A/N: Whoa, this was a long one but I'm beginning to enjoy it very much. Don't know where everything is coming from, thinking how this whole fanfic series started with basically plain crack! Now is almost serious… almost anyways. If all goes well, I'll have the next chapter in the next couple of days.

Enjoy!

Chapter VII:

John was angry, angry at the whole situation. It was unfair, to finally find someone who is strong enough to stand him and understand him. He didn't have to keep secrets about his job and that was a plus. But then she had to be his boss. Yes sometimes it was complicated, but they had managed to make it work, and he wanted to keep on doing it.

John walked into the transport, once on the other side he walked out to the hall way and turned left. He started hearing footsteps; someone was running. John frowned and tried to follow the footsteps that were now sprinting. Why he followed it, he had no idea, curiosity, maybe the urge to forget his current problems."

The Colonel went around the hallways and the footsteps were leading him back into the transport. But as he turned on a corner he had to stop so suddenly he almost lost his balance. Then just as quick John backed away.

Commander Acastus Kolya was in the city… how?

The person he was following was Stella who was now with Kolya's people. That presented a problem, because if Kolya was this far undetected, it meant that he must have more people captive.

Having a large group down at the mess hall, that was going to be a problem. And he should keep radio silence, just in case they were being monitored. The night was going from mildly annoying to bad then jumped into horrible in just a couple of minutes.

Keeping himself out of sight, John made a decision and ran towards the armory.

-0-0-0-0-0-

"Dr. Weir is so nice to see you again." Kolya said with a particular sneer on his face. Then he turned to Rodney. "You too Dr. McKay."

"What the hell are you doing here?" Rodney said before he could control himself. Kolya looked at the scientist in plain amusement. "Well Doctor, we got along so well the last time we saw each other, that I wanted to see you all again." Kolya scanned the room and his expression went from confident to angry in seconds. "Where is Colonel Sheppard?"

Elizabeth glanced at Rodney, but remained silent. Kolya moved in closer. "I asked a question Dr. Weir."

Elizabeth remained steady and silent; Kolya then stood right in front of her, took out his gun and pointed it at her face. "I'm not going to ask again."

Rodney was now staring at her, Elizabeth then focused on the man in front of her. "I don't know where he is."

There was a long silence where everyone seemed to assimilate what was going on. The off duty soldiers in the room exchanged glances, trying to come up with a good solution. But Kolya's men were too many and almost no one in the room was heavily armed.

Kolya lowered the gun. "Then before he graces us with his presence, you and I are going to have a little chat."

Kolya then looked at a tall, blonde guard behind him. "Cali, divide them into groups. Then send a team to search the common areas. I want every citizen to be unarmed and neutralized. Especially Colonel Sheppard, once you find him bring him to me."

"Yes, sir." Cali responded quickly.

Kolya then turned to Elizabeth. "Shall we?"

Suddenly Caldwell tried to get closer but failed when a Genii guard stood in his way with a big weapon. Instead the Colonel looked at Kolya. "What the hell do you want?"

Kolya looked at Caldwell in amusement. "You must be new," Kolya smiled, as he seemed to consider the question. "Same as always; power, control, beautiful women." As he said the last words he tightens his grip on Elizabeth.

Caldwell frowned. "If you harm her, you won't get anything."

"Sir, I think this woman is already claimed. Let him do the threats."

Elizabeth threw Caldwell a grateful glance. He had tried to help her, even with all the other stuff that was going on. She had a mixed swirl of emotions going on inside of her. For one, she was going to be alone with Kolya again, that was never a pleasant thought. Then Kolya's comment to Caldwell about her, that she was claimed. Life had an unpleasant way to show you the bad times; they were always one on top of the other.

Before she walked out, Caldwell shot her a look, which Elizabeth couldn't figure out. Kolya started dragging her away and the last thing Elizabeth saw was the worried glances of Rodney and Teyla as she walked out of the mess hall.

-0-0-0-0-0-

For the first time since he moved to Atlantis, Ronon felt the need to say something to Colonel Sheppard. The whole situation with Colonel Caldwell was stupid, immature at best. Ronon understood the problems a relationship like the one Sheppard and Dr. Weir had, could bring to the place.

If he had been in the city, when they had started it Ronon was almost sure he would have been against it. Leadership cannot be controlled by emotions, especially if the two leaders were a couple.

But since he walked into the city, Ronon had never seen them showing their affection for each other publicly. Or even have their relationship interfere on important matters.

Now he felt the need to intervene on something that had transformed into a childish situation.

Ronon stepped into the transport, once on the other side Ronon turned left towards McKay's lab. He heard footsteps, more than two, it almost felt like a group marching, but someone was definitely running. Ronon followed them, and then he heard a voice, a woman gasping.

Ronon followed the sound; it didn't feel good in his instincts. On the next corner he found a group of people, an unconscious young woman was being carried by a soldier in a strange uniform. There were at least 30 soldiers and in front the leader, who said, "Aiffel, can you give me Sheppard's location?"

Ronon didn't wait for the answer; he was quickly on the move. These people were now headed towards the mess hall. That meant that they should have more areas of Atlantis under their control.

They didn't know where Sheppard was, so he needed to find the Colonel in order to organize those who weren't captive yet. If they had managed to get so far without anyone noticing, it was a sure bet that the radios were compromised. There was no point in returning back to the hall; he would only manage to get caught.

Ronon saw the group split when they reached the transport. Attacking the leader now was useless, because he didn't know just how many of them where already in Atlantis. So Ronon decided to follow the small group heading towards the control room.

Ronon took another way to get there; it was quicker and less known. If the control room was still under Earth's control, he'll be able to warn them about the intruders. But as he arrived, the outcome was otherwise; the intruders had control of the gate. All the security guards and technicians were gathered on a corner of the upper level. The young woman joined them shortly, after the guard placed her with the others.

They were all unconscious, or so Ronon hoped. Because if they were dead, the situation was worst that he originally thought. But then the guard started kicking the legs of most of the captives. They started to wake up, and Ronon breathed in relief.

He needed to do something, but before he could think of something, he heard someone approaching him.

-0-0-0-0-0-0-

The walk with Kolya was made in silence; Elizabeth already knew how the man worked. He liked to be stealthy, rude and calculated. Although he never succeeded in both the opportunities he had to take something out of the expedition. Kolya had always managed to do some real damage.

In some way Elizabeth hoped that this time it would be the same, minus the damage part. She knew what he was capable of, and if someone tried any sort of rescue at this point it would be scary. By experience, she was aware that he had no problem in gabling with her life.

By the time Elizabeth realized where they were going, she felt a bit aghast. The gate room was in their control. Instead of the usual soldiers, Genii guards were by the gate. The oversized guns looked more menacing than their owners.

But still… they were armed men, always a dangerous thing.

As they walked up the stairs and he led her to her office, there was a commotion on the far left side of the second level. A Genii guard was looking very annoyed, the Atlantis soldiers were looking amused and someone was laying their head on a console.

It was enough for Kolya to take notice. "Jole! What is going on?"

Jole turned around, so he covered the person that was lying on the console. Elizabeth couldn't identify the person, but the clothes revealed that it was one of hers. The guard looked even more mortified when Kolya addressed him, but he replied, "Nothing sir, everything is under control."

A loud muffled laugh came up from behind him; Jole's face went ten shades of red.

Kolya eyed the soldier carefully. "I want that console up and running as soon as possible."

The answer was a confident face, with a nervous voice. "Yes, sir."

The laugh was fainter this time, but still there. Kolya grabbed Elizabeth by the arm and led her towards her office. Once inside, he closed the door. "Your people are very efficient; someone blocked the console that shows where people are in the city. That will be resolved shortly."

Kolya motioned her to sit down on one of the chairs in front of the desk; he rested against the desk facing Elizabeth. "How are things?"

Elizabeth felt like stabbing the man, the man just sat there and wanted to talk like old friends. She managed to retain a calmed face. "They were fine Commander, until you showed up."

"Are you sure? You weren't looking so good when I walked in." There was amusement in his voice. Elizabeth ignored the hint. "Why are you here?"

"Straight to business." Kolya said with a smile.

"With you is always is always business."

"Where is Sheppard?"

"I told you, I don't know."

Kolya crossed his arms and let out a sigh. "Then I want to talk to your superiors."

Elizabeth stared at Kolya. "My superiors are very far away."

"I know, but I also know that you're able to communicate with them."

"No," Elizabeth knew the answer might cost her a lot, and she feared it once Kolya stood up. "Dr. Weir, it will help greatly if you cooperate."

Elizabeth remained silent; Kolya took a step towards her. "Then tell me where Colonel Sheppard is."

"I'm not going to say it again, I don't know."

"Then he better show up soon."

There was a commotion outside, Kolya turned around and Elizabeth saw that someone was hitting the guard called Jole. Elizabeth smirked, "On the other hand… I should tell you where to look for him. Every time your plans have failed, is because of him. Hopefully this time it will be the same."

Elizabeth never saw it coming; the slap on her face left her cheek stinging. She could feel each finger almost etched on her face. But it gave her satisfaction to see Kolya's face.

-0-0-0-0-0-0-0-

Arriving near the armory, John decided not to go right in. If Kolya's men were all over the city, this would be a place he would set up guard very quickly. John had no life signs detector with him, so there was no way to know or sure if there were hostiles on the room. John peeked around a corner and looked at the armory doors. The corridor was empty, not a soul around.

John moved in carefully, he didn't want to walk into an ambush. But as he moved closer he found no one. He opened the door and walked inside, he was lucky, it was empty. John quickly grabbed a life signs detector, ammunition, a P90 and a small wraith stun gun.

He turned the detector on and saw two figures heading his way. Either Kolya had found him, or just his guards were making rounds. John needed to think quickly, he hid inside the room; the Colonel took another look at his LS detector and waited.

When the guards arrived, they were startled to find the doors open. Quickly they started searching the room. John had made sure that his hiding place was one they would search quickly. When the first guard looked behind a big box, there he found Colonel Sheppard sitting on the floor with a stun gun in hand.

The next thing that happened was two quick shots, and the guards were on the floor. Sheppard stood up and looked around, to make sure this would not be discovered so quickly. John hid the unconscious guards on a nearby storage closet and then headed towards the gate room.

He checked his detector, no one was near him, John thought for a moment to move towards the mess hall, but there were a lot of people there. And most likely there were many guards as well. Hidden shortcuts and corridors were always the best option, as he moved in closer he could see the Genii guards moving around. He searched for the LS detector, but as he turned on a corner, a gun was placed on his head.

Taking a quick look he realized that it was Ronon.

Both soldiers sighted in relief at the sight of each other, and then Ronon have him a small smirk. "I almost blew your head off."

"Well don't try anytime soon." John said as he shook his head.

Ronon put his gun away and walked towards the gate room. "Who are these people?"

"They're Genii, I can bet they're with Kolya," Sensing Ronon's questioning gaze he added, "bad guy, long story."

"We need reinforcements."

John nodded. "We need to get to the Daedalus. I don't know why they haven't done anything but Kolya can't have that much man power to overrun the ship as well. We need to get in there before someone finds us."

"What do you want to do?" Ronon asked as he took another glance to the gate room.

"Let's go to the ship, and then we'll deal with the bad guys. Also, we need…" John didn't finish his sentence, he was looking at the gate room and he just spotted Kolya on Elizabeth's office and he had her. That set off a fire inside of him, Ronon knew him well, as the Runner said, "Let it be, we need to get more people."

"He'll hurt her… I know he will."

"Sheppard, you need to be sharp. He wants you…"

But John never allowed Ronon to finish his sentence. "Precisely."

There was a commotion to Ronon's left, on the second level where the captive soldiers were. He then turned to the Colonel. "Sheppard…"

Seeing Sheppard's angered face, Ronon took another glance towards Dr. Weir's office, and at that moment Kolya slapped the Doctor on the face. When Ronon turned to look at John, he wasn't there, he was moving into the open.

John couldn't fight the anger within him, and he made a choice he might regret later. He saw Ronon following him, he turned and said, "Ronon, get the others, that's an order."

"Sheppard!"

"I gave you an order. DO IT!" Then John Sheppard walked into the gate room.

TBC…