Hello, Stargate Lovers!

Oh, my! This episode is amazing! One of my favourites of the season, it's funny and bit angsty at the same time. So, of course, I had to pitch in with a bit of softness towards the end, so we could have a lot of angst in the next chapter, which is an original from me.

This one was a bit hard to write and develop, because of how the A.I. connects with John, Woolsey and Rodney, but I wanted Alexandra to watch John's torture and one of his worst enemies in action. So, I hope what I did makes sense.

I hope you enjoy this one!

Chapter 50: Episode 5x15

"Mr. Woolsey. He seems lonely. He never takes part in any of the city's social activities. He always eats alone. Either in his office or in his quarters." She kept going, staring at the older commander of Atlantis by the breakfast table.

"Maybe he has work to do, you know? Some of us are busy people." Rodney answered, nonchalantly, as he started his own breakfast.

With a serious look, Ronon turned to him.

"Sometimes, when I walk by his quarters at night, I hear him crying."

"What? Really?" Suddenly, the scientist was worried.

"No." The satedan simply said with a mocking laugh.

"Mr. Woolsey, would you care to join us?" Both heard Teyla ask and Ronon took his feet off the free chair.

"Well, thank you. But I'll be taking my breakfast in my quarters today. I still have some final preparations for my impending performance evaluation. I'm a little apprehensive." Woolsey approached them upon her greeting.

"You shouldn't be. You've done a wonderful job as our new commander." She continued with a soft smile.

"Well, let's hope the I.O.A. agrees."

"There you go. He prefers to be on his own. Speaking of which, where's Sheppard?" McKay kept going as he started to eat, finding strange the colonel was not amongst them.

"He flew some astrobiologists to the mainland this morning." Teyla answered.

"And volunteered to stay with them over night." Ronon completed.

"Why would he do that?" Rodney frowned, not understanding the look his two friends shared.

While she too took the opportunity to explore the mainland, Alexandra smiled at the attempts John was making at flirting with one of the new female scientists. It didn't freak her out as much as she thought. Or hurt. She was more amused than anything else, really. And she felt like John was having fun.

Not far from where she was, John glanced back at her at some point. Alexandra was writing, taking pictures and he couldn't help but notice that she looked more relaxed as the days went by in the ancient city. And if he was honest with himself, he felt relaxed as well.

For the past three weeks, they were back to their usual banter, talking, laughing, having meals together... And he liked that. He enjoyed anything she would give him. Even if it surprised him at how quickly, and affirmative, she had replied to his question about accompany him and the astrobiologists to the mainland. And he wouldn't ruin her mood in their first mission together after everything that happened between them.

"You could help, you know?" He sauntered closer to her, after giving up on the other scientist.

"What?" She glanced up at him with a smile. "And let myself miss out on a show? No way, flyboy." Alexandra teased him.

"Shut up…" John heard her snort as he followed her into the woods. "You like seeing me suffer, don't you? Confess!"

Alexandra shrugged with a mocking smile.

Suddenly, a sound was heard not far from where they stood and both got into attention.

"Stay here." He said.

"You're not going alone." She countered with a frown.

But neither one got too far as both were put uncounscious with a stun gun shot.

In Atlantis...

Meanwhile, Rodney found something very interesting at the bottom of the sea, per Radek's idea.

"Keep looking. There's nowhere for them to go. They're scientists."

At Kolya's voice, John opened his eyes, a headache blooming on the side of his head and feeling himself bound against a tree. Immediately, hazel eyes spot an uncouscious Alexandra not far from him.

"You're awake. Save your energy, you're not getting away this time, John." The older commander's eyes go from the pilot to Alexandra. "She's okay, if you're wondering."

"I killed you." There was a confused tone to John's voice.

"You shot me. There's a difference." There was a shrug in Kolya's words.

"No. I killed you. Beckett confirmed it. You were dead." The pilot insisted, remembering the day in question very well.

"Yeah. I'm sure that's what he thought. Let's just say that your friend... what was his name? Lucius? He wasn't the only one using Ancient technology that day."

"How did you get here? How did you find us?"

"Turns out some of your offworld contacts aren't as trustworthy as you think. Your secret's out, Sheppard. Even the one of your lady friend." Kolya approached Alexandra as she had come to herself in the last couple of seconds. "You should introduce me, John."

"What do you want, Kolya?" John tried to take the older man's attention away from her.

The enemy smirked slightly looking back at the pilot.

"A half's day walk in that direction will bring us to the edge of the mainland. I figure it'll take us maybe two days to reach Atlantis by boat."

"Before you even get to the city, they're going to blow you out of the water." A dark shadown was slowly creeping into John's eyes.

"No. They won't even see us coming. They'll be to busy couting their dead."

"What are you going to do?" The scientist spoke.

"Cripple their defenses with an explosive device. But first I need something from you. An IDC."

"Go to hell." The colonel simply said.

"Figured you needed some convincing." Then, Kolya struck John, that grunted in pain.

Again.

And again.

«Why can't I use my powers? I feel... strange.» Alexandra frowned, moving her hands to find a weakness to her binds as she witness John's torture.

"You can tolerate more than any man I've ever known." Kolya finally spoke after a few minutes. "Now, why is that?"

"Well, I was married once." John retorted, hearing the other man chuckle.

"I heard about you, Commander Kolya." Alexandra started, her heart jumping in her chest. "You want Atlantis, but she's always out of your reach."

"Don't you dare touch her, Kolya!" John spit blood as the older man stopped and approached the scientist with a sadistic smile on his lips.

"I am not in a mood for bargaining, Dr. O'Neill." Then, Kolya trapped her chin in his hand. Hard.

"I'm not bargaining. I'm sure you know we don't trade with terrorists. Just stating the facts." She shrugged.

"You're feisty. I like you." Kolya chuckled, releasing her, upon seeing the fire in her eyes.

"Kolya!" The pilot got the commander's attention.

"Very protective, are you, John? I wonder what Dr. Weir would think about that. After all, you were very protective of her as well and look what happened to her."

In a second, John leaned against the tree, quietly, disheartened. Kolya smiled as if he was winning.

"You're here in the Pegasus Galaxy to protect your people, but half the time you can't even do that." The two shared a look. "That's what drives you, isn't it? Your past failures."

"Don't listen to him, John!" Alexandra frowned at his sudden quietness.

With a flick of his wrist, one of Kolya's soldiers placed a rag in Alexandra's mouth to prevent her from speaking. Then, they unbounded John and placed him on his kneeds while Kolya picked up a machete. She grunted and fought against her own bounds, but with no changes in her powers. She felt like she had drank too much and a sense of wooziness overwhelmed her.

"Last chance, Johnny boy. You going to give me that IDC?"

For the first time, the pilot looked afraid, already anticipating what was going to happen. He couldn't look back but Alexandra's muffled screams were heart wrenching.

"Didn't think so."

There was a dry sound and then nothing.

Minutes later, as John opened his eyes in pain, his hazel eyes found Alexandra's. There was sadness in them.

Then, he looked at his severed arm.

"You're an interesting man, Sheppard." Kolya was looking at his foe with a curious glint in his eyes. "You travel to another galaxy, risk your life for a bunch of people you don't even know. If you ask me, you're either someone with a death wish, or someone running away from something. So, tell me, what are you running away from?"

There was no answer.

In Atlantis...

Meanwhile, in the ancient city, Rodney finally found the information he needed about the curious pod he and Radek rescued from the bottom of the sea.

"It's a mechanism to spread living organisms that can become sentient beings, once released."

And, now, a choice is presented. Getting the information from the pod or sending it back into space, back onto it's course for a new home.

"Even those two scientists you came with put up more of a fight. Perhaps I should have a private conversation with Dr. O'Neill." Kolya glanced away from John, who had a ragged breath as he exchanged looks with Alexandra. "Boys, bring the doctor with us." The commander ordered.

However, as Kolya turned to John once more, the pilot had disappeared into the forest, trying to give Alexandra time to escape. His senses made him question on the reason why she hadn't used her powers yet.

"After him!" The commander demanded, leaving Alexandra bound against the tree.

As minutes of fighting and gunfire ensues, at some point, John fell down a precipice, holding on with just his good hand.

"Use your other hand." Kolya shouted as he appeared from above, watching John struggle.

Frowning, the pilot looked at his severed arm and saw his hand back.

"Go on. I have no intention of letting you die. Now, climb back up, John."

As soon as he's out of danger, the pilot pulls up his hand gun and looks Kolya up and down.

"What the hell's going on here?"

"Before I explain myself, we should check on Dr. O'Neill."

With a confused nod and frown, John ran into the forest, to where he had left Alexandra and found her uncouscious, no ropes in sight.

"Alex..." His voice was soft as his hand touched her cheek and relief flooded his chest, seeing her eyes open and focused on him.

"John? What happened? Your hand…"

"I'm fine. See?" He showed her his hand. "Are you okay?" He saw her nod and helped her up as she seemed light-headed.

"I am sorry for putting both of you through this. But I needed to know." Kolya's voice sounded behind them.

Both turned to Kolya, silently.

"I am the artificial intelligence of a seed carrier from a race called Sekkaris. I am their last hope to achieve the unit's assignement." At their nods, the entity continued. "It contains millions of my species. We have foreseen our extinction and decided that wouldn't be our fate. The pods that were sent have the History and the Science that will recreate my people in a new planet. But to do that we had to find the ones that could help us on our way. This ruse was to see if you were worthy for us to ask for your help. As a soldier, John, you were threat. If anyone was to use force to secure the repository, it would have been you. So I connected with your mind to distract you."

"Distract me?" John leaned his head to the side, feeling shaken about the experience.

"My apologies, Col. Sheppard. It was necessary to keep your mind occupied."

"And that's what you chose?"

"What you chose." The entity pressed. "I didn't have full control over your hallucination. Or the direction that it took. It was your mind driving the diversion. I merely played along."

"Are you saying I tortured myself?"

"You torture yourself everyday. But in this case, it was your mind manifesting your darkest fears."

For a moment, John was surprised, and not in a good way. He glanced back at Alexandra, that had been listening quietly.

"That's why I couldn't use my powers. Or why I feel dizzy." The scientist suddenly said. "You couldn't enter my mind."

"Exactly, Dr. O'Neill. Connecting with you was very hard." The Kolya image turned to her. "So, I used the information I got from John's mind. I tried something very similar to what Kal did to you when you found his body." Alexandra frowned at the memory. "I used what John was seeing to distract you, while attacking your mind in the process, so you would play along, as you would say. You will have a bad headache in the morning. I am sorry for it."

At her quiet nod, directed at the A.I., John cleared his throat.

"We should go. Warn Woolsey and see what we can do."

And they were left alone at his words.

Before he could walk ahead, Alexandra grabbed his arm.

The pilot looked down at her. He saw something he didn't want to see. Not now, when they were back at being friends. Not when he had a lot to ask and was trying to find a way to breach the walls he had put between the two.

"Later. We have to go."

With another silent nod, Alexandra followed him, finding the other two scientists safe and well, ready to go back to the ancient city after the colonel's and the lead scientist disappearance for hours.

In Atlantis...

"I'll start the process that will give life to the Sekkari, and then I'll go to sleep until a time when I'm needed again."

Woolsey nodded with a smile at the entity in front of him.

"John, I realize it may have been an unpleasant experience."

"Yeah. Well, just a little bit." The colonel's shrugged, trying to shake the odd feeling lingering inside of him.

"And I want you to know I'm sorry for what you had to go through."

The pilot nodded.

Then, the woman that had been Woolsey image turned to Alexandra.

"And, Dr. O'Neill, you should trust more in others."

"I'll try to remember that." Alexandra offered a smile, wondering what the entity had seen in John's mind.

"I'm sorry. I don't mean to complain or anything. It's just that I have spent the better part of a day making sure this was in working order. It would be kind of nice to just get a little face time with the..."

"Here you are, Dr. McKay. The true form of the Sekkari."

And then the woman turned into a silvery glass looking kind of humanoide.

"Good luck." Woolsey ended.

Then, the Apollo beaming light appeared and took the pod away from the city.

As John and Rodney left the hallway, Alexandra smiled at the older man.

"Are you okay, Mr. Woolsey?"

"I am, Dr. O'Neill. Thank you."

And evening time rolled along, Woolsey ended up joining Atlantis main team for dinner, finding that Zelenka had been Rodney's Sekkari's image for the day.

Later that night, Alexandra couldn't sleep, so she went for a walk, finding one of the balconies doors open. There, she found John, leaning against the railing.

"Can't sleep?" She asked softly, stepping closer to him. And saw him shake his head. "John…"

"Can we please not talk about it? Not tonight, at least." He kept his eyes on the moons of the planet.

"You can be all somber and broody with the others, and I know they've seen a lot from you, but don't be like that with me. Not after what I've seen today."

John let his head fall at her words.

"You can't really believe in everything the Sekkari said."

"I've read your file, remember? I've seen you in action... In a more personal way. John, you can't really think all of that of you. I've told you..."

"Why can't I?" He still didn't look at her. "I'm impulsive. Teyla got abducted. Ronon almost died. Same with Rodney. Elizabeth… I failed her. Atlantis…"

"Atlantis is safe! Because of you, John. Because you have a good heart. You don't give up. Look what the Sekkari did, they trusted you." She placed her hand on his arm. "Look, I won't deny that you don't have a dark side. Everyone has one. Some more passionate than others. That's why Atlantis is still here. Why everyone looks up at you for leading. Even Woolsey."

"C'mon…" John half snorted as he glanced at her.

"It's the truth. Even my uncle trusts you because he saw something in you, John. And I look up to him, so..."

"Michael took you." Finally, his eyes landed on hers.

"And you got me back." He was about to protest when she took a step closer, making him look down. "Listen to me, John Sheppard." He saw fire in her eyes. "You are a good man. You have a good heart. Did you do bad things? Deal with it. Did you made mistakes? Deal with it."

"I hurt you."

"And I came back. Maybe my uncle ordered it, but I wanted to come back. I missed you... All of you, I mean." She shrugged. "I'm complicated."

"So am i." He saw a hint of a smile on her lips.

"And if an Ancient tells you that you are a good man, a good leader, you accept it."

"I thought Ancients were sneaky llittle bastards…"

"Well..." She shrugged, taking her hand off his arm and looking out to the moonlit horizon. Immediately, he missed her touch, even if he could feel her body heat next to him.

He gave her a smile and then frowned. How could he tell her that another Ancient had told him otherwise.

"Why are you my friend?" The question just went out.

"Because I don't trust people that don't have a dark side."

"That's why you don't like the Ancients?"

"Trust me. They have bad sides. But theirs is of a different kind. But I do believe me and Janus would get along quite well."

John chuckled at that.

And when silence settled around them, like so many months ago, Alexandra settled next to him, almost pulled by his now relaxed stance.

And the trials of the day slowly caught up to them.

Ps: Thoughts?