IMPORTANT AUTHORS NOTE PLEASE READ

-If you are reading this for the first time, you can skip this next part and head to the story- I hope you enjoy it!

-If you started this fic anytime before August 2013, I have deleted all the old chapters and am in the process of completely revamping this fic. I have the old chapters if you still want them but the same storyline still stands. I have split a few chapters in two and essentially rewritten most of the material. If you have already reviewed past chapters (1-13) the site won't let you review the updated versions until I start posting completely new chapters, just a heads up!

You can always PM me if you have any questions or comments whether big or small:] Hope you enjoy the new and updated Restoring Reason!

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Prologue- Day 2 Missing

Clouds wrapped long translucent arms around what should have been a full moon, and the crisp September air was still, as though waiting in anticipation for some event. In a laboratory nearly half a mile underground, the happenings were far from silent.

"Get- yer fuckin' hands, offa me!"

Used to his captive's demands by this point, the scientist paid no heed to his prisoner and proceeded to drag him to the lab table at the far end of the room. Raphael continued tossing out threats and vivid insults, both in Japanese and English, and did not stop struggling against the steel manacles that bound all four of his limbs.

Agent Bishop laughed as he slammed his hostage down on the table and easily slipped him into a full body restraint.

"You, are wasting your breath." He said, planting one hand firmly on the teen's plastron as he pulled and fastened additional chains across his upper arms and both legs. Crap, Raphael had really been hoping for leather or something he could saw through with the shuriken he still had hidden in his belt.

He watched Bishop warily as the man turned to open the drawer in a tall closet. When he turned back, he was holding a syringe filled with something clear. Raphael glared at him and continued to squirm- for show mostly- against his bonds. He held back a wince as the chains dug into his already bruised skin, and finally braced himself for the worst.

Bishop moved forward and neatly plunged the needle of the syringe into Raphael's shoulder. Almost instantly after removing it, a fiery sensation started pulsing through his veins as whatever Bishop had injected him with spread throughout his bloodstream.

Raphael couldn't keep from tensing up instinctively at the pain, inhaling sharply and trying not to watch Bishop record notes on a clipboard. "What is this?" he hissed, more to himself than anything but not realizing he'd voiced the thought aloud.

Bishop's lip curled at seeing his obvious discomfort, "I guess you don't remember. Of course, you were unconscious when it happened. But you can thank me for what's been happening to you for the past six months- well, for the two years really. I can assure you I've never forgotten."

Raphael's eyes flashed and narrowed dangerously, "You'd better start makin' some sense ya maniac-"

"Or what?" Bishop quirked an eyebrow in mild amusement, "Delude yourself all you want with dreams of escape Raphael."

Oh how he hated hearing his name being uttered by that despicable set of lips.

"Or you'll regret it!" Raphael finished lamely, and unable to bury his sudden curiosity, "What d'ya mean- 'what's been happenin' ta me?"

"Oh you know," Bishop flipped back to the beginning of his notebook, "Night terrors, mood swings, a sense of territoriality coupled with a sense of impending doom. Ah and my personal favorite, a significant increase in your entomophobia."

Raphael froze and he frowned slightly, how did he-? He stuttered, trying to regain his composure, "None o' that's new- s'just me." The confusion still must have been plain on his face for Bishop chuckled, "Oh Raphael, looks like we'll have to bring you up to speed again."

He dropped his clipboard on a nearby table, and rolled out a cart with an impressive array of test tubes, vials, and syringes. Raphael recognized IV bags filled with bright blue fluid in the shelf beneath the first, and realized with a horrible jolt that he could no longer feel his arms or legs.

Bishop saw the brief flicker of worry in Raphael's eyes and laughed again, "This? It's to keep you still while I work. Don't worry, I'm not killing you, I am merely going to do a few experiments, you will take a few tests. We're going to have fun."

"It will be Saki's decision whether or not to kill you after I hand you over to him as was my part of the bargain." He finished, filling up a syringe.

Raphael felt a cold hand clutch his heart when he heard the Shredder's name. That can't be good, he thought, feeling a pit of dread open up in his stomach, what the hell could he possibly want with me?

Bishop watched Raphael's confusion as though deeply amused, "You'll see turtle. Fascinating things come to those who wait."

TBC

A/N: What d'you think? Reviews make my day no matter how short they are:)