Hello, Stargate Lovers!

Hope you're doing well!

I'm glad that you are all enjoying this story... Probably, gonna post one chapter a week, since life is happening... and work gets in the way... But the important part is, I'm going to keep writing this story, since is giving me a lot of pleasure to do so.

"Ghost in the Machine" is a sad episode, right for the mood of the current events of this story.

Thank you for the follows!

Chapter 38: Chapter 5x05

His feet took him directly to the infirmary. It had become a habit for the past week, even before going on a mission.

Even if he never went to actually talk to her after she woke up the first day.

"How is she, doc?" John asked as he felt Jennifer stop next to him. His hazel eyes were on Alexandra, who was talking to one of the doctors.

"Much better. Her energy levels are normal for the past couple of days. I'm actually on my way to discharge her." The pilot nodded. "However, in my opinion, I feel like she's detaching herself from what happened."

"What do you mean?" He frowned, confused, and turned completely towards the other woman.

"Well, I tried to make her do something with her abilities. And she refused." Jennifer looked from Alexandra to John. "Dr. Simmons cleared her already, saying that what she was feeling was normal given what happened. He gave her a couple of sessions with him just in case and no off world missions for now. But she can go back to desk duty." Jennifer watched the pilot that had turned back to the person in question. "Perhaps you should talk with her, Colonel."

Now, there was a worried frown in John's expression.

There was a moment of silence, before the military commander gave the doctor a quick smile.

"I'll talk with her later, doc. Thank you." And with that, he disappeared from the infirmary in direction of the control room.

Seven days of seeing her at a distance. He still wasn't ready to talk to her. He didn't know what to say and his feelings were all over the place and he didn't want to do or say something that would spook her after what Kal did to her. To them.

Hours later

The puddle jumper hit the space Stargate and it was losing altitude, with the possibility of burning up in the planet's atmosphere... the planet with the flying monkeys... that was an odd way to go, if he was honest.

Rodney was talking incessantly, looking between his working tablet and the jumper's controls, even if they were powered down given the surge of electricity that his team was suddenly caught in.

What the hell was going on?

It was supposed to be a simple mission. In and out. To scout for an Alpha site if anything happened to Atlantis... even if there were flying monkeys that didn't appear on the Atlantis database.

And that was why they needed her... well, of course Rodney and his team were good on their jobs, always had been. But he had the feeling that she would have found out about the planet's primordial creatures before anyone else.

All of a sudden the jumper came back online and he flew it towards the gate.

Now, they lost the life support.

And... another power surge.

And... they were back online.

What the hell was going on?!

Everyone was safe.

Isolated incident or not, John was glad to be back on Atlantis and off that jumper.

And away from two babbling scientists that were currently doing their thing on its systems.

Right now, as his feet had taken him from the jumper's bay and into the city's corridors, he knew there was one place he wanted to be.

For a moment, John hesitated, thinking about his earlier conversation with Jennifer about Alexandra and her powers. Was she scared? Did she... lose them after her fight with Kal?

Of course that would be the first place she would go to after being discharged, he thought as he leaned against the doorframe of her lab and his hazel eyes caught her sitting by her computer, her glasses back on, a pen twirling between her fingers. It was good seeing her up and about.

"John?" Her voice took him out of his reverie as she stood and noticed him by the entrance. "Everything okay?" Alexandra took a step closer to him, worried. She hadn't seen him in days.

"Yes. I... We had a jumper malfunction."

"Is everyone okay?" Her eyes went over him, but that feeling of her looking into his body wasn't there like the other times she had done that.

"Yeah. We are all okay. McKay and Zelenka are inspecting it right now."

There was a relieved smile on her lips.

"So, you escaped from them?" Her voice was coming out softer than before.

"No… Well, yeah... they get too…"

"Noisy? Babbly?"

"Yeah!"

Alexandra snorted and rolled her eyes, mostly to look away from him. There was this feeling of distance between the two. And she wondered if she was the one doing it or him. And the fact that she didn't remember a lot of what happened, was making her walk in eggshells.

"You're up and about." John entered the lab fully, his eyes completely on her as he approached her.

"I was tired of being coddled by the nurses. And you placing Lorne and his team by the door, didn't help." The scientist gave him a look that made him scratch his neck with a sheepish look.

"I was just being careful. Not because of you..."

"I know." She said it so softly and avoiding his eyes that he had the urge to pull her against him and wrap his arms around her. There was a fragility in her that he didn't know how to respond to. So, he placed his hands in his pockets.

"Alex..."

There was a flickering of light.

Both looked around the room.

"Rodney?" John said to his radio.

[Go ahead.]

"Are you messing around with the power again? The lights are flickering."

[Yeah, I'm getting reports from all over the place.]

Then a bolt of lightning surged from the walls and pilot and scientist jumped away from each other.

John sighed at the interruption as her brown eyes turned to his. He saw the relief in hers.

"We haven't finished this conversation..." He said before leaving to meet Rodney.

Alexandra's eyes followed him out and she sat back down, letting out sigh.

"We thought you were dead." John hesitated on saying those words as he already had dealt with that pain, even if it was still there.

"I suppose I am. My physical body, anyway, but my consciousness is still intact." The computer voice said.

"Right. So what happened?" The pilot continued.

"Do you remember the day I ordered you to leave me behind?"

"Yeah. Yeah. I remember."

"Well, after that, the Replicators took me to a lab. The nanites in my body were unleashed and allowed to replicate. I joined the population but even in my new form, my original consciousness was still there. I was still me. I tried to hide it, but a few of the others could sense it. They were remnants of Niam's old group. I believe you encountered some of their handiwork. Replicator-built human versions of me and your team."

Woolsey was angry at the possibility of giving more power to a Replicator as he turned to Rodney. Even if that replicator happened to be Elizabeth Weir.

"Replicators are far too powerful to even think about trusting them. They've been the scourge of two galaxies. You know better than anyone how difficult it was to get rid of them."

As she heard this, Alexandra entered the control room balcony where the team was reunited with Woolsey.

"Is it really her?" She whispered, stopping next to John. She had been keeping her distance from what was happening, but hearing that Elizabeth was back had been stronger than her.

"It is." He kept his eyes on Woolsey and Mckay going at each other. "Well, maybe we can upload her or it or whatever this thing is into a virtual reality, like we did with Ava?" The pilot mentioned.

"That could work, but it wouldn't be easy, especially if she doesn't want to go." Rodney sighed.

"We'll talk to her." John continued.

"What about you, Alex? Perhaps she would listen to you." Teyla turned to the most recent addition to the conversation.

Four other faces turned to her. However, Zelenka interrupted the small meeting before she could answer. And, as they all realized what Elizabeth was trying to do, the south pier was the next destination for Atlantis main team.

There was something about the person sitting in front of her. It didn't look like any other replicator she had encountered before in the Milky Way System. And she had never actually met the Asuran Replicators, spite reading about them.

"I'm glad you're here, Alex." The former Atlantis leader smiled at her friend.

The scientist approached the replicator and sat. She was the second one to visit her and she was curious by the goal that particular replicator group wanted to achieve. Ascension.

"I'm glad as well. I've learned so much since I've stayed. I'm only sorry I couldn't help John and the others to save you back then."

"I'm sure they appreciate your help now."

"I do hope so." The woman smiled. "You've done a wonderful job, Elizabeth. Atlantis and its people are what they are because of your command."

"It wasn't just me. John helped as well. If he hadn't trust me five years ago, the military would have never obeyed my orders."

"True. There's mutual devotion on both parts." Alexandra tilted her head to the side. "They all miss you."

Elizabeth smiled, sheepishly.

"How has it been working with him? I remember you two got along back on Earth, while you were training him."

"Easy. He's a very easy leader to follow." Alexandra said, trying to keep her tone neutral.

"Yes. He inspires something in people. And the proof is Teyla and Ronon."

"Yes. They would do anything for him."

The replicator nodded. Her keen eyes watching the scientist closely.

As John entered the room, Alexandra turned briefly to him, which made Elizabeth raise a curious brow when the young woman stood to give the pilot his turn.

"Sorry to interrupt."

"It's alright. We'll talk more later, Elizabeth."

"Of course." The replicator smiled and saw how the pilot watched the scientist leave the room.

"Uh, sorry about all this." John started.

"It's okay. I understand. Amazing news about Teyla." She continued.

"Yeah."

"And Dr. O'Neill staying... It was a good addition to the team, I imagine. After all, she was supposed to accompany us from the start."

"Yeah... She brought something more to the city." John rubbed behind his ear. "Look, we all want to believe you are who you say you are."

"I understand. You have to be cautions. But it really is me, John." They looked at each other for a moment. "You just have to give me time. You'll see that..." Elizabeth stopped and turned serious. "Oh, no."

"What's wrong?" John opened his arms to make the security team stand down as they held their weapons up as she stood.

"They've found me."

"Who?"

"The other Replicators. They're on their way to Atlantis."

"We've established contact with the Replicator known as Koracen." Woolsey informed John as he appeared with Elizabeth and Ronon, followed by a security team.

The negotiations were going nowhere and suddenly the city was sinking into the ocean.

"Can't you do anything, Dr. O'Neill?" Woolsey turned to Alexandra that had stayed quiet at the edge of the control room, knowing there wasn't much she could do. This threat was one she couldn't fight against, even if she wanted to.

"I can't. And I would advise against it, Mr. Woolsey. As you well know, my powers never worked with the Replicators and only powered them. And it would probably do more harm to the city." Her eyes went from Woolsey to John, feeling lost. For a moment, she felt Teyla's reassuring hand on her shoulder.

Woolsey sighed, nodding at the scientist.

"Send them a message." The Atlantis leader started.

"They won't stop." Elizabeth responded.

"Fine. Then we'll all die together."

For a moment there was a silence.

Then a bleep.

"They're powering down the ZPM. The city's stabilizing."

There was a collective sigh of relief.

"All right. Now we can negotiate."

"How are they doing?" Alexandra approached Ronon that hummed an answer, not taking his eyes from the lab room the replicators occupied. "Good." She says back, patting his arm after a few moments, and smiled watching Rodney sleeping.

"Big guy not saying much, is he?" John asked, finding her in the corridor.

"Nope." She gave him a quick smile.

"Alex, what happened earlier?"

"It's just... complicated."

"Alex, c'mon..."

"Let's just end this day first, okay?" She gave him a nod and left, leaving a lost pilot behind.

A plan was made.

"I heard you're head of a department now. You didn't mention it earlier." On her way to where her fellow replicators were being held, Elizabeth had found Alexandra in her lab.

"Still getting used to it, I guess." The scientist shrugged. "Woolsey made it happen."

"I'm glad you agreed to it. I always thought you were meant for more. Being an Ancient or not." Elizabeth smiled as the other woman shoulders relaxed. "I couldn't help but notice some tension between you and Col. Sheppard."

The scientist stood from her chair.

"We had a situation about a week ago. It sort of turned us against each other. And, now, he's being…"

"Cautious?" Elizabeth raised a brow. Then she saw something in Alexandra's stance. "I see. He's being something more. I was his commanding officer for three years, Alex. I know how he is. It's not difficult for him to get protective with the people he cares about. But another thing is to have his eyes fully on you, watching your every move, listening to your every word."

"Wait, did you two…" Alexandra frowned, leaning against the table.

"No. And I knew his reputation. Women talk, you know?" Elizabeth winked, seeing her nod. "And let me tell you there was only one woman that captured his attention like that."

There was sort of a snort from the scientist.

"And she was an Ancient." Alexandra sighed. "Elizabeth..."

"Your powers are back." The Replicator simply said.

"How do you..." Alexandra stopped. "You read it in the data base." Elizabeth nodded. "Yes, they are growing. Just like when it happened with Cam."

"The Ancients..."

"Let me worry about the Ancients. And all he has to worry about are the Wraith or other threats coming Atlantis way."

"Alex."

"I know, I know." Alexandra gave her friend a tired smile and then approached her for a hug. "Are you sure you want to do this?" She already knew about the plan in motion.

"On my way to tell them."

"If I could do something..."

"I know. And if what you feel is true… It can be a good thing. Even if the Ancients are meddling with your life again." Elizabeth smiled, seeing her nod, before leaving.

Hours later, everyone gathered in the gate room.

Heartbroken, the team watched as her old friend entered the gate and disappeared.

Alexandra's brown eyes went to a certain a pilot that had stepped closer to the gate and stayed with his eyes locked on it as his friend left once again and the blue pool disengaged.

She ended up leaving, escaping questions and wanting to be alone.

It was hours later and he was in a jumble after that day. Talking with Elizabeth again, losing her once more. It was too much for the average human. After everything that happened in the past few weeks, he was just tired. And was ready to sleep, when the door to his quarters ringed.

"Alex?" She was the last person he had thought of, especially after her disappearance from the gate room earlier.

"Hey. I'm sorry. I know it's late. And you probably want to be left alone... after everything and after seeing Elizabeth leave again..."

"Is something wrong?" It was the first time in months he saw her hesitant.

"No, no… I just… I thought... we never got to finish our conversation. And I wanted to apologize, John. For everything I 've been putting you through. You must think I'm a bad person, or friend, or whatever we are right now. I still can't remember much but I'm pretty sure I said some mean things that you didn't deserve…"

He was not ready to a mumbling Alexandra right now.

"It's alright, Alex. We are friends, first of all. I know you didn't mean any of those things." His hand rubbed the back of his neck.

"But that's the thing, isn't it? What Kal said… It made me think... I don't know who I am anymore. What I am… What if he comes back?"

He frowned, his anger simmering towards that particular Ancient.

"Stop. Come here." John pulled her inside his quarters and the door closed. "Sit. Look at me." He made her sit on his bed and his hands grabbed hers, gently, as he squat down in front of her.

Alexandra did as he asked, locking her eyes on his for the first time since he opened the door.

"You are overwhelmed. You are scared. And I get it. But he's not coming back and he's definetely not going to get you. I promise."

"What if I'm not fit for field duty anymore?"

"You will be."

"And my powers..." She took a deep breath. "They're... all over the place... That's why I didn't use them... when Woolsey asked me. Or Keller... I'm afraid, John."

"Alex, you are safe. You said it yourself. You have your own protection. And it worked. And what you feel will go away. Your powers are a mess, because you feel like that too."

She closed her eyes for a moment.

"He messed with my head first! It already happened once, with Anubis, and I promised that wouldn't happen again. And it did. And I almost hurt Atlantis…" She looked at him. "You." John's hazel eyes locked on hers and his hand brought hers against his chest as if to reassure her he was alright. She could feel his heartbeat. "That's how I knew. There was something that clicked when he threatened you. He said you were the only one who didn't believe him."

"He was right. Sneaky little…"

"Bastard." She ended, giving him a small smile.

John smiled too and sat down next to her.

"Do you know why he wanted you?"

"When he was inside your mind, he wanted my powers. From what I gather, and from the pieces I remember, when I released him from you, his ascended form got powered by my energy and he went to find his body. However, he couldn't release it from stasis. So he waited. Until, I found that adress on the database. He told me this, thinking he was already manipulating my mind. And he was, in a way..."

John nodded, thinking back at what happened on the pier.

"Well, not all Ancients can be bad. There's someone looking after you."

"What do you mean?" Alexandra was confused.

"When I was trying to find you, a light appeared on the transporter screen. Someone knew where I could find you."

She went over his words for a moment. Then, she saw him yawn.

"I should let you rest." And was about to stand, when his hand grabbed hers again and pulled her down onto the bed at the same time he leaned back.

"Stay..." He had his eyes closed.

"John... I don't think I should..."

"It will make me sleep easier." His arms locked her against his body, giving no space for arguing. "Please." He gave a tired a sigh.

With her head on his chest and her body pressed onto his, his warmth seeped into her own and his breathing lulled her to sleep.

She shouldn't stay, but she did.

The scent of her pillow was different. The bed was different. The light. Where was she?

"Morning."

Her eyes opened to a shirtless and wet haired John Sheppard appearing from the bathroom with only sweat pants on.

"God, John… what are you doing?"

"You do remember what happened last night, right?" He smirked, cheeky.

"What?" Looking down, she saw she was fully dressed. "Oh, shut up." John laughed as she sat up and pulled her knees against her chest.

"How are you feeling?" He sat at the edge of the bed.

"Better. Thank you. Thank you for the peptalk. And everything in general."

"You're welcome." He shrugged, nonchalantly. "Anytime. That's what I'm here for." There was a bitterness to his tone she picked up on.

"I'm serious... All I want now is to move forward. Get better and figure out the things he said to me. To remember."

"You know you're not alone. Me, Teyla, Ronon, Rodney, we are here for you."

"I know." She leaned forward a bit and kissed his cheek, lingering for a second more than necessary. "Thank you for saving me. For pulling me from the darkness." There was more than one meaning to her words.

John rubbed the back of his neck as his eyes found hers and then saw her stand.

"I better leave before someone sees me here and get any ideas." She stopped by the door looking out. Clear. "And, please, John, put a shirt on because that's not distracting at all."

The pilot smirked upon seeing her teasing smile before leaving his quarters. She would be back to normal in no time.

Ps: I know it's not the best chapter... but didn't want to lose the opportunity for Alexandra to talk with Elizabeth. So... thoughts?