Disclaimer: Sadly, I do not own any of these characters. I only take them out to play.

Timeline/Spoilers: Takes place in Season Two, sometime after "The Hive" and before "Micheal." Contains spoilers for "Instinct" and "Conversion" and minor spoilers for other episodes.

Author's Note: This is my first post in a long time, though I actually started this story last year. The original idea was conceived for Ree'an, my original character, but I have changed it around and like it better without her. It does contain Jamie from my other stories: "Dragons of the Deep" and "Dolittle Device."

Many thanks to NalanaSpinderOfSouls and my other friends for beta reading! Hope you people enjoy it and please review and tell me what you think! Reviews make me happy and happy writers write better stories!

Gene Warfare

By Rowana Farrin

Chapter One

Silence. It penetrated every hallway of the dark city. Not a sound echoed in the unending corridors. Nothing moved. Even the shadows did not so much as quiver. All was quiet, wrapped in a blanket of disturbing silence. Darkness too haunted the halls. Thick and intangible, it hung like a cloud over the city. Lights that dared shine were immediately swallowed by the unforgiving dark.

Amidst the darkness and silence, an evil lurked. Its presence was clear against the tranquility of the city and the sea that surrounded it. The evil stalked the corridors, searching. Searching for something that it needed to find. Something that it needed to spread its menace throughout the worlds. It was hungry. It was thirsting for the lifeblood of innocents and their screams of terror as they died.

Teyla woke with a start, the memory of the nightmare still fresh in her mind. Something was horribly wrong. Something was here; something that should never have been here. She threw off her covers and raced down the halls. Her running feet and panting breath broke the blanket of silence. The city was suddenly alive again with the noise that normally plagued it. She pelted around corners and down dark passageways until she finally reached her goal. She knocked frantically on the door, as the cold dread in her mind grew.

"Colonel Sheppard! Wake up now!"

John woke with a start. It figured that the one night he seemed to be having a peaceful sleep, someone would knock on his door. He groaned, rolled over, and rose quickly to deal with whatever emergency had come up this time. He grabbed his gun and opened the door to find a barely dressed Teyla. Before he could ask what was wrong, she answered the question: "Wraith. In the city."

He frowned and instantly reached for his gear. "Are you sure about that?"

"Yes. I do not know how, but they are here." She froze suddenly. "Wait..."

"What is it?" He glanced around the corridor, gun ready to shoot anything that threatened.

"I believe they have gone. But they were here!" she insisted.

"Right." He made a quick discussion. "Go and wake Dr. Weir, tell her what's going on and to meet me in command." He grabbed an extra gun and radio from his room and handed them to her. "Be careful."

Teyla nodded and headed off. John ran for command, checking each corridor as he went. All was quiet and looked normal. He knocked urgently on his new second in command's door.

"Wraith in the city," he told a startled Major Lorne when he opened the door. "Have security teams sweep every inch of the city. Check in every ten minutes."

"Yes, sir." Lorne immediately began to radio his men while he pulled on his combat vest. Sheppard didn't wait, but hurried quickly on towards the command center.

Teyla and Dr. Weir were already waiting for him when he got there. Dr. McKay had also been awake, doing late night lab, work and was now typing frantically on one of the laptops. Sheppard immediately started pumping the night crew with questions: "What's our status?"

The tech on duty shook his head in confusion. "Scans are clear, sir."

"Are any of the systems affected," Dr. Weir asked.

McKay barely looked up. "It's going to take a while to run full diagnostics. But there are hundreds of systems to go through and we have no idea what the Wraith could have done to affect them." He sounded nervous, but so far was keeping himself under control. "What worries me more is how they got in without anyone knowing. The scans should have warned us of if any showed up."

Sheppard frowned and started pacing the floor. His instincts were screaming that something was wrong, but he couldn't put his finger on it. He clicked his radio. "Lorne, report."

"No sign of the Wraith, sir," the Major replied. "Everything seems quiet."

"Start checking the crew quarters. I want a full head count on all personnel and let me know the minute anyone is missing."

"Yes, sir."

Impatient for results, Sheppard and Teyla took off and met up with Lorne and Lt. Cadman in the South hall. Sheppard and Major Lorne started down the living quarters taking a count of each person. Teyla and Cadman did the same in the women's quarters. Most of the other personnel were asleep and the rest were more than willing to stay in bed until danger had passed.

After several minutes without incident, John was beginning to think they had gotten away clean this time. McKay reported that the computer and technical systems were untouched and so far all the patrols had come up negative. It bothered John that the Wraith didn't seem to have done anything. Sneaking around wasn't like them in the first place and to leave without hurting anyone or anything was definitely out of character. Still, he had a few more corridors to search.

He turned a corner and immediately knew something was wrong. The hall looked the same as all the others, but something was definitely not right. Major Lorne started checking doors. Everyone was asleep and most didn't even notice the soldier checking on them. Sheppard walked ahead uneasily, weapon armed and ready. Suddenly his foot hit something that skidded loudly across the floor. Lorne looked over, gun ready, but Sheppard held up his hand in a silent command to wait. He knelt and picked up the object. It was a hunting knife with a wood and leather hilt.

'This is Ronon's knife,' he thought in puzzlement. 'What would he be doing here in the middle of the night?' He felt a sinking feeling in his gut. The knife was covered in fresh red blood.

"What is it?" Lorne asked softly.

"I don't know." He turned quickly to the door that the knife had been by and quickly palmed it open. In an instant his worst fears were realized. The room was in shambles. Sheets had been torn off the bed and thrown carelessly aside. The side table had been knocked over and personal affects were strewn all over the small room.

John looked at the scene in horror and barely heard Lorne's next question: "Whose room is this?"

He felt his heart sink even more as the answer came to him: "Dr. Beckett's."

To be continued….