I thought you said she was being taken for stasis –" Rodney began.

"There has been a slight change of plans," the black-haired Replicator replied, its tone emotionless.

There was a portentous hum as the force field to the brig was turned off and the door slid open. The Replicators stood aside, and without hesitation, Elizabeth entered the brig and approached John. She raised his arm, and John felt a powerful pain in his gut as she threw him a violent punch. Doubled over and barely able to breathe, he looked up to see Elizabeth standing above him, her eyes hardened, her face completely inexpressive. She hit him again, this time in the face, and he fell over. His vision was fading to black, and he couldn't make any words come out of his mouth, barely able to endure the storm that was raging uncontrollably in his heart.

"John? John, are you all right?" John was sprawled on the ground, and he heard a voice. He slowly rolled onto his back, groaning softly at an ache in his abdomen and the left side of his jaw. He opened his eyes, and he saw Elizabeth's concerned face.

"I'm very sorry. I had to make it look convincing," Elizabeth said, her tone apologetic. John looked around him, and he saw his teammates standing behind her, looking just as bewildered as he felt.

"Elizabeth? What just happened?" he asked.

"Elizabeth attacked you, and you passed out again," Rodney's voice came from a few feet away, though his griping tone still sounded uneasy.

"That's the third time today," John muttered. His mind still felt unclear, but he noticed that the door to the brig was open, and there were no Replicators in the room. He looked back at Elizabeth. "What happened to you, and where are the rest of them?"

Elizabeth sighed. "I had to make a very convincing argument to them to leave me alone with you and your team." She looked around at John and his teammates. "Look, we don't have much time," she said. "I transferred to the Replicators the gate address to an uninhabited planet – they don't know where Atlantis really is." John squinted at her.

"Are you saying –"

"That I was never taken control of by the Replicators? Yes." Elizabeth looked repentant. "Probing your mind – not exactly the most pleasant task that I've been forced to carry out with you, but I couldn't risk them gathering accurate information about Atlantis." There was a surprised exclaim from behind her, and John looked over her shoulder to see Rodney's stricken face.

"Wh – I can't believe –" Rodney stammered. "– You hoodwinked them!"

"And us," Ronon grunted. John looked back at Elizabeth.

"They don't know?" he rasped.

"No. Not yet at least," Elizabeth responded, her voice firm. "They haven't discovered the false gate address yet, but they will once they get there." She paused for a moment. "Unfortunately, I wasn't able to tap into the system to alter Rodney's information about the Wraith attack command code, so they are working on making changes to their base code to shut off the command right now."

"Well, we can't do anything about that right now," John said. "We need to get out of here."

"I need to stop them." Shocked, John looked at Elizabeth's determined face, as if he couldn't believe her words. "John, if the Replicators successfully shut off that attack command, they and the Wraith will no longer be in conflict with each other –"

"No!" John cut Elizabeth off. He sat up suddenly to meet Elizabeth's level gaze beside him. "I'm not about to let Rodney loose in the city to work on that anymore, and you're not going to, either. We need to get out of here, and I'm not about to do anything that means giving up one of my own people – again."

"John, you can't stop me," Elizabeth insisted.

"Don't argue with me!" John shouted, standing up, and Elizabeth rose to her feet with him. "You're coming with us, even if we have to stun you and carry you back to the Jumper. We're leaving right now."

Then no one spoke, and an uneasy silence filled the air. John looked straight into Elizabeth's adamant eyes and saw that her expression had hardened with stubbornness. He felt a sense of fury nearly boiling over within him.

"Sheppard, how do we know she hasn't been playing us the whole time?" Ronon's voice broke the strained silence. John continued to look at Elizabeth, though he felt something in his heart beginning to fade.

"John, Ronon is correct." It was Teyla speaking now, and her voice was soft. "As much as we would like to trust Elizabeth, we have reason to be skeptical now."

"You have every reason not to trust me," Elizabeth spoke aloud, still staring at John. "In a way, I'm almost relieved to finally hear that."

There was the sound of a distant explosion, and the ground trembled slightly. John looked up, hearing faint sounds of something crashing down above them.

"What was that?" Teyla breathed.

"I don't know," John replied, "but the Wraith did say that they had detonators planted in the city. Must have been their back-up plan to blow this place up if they had to do it remotely." He looked at his teammates. "We need to go," he said, and they nodded and hurried out of the brig and into the hallway. Elizabeth was still standing next to him, and he looked at her, whose expression remained hardened. Wordlessly, she turned away from him and ran out the door, and he followed her.

He led his team through the dim hallways that were growing more unsteady with every passing second. There were no Replicators around now, and they climbed a stairwell, then turned a corner and spotted the ladder to the hatch from which they had entered. Guarding their six, John motioned for Teyla ascend first, followed by Rodney and Ronon. He signaled to Elizabeth to go, and she turned around, her expression obstinate.

"Elizabeth?" He looked at her, his eyes fearful of what she was about to say.

"John, if the Wraith are about to destroy this city, then it's best that I remain behind."

"No, it's not. You're coming with us!"

"No, I won't!" Elizabeth shouted. John was startled by her outburst, and his face slightly fell. He watched as she narrowed her eyes before she spoke again.

"It's better for the both of us."

John felt something inside of him snap.

"Then you leave me with no choice." In a single motion, John pulled out his 9 mil and pointed it at Elizabeth's leg. A shot rang through the air, and Elizabeth gasped, her eyes widening, suddenly lurching to one side as she lost her balance. John caught her before she fell, then hoisted her over his shoulder as he climbed the ladder himself.

"Sheppard, we thought you'd been killed!" Rodney exclaimed as John emerged with Elizabeth. John felt Elizabeth struggling against his arms, her breathing sounding panicked, and he saw Rodney's eyes widen. "Wh –"

"Elizabeth was about to run off, and I wasn't gonna let her." John suddenly felt a powerful pain as Elizabeth punched him hard again in the side, and he was forced to set Elizabeth down on the ground, then staggered forward, breathing heavily, fury nearly bursting out of him, out of control.

"Will you just –"

"John, I won't go," Elizabeth interrupted. John watched in startled amazement as she rose to her feet, the flesh wound in her leg apparently healed. "As long as my nanites are active, they make me dangerous, and you need to accept that there is absolutely nothing you can do to change that."

"Look, when we get back, we'll put you in isolation, and Rodney will figure out how to repair your cells and shut down the nanites –"

"No, John," Elizabeth cut him off, her tone uncompromising. "Even if they are shut down, you can't ensure that they will never be reactivated again and used against us." John felt the rooftop they were standing on begin to tremble, and he took a step toward her, clenching and unclenching his fists.

"Look – you're a member of my team, and at the end of the day, no matter what happens to any of us, we don't give up on each other."

"John, this mission was a mistake." Elizabeth's tone was accusatory. "You've endangered the entire Atlantis base as well as the lives of you and your team, and you appear to have not even considered the possibility that being rescued was not at all what I wanted." Her expression appeared injured. "The least you can do now is to allow me the dignity to choose my own fate."

"You want to throw your life away, just like that?" John retorted, taking another step toward her. "I'm not buying it, not while there's still a chance that we can save you." His eyes bored into Elizabeth's. "You didn't deserve this, and what happened to you wasn't your choice!"

"You're right." Elizabeth held John's gaze, her eyes resolute. "It wasn't my choice. Had I had any say in the matter, I would have died rather than allow something immeasurably dangerous to keep me alive. But that clearly wasn't my decision to make." She stepped closer to him, and he could feel a mixture of negative emotions washing off of her. "But I had the choice of going on the mission to this planet to save our city, and I did what was necessary to allow you and your team to escape – even if that meant not coming back."

The sound of explosions began going off all over the city, and John distantly heard the voices of his other teammates, pleading to him that they needed to leave. It felt as though he had already lost, and he was only clinging on to the last shred of hope before the inevitable happened. As the ground beneath him became increasingly unstable, he suddenly felt the intense frustration and anger, everything that had been building up all this time, a whirlwind of painful emotions that he had tried so hard to suppress.

"Elizabeth, I went through this with Ford." John seized Elizabeth's arms as if his life depended on it. "I assumed every possible risk in this damned galaxy in order to come back for you. Why? Because we don't leave our people behind, no matter what happens to them, no matter the cost." His eyes became desperate. "I already left you once. Don't make me go through that again." Elizabeth looked at him, and he saw that her expression had changed, her adamant resolve having faded away to something akin to remorse.

"John, you knew when my nanites were reactivated that there would be consequences. They're here now – and we have to accept them." John felt something inside him wither.

"Elizabeth –"

"I'm sorry, John. You can't save me." Elizabeth looked at him once more, her expression pained. "You read my letter. Even if I go back, there's no going back to the way it was before all this happened, and you need to accept that." She broke free of his grip and whirled away from him, her hair flying around her, and John watched in horror as she disappeared down the metal hatch.

"Elizabeth!" His shout was drowned out by the sounds of roaring explosions, and he felt arms grasping onto him. He resisted, struggled against their grip as they pulled him away, almost unaware of the fractures forming in the surface beneath his feet. Then there was a deafening detonation, and John felt himself flying through the air, smashing his head against what he assumed was the hull of their Puddle Jumper. His eyelids dropped, and the last thing he saw was the panicked faces of his teammates, minus Elizabeth, before his vision went completely black.

His mind and body felt completely numb. He twitched his fingers, and he sensed bright lights through his closed eyelids. He shifted slightly, and there was a dull aching in his entire head.

"John?" He faintly heard a voice. John raised his eyelids halfway, trying to keep out the light, and he glimpsed Teyla's face, looking concerned.

"John, can you hear me?" Teyla's gentle voice drifted to his ears. His gaze slowly focused on her, looking confused.

"Where am I?" he rasped. Teyla seemed to hesitate for a moment before responding.

"John, you are in the infirmary. You have been here for nearly a day." Her expression seemed disquieted.

"What about Elizabeth?" John asked. He watched as Teyla's eyes widened, as if she was startled, and her expression suddenly turned sober.

"John, you fell unconscious in the Jumper when we were caught in the crossfire between the Wraith and the Replicators. You suffered a severe concussion, and the Jumper was severely damaged." Her voice was soft. "Major Lorne and a team of Marines were in another Jumper when they found us in space, and they escorted us back to the Gate and back to Atlantis." Teyla's gaze was somber.

"John, the mission did not succeed. We never made it to the planet."