Disclaimer I do not own Xenosaga, or its characters in any way. This is just a Novelization of the original game

Chapter 1

The KOS-MOS project

4000 some years later

Year: 4625 S.E.

Aboard the Federation ship Woglinde

Shion Uzuki was not a typical Vector Industries employee. For example, she was accepted into the highest raking area of Vector industries at the age of eighteen, directly after she graduated high school. Vector's First R&D division was the hardest class of Vector to get into. They worked on top secret military and government projects that were not to be revealed to anyone outside the company. Even for a Bormeo University graduate, it was hard for them to get accepted into a rank so high. It left lower class employees of Vector questioning how a high school graduate like Shion could place so easily as Co-Chief of the First R&D division without any college education. It was a question Shion asked herself many times.

Now at the age of twenty-two she had taken on the role of Chief engineer of Vector's first R&D division and was currently working on a project that she poured her heart and soul into…the KOS-MOS project. The KOS-MOS project was an android that could be capable of practically unlimited battle capacities.

Now that all of humanity was living in space and on distant planets in this day and age, a new threat had arisen. Humanity faced the threat of the Gnosis. Gnosis were alien creatures that show great hostility toward humans. Vector Industries CEO Wilhelm had suggested that they create an android prototype that would have the abilities to defeat the Gnosis if they ever were to attack. And so the KOS-MOS project had begun.

Ready for another day's worth of testing Shion Uzuki proceeded to begin the Encephalon dive. The Encephalon dive could transport the human consciousness to a dream like virtual reality world. Dressed in her Vector Industry uniform she took her seat on the VX-2000 Encephalon dive chair, and pulled the harness over her head. She looked at her partner Allen Ridgeley for backup. He gave her a quick nod and asked her to proceed.

"Commencing Start-up experiment. Open up an interconnection." Shion ordered.

"Rodger. Opening interconnection. Connecting with dummy protocol." Allen replied.

"A-line protocol secured" another of Shion's wokers, Basil announced.

Togashi another co-worker said, "Opening cage partition, 60 seconds until release. Countdown…. 59…58…57…"

Shion sat in the Encephalon dive chair waiting patiently. She had done this procedure many times before. This time was no different.

"All monitors cleared. Opening cage partition in 3…2…1… Proceeding with the KOS-MOS body formation." An image of a see-through young woman appeared on Togashi's screen. "Proceed to the Penfield mapping."

"Penfield mapping at 78…79…80" Basil replied.

To Shion this was all standard procedure. It was something she did everyday, like she got up every morning at six, and brushed her reddish brown hair into the same hairstyle every day (A braid on her left side and a clip on the right.). To Shion this day was no different than any other day. She sighed and took off her glasses.

Shion was shook from her thoughts when Allen cried out "There's noise appearing in the temporal lobe."

Shion looked at her co-worker with concern. "What's the problem?"

Allen turned to look at Shion's green eyes. "Its on the left side of the temporal lobe. I'm showing slight signs of stimulation to the synapses in section 818… its within permissible bounds though. Do you want to abort?"

Shion answered this automatically. "No. Lets keep going. Just stick to the menu. I'll try from a direct approach." If there was one thing Shion hated the most, is pausing her job because of problems. The deadline for the next amount of data was due today and the commander would have her head if he didn't get it.

"Roger. Launching NATARAJA connection system." Allen replied.

Shion waited patiently again as the start-up system began again. The screen within the harness flashed asking for the connection password. With a slight smile she typed in "Ye Shall Be As Gods."

"Password Accepted…commencing NATARAJA boot up sequence" the automatic computer like voice replied.

Before Shion knew what was happening she felt her vision go blurry and her body get very heavy. She felt like the walls were closing in upon her and the air grew harder and harder to breathe in. Shion never liked this part of the start-up sequence, but before she had time to panic she felt her body being pulled in a strong jolt. It was as if someone pulled out her insides. The sickening feeling however stopped, as quickly as it started, and Shion's consciousness stood in a new virtual world constructed by computers leaving her near lifeless body in reality.

Shion focused on her new surroundings. She stood in the center of what looked to be a wrecked warehouse. Electrical lines were pulled down and cut; leaving sparks flickering from the tips. Fires burnt off to the side of the main pathways ignited by fuel tanks. The air smelled acrid with the scent of tar. Chunks of concrete and building seemed to be missing from this already devastated scene.

Shion looked around with more suspicion and found that at the edges of her vision the scene went blurry and static-like. "Allen, there seems to be a problem with the visual field connection."

Allen, who watched the chief engineer from his computer screen in this virtual world looked closely at the monitor. "Hmm… Ah! I see a small break in the MT field, route K12. It looks like the bi-directional link in the V4 field is lagged too. Hold on a minute I'll fix it now…How's that?"

Shion felt an immediate response. Her vision cleared and the virtual world came back into focus. "Looks good. Lets keep going."

Allen smiled. "Rodger. Proceeding with KOS-MOS host separation."

Shion waited patiently for the procedure to begin. After all… this was standard basic procedure. She had been working on KOS-MOS for four years now. Every morning was the same. As was every evening as well. Shion was forced from her thoughts as a bluish gleam filled the space next to her. The light continued to grow brighter and brighter until it formed the shape of a woman. In one blinding flash a human like figure stood next to Shion, her red eyes focused.

Shion took a good look at the android that she had worked so hard in creating. She stood about five and a half feet tall, with long flowing blue hair that reached past her back. Her eyes were intense and determined and her face was utterly expressionless.

"Morning KOS-MOS. How do you feel?" Shion questioned the female.

KOS-MOS looked at her creator. " Good Morning Shion. All systems are normal."

Shion frowned. " How about introducing yourself?"

The android nodded, yet still expressed no emotions. "I am an anti-Gnosis Humanoid Fighting system. Serial number 00-00-00-00-1. Development name KP-X, abbreviated name KOS-MOS. As I am currently configured for simulated battle, my output is limited to 22 of its normal capacity. My estimated weapon specifications are…"

Shion interrupted the android. "All right, that's good enough. Thanks."

KOS-MOS remained still. "You are welcome." Her robotic voice made it hard to believe that she could ever feel any emotion.

Shion turned away from the overbearing red eyes of the android. "I'm afraid all I have for you today are the usual start up tests. Sorry to wake you up just for that. You'll have to go back to sleep once everything is checked out."

"I see."

"Do you feel… sad or anything?" Shion questioned.

KOS-MOS didn't even look at Shion this time she spoke. "A predetermined set of emotions has been hard-coded into my emotion module to better facilitate interactions with humans. In order to facilitate a relationship with you- Chief Engineer Shion Uzuki of the KOS-MOS project, Vector Industries first R&D division- I will emit an expression such as sadness only when that response deemed necessary. However, the emotion module of my program has determined that this is not necessary at this time."

Shion let out a small giggle. "I guess your right. I of all people should have known that."

KOS-MOS looked once more at her creator. "Your understanding is appreciated."

Shion didn't reply at first, but instead went deep in thought. KOS-MOS waited patiently for an answer. Finally the young engineer replied. " But you know, KOS-MOS… I've got mixed feelings about all of this. Of course I'm happy your awake, but the fact that you'll go back to sleep makes me a bit sad. On the other hand the next time you wake up, it may be a time of much bloodshed, so deep down inside… I hope that day never comes. Understand?"

KOS-MOS looked at Shion innocently. She processed the information that her creator had told her, and replied. " The algorithms I have been programmed with do not support the comprehension of illogical thought."

Shion let out a sigh. "Well, I hope someday you'll be able to understand."

KOS-MOS nodded. "I will try my best."

With a bit of disappointment Shion pulled out her connection gear and activated the computer screen. "Alright KOS-MOS shall we get started? Allen lets pick up from process 277 where we last left off."

"Rodger. Placing target drones in the encephalon. The drones are set to 'random movement' and 'enemy ambush' Allen replied. "How about a test run before the mission chief?"

Shion thought a moment and nodded. "Lets do that. Did you get that KOS-MOS?"

"Affirmative."

Shion proceeded in checking all of KOS-MOS' parts and weaponry. She also tested her logical capabilities and her field combat statuses. As usual everything was working, yet there were still things about the android that even Shion was discovering.

"All processes to 300 cleared" Togashi called.

Allen entered the new data into his computer. "Chief the data transfer is going smoothly. The A-line protocol is looking good."

"It sure is. The response levels are really good." The young engineer replied.

"If we can maintain these levels, we'll have some really good results soon." Allen commented.

"Yeah…" she began, but her voice wandered as she looked at KOS-MOS.

"Chief?" Allen questioned. He clearly hated when she talked like that. It usually meant she was going to suggest a foolish idea.

Shion was silent for a moment but spoke up. "Hey Allen… lets skip all 300 level processes and start from 400!"

"Huh? 400, Chief, but that's…"

She waved her hand in the air. "I feel pretty confident this time."

Allen protested. He wasn't going to let this happen without a fight. "But Chief! Remember what happened the last time? Had we waited ten more seconds to intervene, we wouldn't have been able to get you back at all. Can't we at lest test it out in objective mode?"

Shion winced. She remembered all to clearly what happened the last time. She had waited till the last second to pull herself out of the encephalon. She had risked her life for the data KOS-MOS was giving off. If she hadn't gotten out of the encephalon before it deteriorated, her consciousness would have been lost in the space time anomaly forever, leaving her physical body lifeless. Yet she still didn't want to do the boring tests over again. And it was true that she felt confident about KOS-MOS' abilities this time.

"You know we can't get precise data that way! I'll be fine. If something happens I'll get myself out. Besides you want to test it out as well, don't you? We spent all night building that native A-line protocol."

Allen sighed in a frustrated tone. He hated it when she came up with better ideas than he did. "Well, yeah…but…"

"Then that settles it! Lets get started."

Allen raked his hand through his hair. "Alright, but if anything happens, I'm going to shut it down from here, so don't press your luck."

"All right, all right." Shion replied impatiently.

"And don't deviate from the program." He added.

"Okay mom!" she replied firmly.

Allen took off his headset and relaxed a bit. "Jeez this is so typical of her. Will she ever stop to think about the hell I go through for her?"

A nearby worker by the name of Evelyn wandered over to Allen. "You know sir, the way you worry about Chief Uzuki all the time, I'm surprised you haven't keeled over already."

Allen's face turned as red as his reddish brown hair. "H-hey that's enough! Is the 400 program ready to go?"

"Anytime sir" Togashi replied.

Allen stood up in a boss like manner. "Then start up the program! I want detailed reports from every monitoring station. Any abnormalities and I'm shutting down immediately."

KOS-MOS had proceeded through the broken-down warehouse and began to eliminate any enemy target. Shion followed silently and recorded all the data that was being shown. So far everything was going better than usual. Perhaps that A-line protocol had done some good for KOS-MOS' system.

When KOS-MOS had finished eliminating all enemy targets in the surrounding area she gracefully made her way toward Shion.

"KOS-MOS let me explain a little about this place and your mission. This is place is an imaginary space constructed within the network. It's modeled off of some ruins in some early 2000 A.D. Your mission is to fight the man target within the dilapidated building. Now then shall we continue?

"Yes, understood" the android replied.

KOS-MOS led Shion deeper into the rundown warehouse using the vaporizer plug in she was equipped with to knock things out of the way. Any target drones that made their way toward her, were defeated with one blow from the weaponry she carried. By the time KOS-MOS had reached the checkpoint within the warehouse she had easily glided through every level up till 431. That was when Allen stepped in.

"Replacing the targets with Type Gnosis drones. I've changed the settings on the drones. They will only attack you if you make noise." Allen reported to Shion.

"Good. Ready KOS-MOS?"

KOS-MOS nodded. "Proceeding to finish the mission. I have found the mission key to get into the central room." And with that she used the key to get through a highly barricaded door. With ease KOS-MOS glided into the room as Shion followed. She held her breath as she began to take careful observation of KOS-MOS' neural networks. This was the exact spot that had caused problems last time.

Allen watched his computer screen carefully. "Here we go." He announced with a deep sigh.

In the small central room of the warehouse, a dark aura filled its space. The air grew thick and hard to breathe in. The lights above flickered a bit with the pulsing energy that curled around them. In the direct center of the room a large Gnosis Drone appeared. Its body was transparent and seemed to ripple with energy. It's large eyes looked at them with hate. It raised one of its thickly muscled arms to reveal sharp claws. Shion took down the data that KOS-MOS was experiencing. In all but an instant KOS-MOS' body twitched uncontrollably when she reacted to the Gnosis standing in front of her. Shion looked at her in alarm. Something was wrong, yet she continued anyway.

"So far so good" Shion lied, hoping Allen wouldn't catch the small problem. "Allen please shift the target to real mode. We'll test the Hilbert Effect."

The Hilbert Effect was a technique that humans had devised, as resistance against the Gnosis. Gnosis lived in an imaginary world, so it was impossible to destroy them if they ever attacked. It was living in this imaginary world that gave them their transparent rippling ghost-like effect. The Hilbert Effect used inverted wavelengths to draw the Gnosis out of the imaginary world and into the real world where they could be destroyed. It also shut down most of the Gnosis outer sensory organs.

"What! Chief, you're supposed to follow the program!"

Shion ignored him and turned to the blue haired android. "KOS-MOS, activate Hilbert.

"Activating Hilbert Effect." KOS-MOS replied. She faced the Gnosis Drone and let out a huge blue wave of light in a large circle around her body. The Drone reacted to the light and let out a scream of pain. Its body was no longer transparent. KOS-MOS prepared herself to fight the Gnosis drone, but as she did the space around her began to disintegrate. Shion's computer let out multiple warning signals. She knew it was happening again. The Hilbert Effect had triggered a serious problem with the encephalon.

Allen who watched the screen let out a yelp. "I knew this would happen! Status!"

"This is bad," Basil announced. "Something is wrong in the encephalon. The whole thing could collapse at any moment."

"What? What about the chief?" Allen blurted out in clear panic. A sweat broke across his forehead. He turned toward his monitoring station and looked at Chief Uzuki standing there clicking away at her holographic screen. "Chief! You're in danger, get out of there now."

Shion heard Allen loud and clear, but she refused to loose such great data. " Hold on! Just a little longer!"

"Chief!" Allen screamed.

Basil turned to Allen; his face was streaked with sweat. "Nerve impulses in the limbic system. A brand new network is being created within the KOS-MOS mainframe. We've never had a reaction like this before. This is incredible… I've never seen a network grow so fast. Look sir, parts of the encephalon map are evolving."

Allen had made up his mind what to do. He had warned her that he would shut down the system if something were wrong, and that's just what he intended to do. "That's enough! Shut it down and pull her out of there, now!"

Basil nodded. "Rodger. Entering shutdown command." He jammed multiple buttons on his screen but couldn't seem to activate the code. "It's been rejected. The Chief is overriding us. We can't control it from here."

Allen let out a horrified gasp.

"Ten seconds until encephalon collapse sir." Togashi informed him.

"Damn it!" he cursed. He rushed over to his desk and grabbed a pair of red glasses. "I'm using the simple dive gear to get her out of there."

Shion was moving her fingers madly on the holographic keypad taking in all the data. Just a little longer she thought to herself. A little more and the mission will be a success. She ignored Allen's screaming in the background. Sure she knew the risks, but she was so close to success, she couldn't let it go. It was then she noticed the Gnosis drone was glowing a white gold color. Standing in the center of the Gnosis was a young girl. Her long blonde hair reached her lower back. Her eyes were a deep shade of blue, and she wore nothing but a sensible white dress with a cross necklace.

"A girl… here?" Shion wondered. "How is that possible?" She was so distracted she didn't notice that the ground below her feet was disappearing into a deep nothingness. She kept her green eyes focused on the little girl's blue ones.

"Chief!" Allen screamed.

Shion broke eye contact with the girl and looked at Allen. He grabbed her arm and gave her a hard yank. She took one last glance at the Gnosis drone to see nothing there. Abruptly she felt a jolt and she felt as if someone was dragging her by the hair backwards. The air grew heavy and tight. The walls closed in around her, and as soon as it began it stopped.

Shion slowly opened her eyes of her physical body and let out a groan. She lifted the harness over her head and stood up. Immediately her knees gave out on her and she fell into Allen's arms.

"Are you okay Chief?" Allen questioned with relief.

Shion looked at her co-worker with concern. "Yeah thanks. Did I push my luck a little to far this time?"

Allen let out a sigh. " You can't keep doing this Chief. I thought I was going to have a heart attack."

Shion smiled and stood on her own feet again. "Sorry about that, but the data is really good, besides…"

Allen looked at her with concern. "Was there something else?"

Shion couldn't help but think of the image of the little girl she saw. It was so bizarre, she didn't know if it was true or not. For now she decided to keep it a secret. "No, its nothing. We better get started on that data. Today's the deadline, they'll be asking for it soon."

As Shion took her seat at her own computer an announcement came overhead. "Attention please. We are scheduled to gate out in approximately three minutes all hands please return to your designated areas immediately.

Shion let out a smile. "We've got a lot of new material to add to the program, so lets get started. They won't call for me until we are safely out of the gate out. We have plenty of time."