Disclaimer: I do not own anything from Xenosaga.

Summary: Written form of the events occurring after MOMO's disappearance from the Kukai Foundation. It will contain scenes both from the game, as well as additional ones to further develop the characters and story line. The 'main character' for this is mostly Jr, and will be written in 3rd person focusing on him. Will be have some mild JrXMOMO, but will be focusing on development towards JrXShion.

A/N: Please give me feedback! :) I'm working on fixing my issues with tense and passive sentences though I'm not sure how much it is working! Also please let me know if you think that I'm writing any of the characters in a way that doesn't fit their personalities; I'm of course especially worried about making Jr too OOC. I would love to hear back what anyone thinks, so please review!

Chapter One: Discovering the Root

When Shion mentioned the song as that very thought passed between Gaignun and Jr's minds, the red head finally believed what his black haired companion had said about her after their first encounter. Jr finds himself frowning as he realizes that his younger brother was right once again, Shion Uzuki was not an ordinary human after all. As his eyes stray to her he realizes that he shouldn't be so surprised, she was young, barely over twenty years old, and was the one in charge of one of Vector First R and D Division's most classified projects; KOS-MOS. Yet her subordinate, Allen, seems not to hear a shred of the song, meaning her abnormality has to be of a source separate from her exposure to the KOS-MOS project. Gaignun summons Jr's attention with his thoughts; Why am I feeling so unsettled? This image...just won't leave my mind...

The words from his brother's mind force him to confront the darkness floating in his own heart as the eerie song drifted throughout space. Jr knows that this is the same song from that day, the one where he'd cast his brothers into madness and death, The Song of Nephilim did naught but drag him through his dark memories. Yet now...there is something deeper to the darkness, something more to the song this time around, and he feels that unless he stops it soon he will be pulled under the surface, into the dark abyss.

Reality suddenly yanks him from his reverie as he and his brother are forced to confront it, the federation fleet's weapons are bearing down on the Foundation and unless they do something, everyone was done for. As his eyes clear he focuses on the screen, seeing that they might already be too late, as the Federation ships had their weapons powered and ready to fire. Is this going to be it? He hates to think such a thing but he can't help it. Better this than the succumbing to the Song, he thinks darkly to himself. Then he finds himself again; he wasn't ready to die or let everyone he cares about be murdered by the suspicion of the Federation. He takes a step forward, ready to address the fleet, to talk their way out of this, to assume command as he was created to do; then a blinding light above them.

"What was that!" he demands but received no reply, as everyone's eyes are trained on the machines that are gating in. Jr watches in awe as the Gnosis around the Foundation are vaporized by what appears to be rings of pulsing light, he can't help but think to himself that he needs to get his hands on that kind of technology. The large ship that had gated in appears to be the main weapon that produced the waves, but it is also flanked by three smaller blue ships, which he can just see have a Vector logo on them. Instinctively his eyes travel to Shion, who had moved to the front of the bridge to watch the light show, he barely hears her surprised voice; "The Dämmerung...?" the name is unfamiliar to him, but before he can ponder further his eyes are drawn back to the four new ships, as they move into a triangular formation. Jr watches in admiration as the large ship shifts and an enormous shockwave blasts out from the four of them, eradicating the entirety of the gnosis assault.

"The Rhine Maiden...so she's operational now..." it was Shion's voice that sounds when the attack was finished; everyone else remaining in stunned silence. Jr can't help but suddenly feel embarrassed, between KOS-MOS and this new weapon, Rhine Maiden, even the Durandal was being put to shame by Vector Industries.

"Chief!" a high pitched voice floats through the connection, and a girl in a red vector uniform materializes on screen. Jr feels the desire to take charge and scrape together control of the situation, but within moments Shion is in the forefront, obviously more familiar than he with whatever the hell is going on. He continues to be surprised by the brunette, and the more he is around her the more he realizes how much they seem to be alike.

"Miyuki? Where are you calling from?" Jr lets the idle chatter slide from his perception as his mind wanders, he lets his sapphire eyes slip shut. The image of darkness in his heart meets him immediately, he lets it engulf him, pushing the fear he feels away, washing himself in the abyss with which he is faced. Guilt consumes his emotions and at once he recognizes the feeling from an event, much more near in his memory than the Miltian Conflict. The Encephelon.

It is the same dark pull that he had faced in that room, it is the past that he had been forced to confront in Febronia's church. Albedo, the brother he had abandoned to madness, he is the creator of this void in Jr's chest, the Song is merely his tool. Opening his eyes again, reality greets him, "some type of force field concentrated near here. There's a very high probability that it's what's attracting the Gnosis." It is the voice of that Vector employee, Miyuki.

Shion is kneeling on the ground not far from him, inspecting a small Vector case with a red weapon cartridge inside, "A force field?" she questions, lifting her head from the content of the case and brushing her hair from her cheek.

"Right. The observational guys said that whatever it is, it's definitely something man-made. Anyway, we can find the..." the girl's reply fades away. Jr already knows what has been causing these phenomena. It is the Song that he's been hearing for hours, summoning the Gnosis and causing the darkness to well up within him, and he now has a good idea of exactly who is responsible for it.

"Do you have any idea what this thing is?" Shion's ignited temper yanks him back to the present once more, and he can't help but smile at the hot-headedness they have in common.

"Of course!" is the other girl's upbeat reply, which is followed up quickly by a not so confident, "...Or so I'd like to claim, but I actually just transferred in, so I'm not really sure."

The carefree, oblivious attitude of Miyuki seems to try Shion's patience as much as Jr's own, "Look, Miyuki...this cartridge is a weapon! It sets off a phase transfer that destroys everything in the area. It may be localized, but you could vaporize an entire star with this thing if you wanted to. You'd have to be insane to try using this in a populated area."

"Shion..." suddenly everyone's attention is drawn by the stoic, often silent blue haired android. Jr feels awe wash over him whenever he looks at KOS-MOS, the first time he'd seen Vector's creation in battle he'd been completely shocked. Such ferocity and raw power had been packed into such a beautiful, fragile exterior; the irony of man's creations continue to impress him.

"What is it, KOS-MOS?" Shion faces the android with a serious expression.

"By limiting the phase transfer mass, I can activate the device without impacting either the federation fleet or the Kukai Foundation." Jr is surprised at how much it bothers him that such a robotic voice emanates from something that appears so much like a normal, human woman.

"You can do that?" the fact that KOS-MOS's main engineer doesn't know the full extent and parameter's of the androids abilities would have been strange in other circumstances. However Jr has seen KOS-MOS undertake the impossible in more than one situation, causing him to believe that there is just something more to her than simply being Vector designed machine; perhaps that thought is just his optimism getting the better of him.

"Affirmative. This is one of my many functions." The almost humorous tone in her voice seems to almost reaffirm his sentiments, but he figures he is merely projecting what he wants believe on to reality.

As if in anticipation of Shion's hesitance, Miyuki speaks up in support; "Even the Rhine Maiden's got a limit to how much she can fire. Let's take out the source before the Gnosis overwhelm us." After witnessing the power of that weapon, Jr finds it hard to imagine anything ever getting past it.

"But..."

The brash nature within him rears its head at the Shion's reluctance, Jr realizes that she needed to be made aware of just how dire their situation is. Just what kind of risks they are taking the longer that they wait. "Shion...This is the Song of Nephilim." He chimes in, curious to see any recognition in her features, "There's no question about it."

There was none, "The Song of Nephilim?" she asks softly, recognizing the hint of fear in his tone, "What is it?"

"The single worst creation that ever resulted from Joachim Mizrahi's research. It was the Song that destroyed Miltia and summoned the Gnosis. We've got to stop it before everything goes out of control." At the mention of Mizrahi, Jr instinctually peers around the room in search of the girl who calls the man Daddy. She is still missing, causing his stomach to drop as another worry is piled on to his shoulders.

"Out of control?" the words are more to herself than anyone else, and Jr is reminded that she, too, had lived through the Miltian Conflict. The delve into KOS-MOS subconscious had reflected her memories as well as his own, making him suddenly curious about her past.

Jr shakes his head, reminding himself of the problems at hand, "And we still haven't found MOMO yet. We've got to move."

"I know but..." at her words he is surprised that his temper and impatience don't take hold, but as he looks into her conflicted eyes he feels nothing but sympathy; so much weight is being placed upon her shoulders, and the root of her hesitancy is in her fear for the risk to innocent lives.

Ziggy seems to have latch on to the question of MOMO's whereabouts, he addresses one of the Durandal's 100 Series Observational Realians assigned with finding the girl, "Any sign of MOMO yet?"

The blue haired, child like Realian replies negatively, "We're still scanning, but we haven't located her yet." Jr couldn't help but feel distraught, he had a promise to keep.

"I see..." behind the cyborg's cold tone, Jr can sense his concern, MOMO had a way of making you care about her no matter who you are, "We've got to make a decision Shion. We can't hold out against another Gnosis attack." Ziggy's continuing the efforts to imbue Shion with new resolve.

Finally she succumbs, sighing in distress, "All right...let's see what we can do."

A/N: First Chapter! I have more written up and it's just a matter of editing and tweaking...and of course encouragement from any readers. ^^