Added (10.October.11, 8:03 PM)
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PART THE SECOND

He could hear screams of panic throughout the ship. He heard many footsteps, clunking on the metal floor. A stampede of men and women, running from somewhere to nowhere in particular. For a moment, he considered joining them.
But he slapped some sense into himself using one of his mom's old phrases:
"Lose your head, Lose your life."
So, he sat and thought. What’s could he do to keep his head straight?
He would fix the engine. There. It is only a simple malfunction, what could go wrong...
~
The corridors got narrower, and the smell of disuse clogged his nostrils. The light got dimmer, and dimmer...
Finally, it plunked out with a "Puff." He was left in the dark.
So, he sat down, and waited for his natural Night vision to come back.
While he was waiting, he thought back to the girl at the Recruitment desk.
She seemed like a nice woman to know. Her perfume smelled like daisys, and her smile was radiant. In fact, he could smell her perfume now.
Wait...He really could.
Standing up, he looked up and down the corridor. Nothing...
Then, he heard a noise, a peculiar noise.
Clack clack clack...
It sounded like a giant spider running with hard feet.
Or a woman running in high heel shoes...
Then a beam of light came from the end of the corridor. His heart froze, and he looked around for a weapon. Seeing a plank of wood on the ground, he picked it up, and help it in front of him.
The light was directly in his eyes, he could only see the dark outline of a humanoid figure.
It was tall, and it's arms were long. A perfect representation of the check-in girl. He was convinced it was her. It had to be.
Then the light went down, and he got a better look at it.
It was not her.
It was...A monster. It's flesh had the same look as a rotted peach, with holes everywhere. The skin was stretched thin. It appeared to be a wonder this...Thing...Was alive.
But the worst part was the face. The eyes were small and beady, most of the face was taken up by the mouth and the massive teeth within. It wore no clothing. It was hideous to behold.
The flashlight went back up to his eyes. It tilted his head a little.
And it charged him. Raising his plank, he screeched like a banshee, and swung it at an ark to it's face.
There was a loud THUNK as it's head got turned sharply to the side. It retaliated by outstretching it's arm, which had only 3 fingers, and scratched his chest. Reeling in pain, he took another swing at it's head.
This time, there was a CRUNCH. He appeared to have done some damage. The creature screeched inhumanly, and pushed him against the wall. He only had time for one final swing.
This one hit the leg, and made it fall over. He pushed off he wall, and ran away from the, what he hoped was a, corpse of the dead thing.
He ran, not bothering to look in front of him or behind him, with only his eye-sight and natural night-vision to see by. He passed some more corridors, keeping his steady pace.
After a while, he laid back against a wall, in tiredness. He looked ahead at the wall opposite...
On the wall was some more words in blue liquid, scrawled. He stood up, and had a better look. They read:
"I see you have met Mr. Willy. Nice, is he not?"
He stood back again, heart racing. Willy?
Who is writing these messages? WHY? WHY would someone name their pet monster Willy!

Added (10.October.11, 8:04 PM)
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He looked back at the writing, and began to walk down the passage again, convinced he had put enough Distance between him and "Willy."
However, on the very next corridor, more blue, scrawled scripture. This read:
"He isn't dead you know, despite your violent efforts."(GLaDoS reference FTW!)
Below it:
"Shame on you."
This was made more horrifying because of the fact that this message was written recently. Quite recently.
And that thing is still out there. Still ready to kill him. He felt like kicking himself: Why did he not finish him off. Why did he not grab the flashlight!
"Lose your head, lose your life." He reminded himself, moving on, a bit slower.
The walls then gained an odd quality. They began to change color, and whenever he put his hand on it, it felt...Rubbery.
Also, a faint noise began to become audible:
Bump Bump Bump Bump Bump

Then, more blue writing.
"Ah well. At least I still have Togo with me."
Togo? What is a Togo?
Suddenly, a hiss from in front of him.
Turning, he made out a shadowy form in front of him.
Then, for one second, the lights turned back on.
It was a "Willy" Thing. Exactly it, down to the teeth.
It leapt at him.
He swung plank upwards, and the horrible thing went flying over his head. It collided against one of the walls, and collapsed.
The bumping increased.
BumpBumpBumpBumpBump
It was like the ship had a heartbeat.
What must be Togo leapt at him again, but he was ready. He struck Togo on the side of the jaw, spittle flying. Togo plowed through it, ramming him down into the ground. He was pinned to the floor, as Togo's jaws slowly opened in a horrifying grin.
This was the end...
NO. It was NOT.
He had the strength to continue, he should use it!
Groaning with effort, he pushed up into Togo's belly, sending him catapulting off His chest, and onto the ground. With one last cry of strain and effort, Togo launched himself at him, only to be met by a plank in the chest.
There was a ripping sound as Togo's chest tore on the end of plank. The blood came out, green and sticky. Togo looked up at him, and fell to the ground, plank still lodged in his chest.
He had no doubt he was dead. He had to be. No-one could survive that.
The rubbery thing on the wall was now more wrinkly and organic...almost like....No...skin? It couldn't be possible. The walls recoiled at the thumps, almost as if it was all connected. As if the entire ship was connected. As the bumping sped up more and more, the ship seemed to move with it. It was horrifying. As he entered the main
hallway of the maintenance deck, plank by his side, still dripping with Togo's green blood, The ship seemed to pulse more and more, faster and faster, and he could have swore as he was walking he saw something stare into his soul. He ignored it though, and continued on.
Then, he saw some more blue liquid on the wall. He looked up at it, struggling to make it out...
It was no recognizable letter he had ever seen.

Added (10.October.11, 8:05 PM)
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PART THE FORTH

Then, he stood back, and realized his error.
It was not a letter. It was a frown, painted in blue liquid.
There was a message below it, in actual English.
"They are my toys, now stop breaking them, before I BREAK YOU..."
The letters seemed to scratch, or more like drip, down the wall at the last bit of the sentence.
So...Whoever did it had the mind of a child. It saw the ship as it's toy box, and the Crew as it's toys. He had to keep moving, to get to the control room. To fix the ship, and to save the crew.
If the crew was still alive.
Which he doubted.
Finally, after what seemed to be ages, he reached the end of the hallway. There was a door at the end.
It had blue-liquid-writing on it.
It said, clearly:
"Welcome, make yourself cozy."
Again.
Nevertheless,
He entered.
And stopped dead.
The room was A giant cylinder. In the very middle, surrounded by glass, was a giant heart, pumping and pumping, making the entire room slightly vibrate. What's worse, there were eyes all over the chamber, growing out of the walls, eyes, big and small, all on him. The walls were red, the color of raw skin, and filled with veins and nerves. But there was also machinery poking out, wires and bulbs. Every once and a while, a bright flash would pass through a wire.
He had reached the heart of the ship. Now, to fix it.
He walked around the heart to a small control panel. But then, as he reached for it, he heard a voice.
"Hi."
It was the voice of a small Girl, a little girl. But there was a sinister note to it.
"You are the one who broke my toy." She said, with the air of annoyance in her voice. "Your a bad dolly."
"I'm not a dolly." He said, as he reached for the panel again, and began to push buttons.
"What are you doing?"
"Stuff." He replied.
"Whatever you are doing, stop it, dolly."
"No." He said casually.
"I said Stop it." She said with the same air of annoyance.
"No." He said.
"Stop!" She wined. The eyes glared harder at him, and what he was doing. "Stop it dolly!"
He kept pushing buttons, despite her increasing protests to stop.
He came to the final sequence.
With the last button pushed, the computer let out an ear-piercing screech.
"DOLLY! WHAT DID YOU DO!"
The entire room began to shake.
"I reprogrammed you. The faulty chip is gone. You are ours now. Stop screaming." He said calmly.
"The ship will go down before I listen to YOU, Dolly!"
"No, there are thousands of people on the ship! You will kill them all!" He said, shocked.
"There is only you left, Dolly. You are my last plaything!" She screamed again. The eyes closed in pain.
"What?" He said, completely floored.

Added (10.October.11, 8:06 PM)
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PART THE FINAL

"I ATE THEM! I ATE THEM ALL!"
"Why?! You are a monster!"
She screamed in pain again.
"for one to survive, some must die, dolly. however, in my case, some meant All, Dolly! I needed the blood, there was not enough. Those Stupid Engineer Dolls gave me too little, I needed more, MORE, Dolly! So I drained them dry! You are the last One!" She screeched, going up an octave. The room began to shake more violently, and the mechanical parts began to spark and explode. Wires fell from the ceiling, and the horrible heart was throbbing at a supersonic rate.
"WHY DOLLY!" She screamed, "WHY! WHAT DID I DO TO YOU!"
"For the record," He said, "My name is not Dolly."
"What is it?" She said, rather quietly.
"I. Am. Garran!"
With a swift movement, he smashed the glass encasing the horrible heart. It busted on one side, blood squirting on the floor. Not just some blood, a massive amount, A flood of it. The heart had been holding the blood of practically everyone on the ship. It claimed to be hungry still, but it was so much....If it continued for a few more minutes, it would flood the ship's room. Luckily, it began slowing down and some just fell to the bottom of the jar. She screeched for the last time, then the chamber started to collapse, flesh on metal, falling around him.
Garran’s only chance was the escape pod. It must be operational.
He sprinted from the room, and noticed that the blue liquid on the door was boiling, squirting out, like pus from a pimple.
Sprinting down the corridors, he passed Togo's dead body. It was starting to soften, and the floor was absorbing it. Another massive shock rocked the ship, and the blue-pus-like liquid was now almost flowing from the walls.
He blindly turned the next corner, and kept running. A sign above him stated that the escape pods were on the left. He swung open the door, and got in a escape pod.
There came the Cachunk of the escape pod going out from the ship, then came a sickly gurgling Glagahaga....He heard a thump, and turned around.
Nothing.
He turned back to look out the window, When a Long, bloody, mutated arm hit him in the back of the head, smashing his head through the glass.
His eyes were sucked out into space, and blood began flowing out as well.
His head was ripped off it's shoulders like two Velcro strips splitting, only, more fleshy and bloody. His blood now came faster than ever, going all over the floor and into space, and there sat Willy, with a sick smile.
WIlly was then Sucked out the Window as well, and he hit a switch.
The escape pod then exploded, guaranteeing death.
He was alive through up until his head came off. All of it. He could have swore he heard one more thing, before he died. While his skin was ripping, he heard a faint whisper of a familiar little girl voice.
When you do something, Dolly, make sure you finish it. With a bang...

~
A squirrel climbed on the log.
It was a squirrel. It liked logs.
At least.
However, it was the only witness for the events that are about to unfold.
The log was smooth, and brown. If you are particularly interested, he was looking for Nuts.
Then, something made him stop his work.
He looked up at the sky.
There was a small ember-ish red dot, growing larger in the twilight sky. As he watched, it grew bigger and bigger.
Until it crashed.
The earth acknowledged this with a loud BOOM, and the shaking of the very dirt beneith it's feet. The humongous monstrosity slid on the dirt, knocking down trees, until it came to a rest. The resulting skid mark stretched a mile.
The squirrel scampered up to it.
The side seemed complexly smooth.
But then, something happened. A section of the smooth hull began to twist. In a circle.
With a loud Pop, the circle fell into the hole it made, inside the massive metal hulk.
The squirrel watched, unblinking.
Then, there was a small Thunk.
As a hand with only 3 fingers slowly came out, and gripped the outside hull...
and from the inside came a quiet voice. Almost the one of a little girl:
"I said that I sucked their blood. That doesn't mean I killed them...They are still my toys...My..Dollies..."

~To be continued~