Scootaloo's Big Daddy

Chapters

Prologue (Edited)
Chapter 1: Never get between a Daddy and his Sister (Edited)
Chapter 2: Problems with a metal giant. (Edited)
Chapter 3: Under the... lake? (Edited)
Chapter 4: Subject Alpha VS Rainbow Dash
Chapter 5: Disarming the situation
Chapter 6: Desperate Measures (Edited)
Chapter 7: Subject Alpha Vs Big Sister (Edited)
Would You Kindly: Would You Kindly?
Chapter 8: Examination
Chapter 9: While the cat's away

Prologue (Edited)

It was a peaceful night in Ponyville, the night sky was clear and beautiful, and all around town ponies were turning in for the night. Scootaloo could almost see the other fillies and colts being tucked in by their moms and dads. Scootaloo looked back inside the cutie mark crusaders tree house and suppressed the tears she felt coming. Normally, she would try to be tough like her hero Rainbow Dash, and she wouldn't have any problems sleeping in the tree house, but tonight was different. Diamond Tiara's voice echoed in her skull again.
"I bet the reason your daddy doesn't come to parent teacher conference is because he is too embarrassed of having you as his filly."
Scootaloo wanted to kick that little brat right on the face, but at the same time she couldn't deny that Tiara was right. Why else would Mom and Dad just leave her on the doorstep of an orphanage with only a note with her name on it? Scootaloo was glad she got out of there; it held too many bad memories. The little orange pegasus walked over to the tree house window and peered up at the night and made a wish.
“I wish I had a daddy. A big daddy, that would make Tiara eat her own words and could go crusading with me and my friends."
Suddenly a shooting star streaked across the night sky and fell with a quiet thud in the Everfree forest. Scootaloo's eyes grew wide, she wasn't entirely sure what had happened but either something cool had just fallen from the sky or she had a new daddy. She grabbed her cape and charged out into the night ready for adventure.

Rapture, 1954
Subject Alpha 9 - 2 Patrolled down the long halls of Rapture with his Little Sister riding on his shoulder. The citizens of Rapture moved out of the way of the seven foot, several hundred pound behemoth, and he wouldn't have liked it any other way. Alpha 9 - 2 was a simple soul of only base intelligence; in fact he didn’t even know his own name. All he knew for sure was that he was supposed to protect and serve his Little Sister.
Today was beginning to look like any other; he would carry his Little Sister around, she would point out things she wanted him to go to, then he would get her food, and finally they would head home to the Little Wonder Educational Facility. Today, as Alpha walked in the alleyways behind Fontaine Futuristics, his little Sister noticed something and tapped on his yellow face plate before she pointed off at an object to his right.
"Mr. Bubbles look over there. Something is glowing."
Alpha slowly turned to face in the direction she was pointing. It wasn't uncommon for her to point out things she wanted him to get for her; however, it was a little strange that she was doing it in a garbage filled back alley and not a toy store. When he finally faced the direction she was pointing he knew without a doubt what she was interested in. Before him, sitting on the ground next to a large dumpster was a Plasmid vial with the word "unstable" taped onto it. It was flashing every color of the rainbow like it was a physical LSD trip. Alpha grabbed his Little Sister and set her on the ground so she could grab the Adam while his mind tried to process what he was seeing. Whenever he found some Adam he would always give it to his Little Sister to drink, and although it looked odd it was still Adam. However, even she was apprehensive of drinking the flashing liquid. She carried the vial over to him and looked up at him with her big yellow glowing puppy dog eyes.
"Mr. Bubbles, can you test it and make sure it is safe, please?"
How could he possibly say no? Taking out a syringe Alpha took a small dose of the strange Adam. While even the most desperate of Splicers would think twice about injecting such a strange concoction into their blood stream Alpha merely obeyed jabbing the syringe through his suit and into his arm.
At first, nothing happened. Alpha emptied the syringe into his arm and Waited for some sort of effect. He was actually worried for a second that he wouldn't get any sort of power from it. His focus shifted to his personal wellbeing when a feeling of agonizing pain and built-up energy threatened to disintegrate him. His body contorted in pain and glowed as the plasmid moved throughout his system. He cried out in agonizing pain and vanished before his Little Sister's eyes.
Alpha found himself falling. Falling between space and time as both began to lose meaning. The planes of existence shifted and let him pass by uninterrupted until he finally caught one head on. Suddenly time, space, and gravity had meaning once more as he landed in a wet marsh. Despite his existential crises Alpha 9 - 2 was perfectly fine, and dragged himself out of the marsh with relative ease. Taking a short break the Big Daddy made a mental checklist to make sure he was in fact unharmed.
'Bones don't feel broken, suit seal is secure, and fingers are nonexistent, wait... What?!'
Alpha looked at where his hands used to be and stared at his new hooves in shock. Instead of fingers there was now a hard stubby end to each of his arms. Even his suit had been changed giving him metal boots instead. It was as if he never had fingers to begin with. His back legs were no different except that he now had an extra joint that made his leg even less familiar. He wondered how he would use his drill and machine gun now. Suddenly his drill swung out from being behind his hoof and the machine gun came out of a square metal box on his back. It proved too much for Alpha. His mind went through various questions and thoughts as he tried to make sense of it all.
'Why am I some kind of horse?! Where did I get this strange gun saddle and drill!?! Ryan! He must have done this to me! He tore me apart and put me back together again as this thing! Probably for his precious little sisters! Curse you Ryan! Curse you Rapture! Curse you Comstock! Wait.... What did I just say?'
The feeling of blood slowly running down his nose brought an end to his brief moment of independent thought. His mind struggled and lagged behind this new universe until he knew who he was. Mainly due to the intense mental programming and conditioning he had received as a Big Daddy.
'I am Subject Alpha 9 - 2. Alpha series Big Daddy. Earth pony. I must protect and serve my Little Sister at any cost.'
His existence now making sense Alpha got onto all fours and began searching for his little sister. He was convinced he had only put her down moments ago, but that was in an alleyway and now he was in a marshy forest. Alpha tried to make sense of it all when he heard the sound of a young girl’s screech echo through the air. Alpha charged full speed towards the source of the screaming with one thought on his mind.
'Protect Little Sister.'

Chapter 1: Never get between a Daddy and his Sister (Edited)

"The mind of the subject will desperately struggle to create memories where none exist…"
―R. Lutece, Barriers to Trans-Dimensional Travel, 1889

Scootaloo wasn't so sure that she had done the smartest thing when she ran into the Everfree in the middle of the night. This was heavily supported by the fact that she was now being chased by eight timberwolves and was completely lost. Sometimes she wondered how she got herself into these situations. Though at the moment the only thing she was wondering was how she was going to get out of this mess alive. She was quickly getting tired, she still couldn't fly, the timberwolves were catching up, and screaming was not helping. Unfortunately, while she was distracted thinking of some way to survive her last option ended due to an unfortunately placed root.
Scootaloo tripped and somersaulted straight into a tree; if it weren't for the fact that she was in a life or death situation she would have thought it was a pretty cool trick. Of course, staring into the angry green glowing eyes of a timber wolf made other thoughts come to her head. In desperation she spoke aloud; pleading with fate to let her live. "I don't know why I deserve this, but I regret everything I've ever done. I'm sorry I went overboard occasionally when I searched for a cutie mark, I'm sorry I'm not going to be able to learn how to fly from you Rainbow Dash, and I'm sorry I went into the Everfree in the middle of the night." Tears streamed down her eyes as she realized that she was doomed. "I just wanted a dad."
While most would see this display and would regret whatever actions they were doing to cause it, the timber wolf did not care. It was going to protect its territory and get a meal at the same time. It stood up on its hind legs and brought its right paw up to end the filly in a single deadly strike. Suddenly a metal helical object bursted through the wooden creature's chest and stopped only a centimeter before Scootaloo's nose. The little filly went cross-eyed staring at the strange new addition to the timber wolf, wondering what in Tartarus had just happened. The wooden wolf slowly turned its head to face the source of the protrusion only to stare into a single large red glowing eye. 'I regret everything.' Was the last thought that entered the once vicious animal's mind.

Alpha let out a loud angry roar and ripped a large chunk of the strange wooden creature's chest before tossing both chunks away from the strange orange Little Sister. At least his mental programing believed she was a little sister. Though consciously he wasn't too sure; she didn't look like any Little Sister he had seen before. 'Aren't Little Sisters supposed to have yellow eyes, black hair, and little fingers to carry…' Alpha shook his head clear once more as another nosebleed dripped down his face under his helmet. 'Must protect Little Sister.'
Alpha recovered from his strange thoughts and positioned himself between the filly and the rest of the wolf pack. The wolves were beginning to encircle him cautiously; they had never encountered anything like the strange metal and leather pony before them. Maybe they planned to attack him from multiple sides at once Alpha didn't care though; it wouldn't work. With a single thought the machine gun harnessed to the right side of his back came out of its protective metal case with AP ammunition loaded. If Alpha could actually feel emotions he would have smiled under his helmet. The Gatling machine gun span up preemptively and pointed to the nearest wolf on his right.
'Now I see why I have been modified like this: I can shoot my machine gun and use my drill at the same time, while also being able to carry my Little Sister easier.' The Mexican stand off lasted a few moments until the wolf on Alpha's left made the first strike. The wolf pounced towards the Hulking pony and was quickly dealt with by his powerful motor drill. Alpha then opened fire on the wolf to his right ripping it into splinters. He quickly turned the gun on the remaining wolves quickly tearing two more apart. The wolves began to panic as the constant thudding of Alpha's powerful machine gun caused even their wooden ears to ring. Alpha moved in to finish the job launching his drill at the nearest timber wolf and pulling the poor creature before ending it with a burst of his machine gun to its head. Although two of the wolves had managed to escape with their lives he was certain that through their wounds and the smoldering heaps of their fellow pack members that they had learned the first rule of Rapture: Never get between a Big Daddy and his Little Sister.
Satisfied that he and his charge wouldn't be bothered again his faceplate glowed yellow once more and he turned to the little filly to ensure she was unharmed. She was cowering in a small nook in the tree with both her front hooves and her small wings covering her ears. 'Serve Little Sister.' Alpha felt a little confused when that mental command spoke out to him. 'She hasn't asked for anything. What am I supposed to serve her for?' It took him a few moments until he realized that he was expected to comfort her; after all, she just had a near death experience. Carefully Alpha sat on his haunches, picked the little filly up onto his lap, and petted her head. After a few moments of making the most soothing sounds he could her breathing slowed, and she stopped crying.
Once more satisfied that he had done his duty Alpha picked her up by her midsection and held her in the air for a moment to look at her. She looked back at him with big curious violet eyes unknowing of the significance of his actions. She was his Little Sister now and he would protect and serve her for as long as she lived. He then pulled her onto his shoulder and began walking towards signs of civilization in search of either a temporary shelter or a Little Wonders Educational Facility.

Chapter 2: Problems with a metal giant. (Edited)

"I love you Mr. Bubbles."
―Unknown

Alpha curled around his Little Sister keeping her warm in the cool night. Although he would have preferred a Little Wonders Educational Facility this wooden shelter was still appropriate for their needs; even if he broke every single ladder rung trying to get on. Alpha shuddered as numerous bad experiences with stairs and ladders leapt forward in his mind. He watched her sleep peacefully as he thought to himself. He never slept, except for during repairs, as he had to always keep guard, but it did allow for him to plan things out and spot out eventual problems. He began a mental list of important questions and problems.
'Where am I? This does not look like any part of Rapture I have seen. Perhaps I'm on the surface. That means I am living among the parasite and away from the source of Adam and Eve. I will have to depend on my little sister to be my source. I am going to have to hide myself from those Greedy Americans and Stupid Socialist Comm-'
A sharp headache and the feeling of yet another warm nosebleed running down his muzzle interrupted his thoughts. He shook his head and tried to recollect himself.
'I am going to have to hide from the Equestrian and Griffin parasites if I am going to keep my little sister safe here on the surface. These headaches and nosebleeds are interrupting my thoughts and jumbling my memories. I almost forgot the day I was given my one and only Little Sister here. I will have to keep track of these nosebleeds and treat them with Adam once she produces enough.'
Alpha inhaled deeply knowing that he would be able to take care of his Little Sister. He inhaled again feeling something was terribly wrong. Alpha made sure that he was breathing air that was being pumped from outside his suit at that very moment, but it was to no avail. His Little Sister was not producing the pheromones necessary to keep him alive.
'What happened? She was producing pheromones just yesterday. Why would she stop? As long as she had Adam she should keep producing them. So why... That's it she just needs a little more Adam! Tomorrow I will put her in a safe location and go grab her an Adam slug.'
Alpha nodded to himself approvingly causing shadows to bounce around the tree house due to his yellow face lamp. Feeling better about his situation he waited for his Little Sister to wake up.

Scootaloo was woken up by her alarm which she quickly silenced. She yawned and talked to herself like most sane individuals.
"I had the weirdest dream last night... I was being chased by timber wolves and a giant fabric and metal cyclops saved me. I’ll have to tell Sweetie Belle and Applebloom about it."
Finally Scootaloo realized that for some reason the floor of the tree house was unusually soft and realized that she was sitting on some kind of strange tan fabric. She quickly realized that the cloth and metal cyclops wasn't a dream after all and she had fallen asleep on it. She did the only sensible thing that every pony in a horror movie failed to do. She ran as fast as she could away from the monster. After running only ten feet away from the tree house her great escape came to an end as the very ground shook violently. When she regained her footing she realized what had happened. The cyclops was so heavy that just by jumping the short distance from the main floor of the tree house to the ground it had caused an earthquake. Scootaloo froze in place and stared up at what had to be the biggest pony she had ever seen; if it even was a pony. The cyclops was at least three feet taller than Big Mac; Scootaloo had seen adult Manticores that weren't as tall as the thing in front of her. Then just when she thought the bulbous metal cyclops couldn't be any more terrifying, it started walking, causing a minor earthquake with each step. Scootaloo was panicking, frozen in place with no idea what to do.
"Stop!" She cried out in desperation, shutting her eyes tightly. Somehow as if by magic the rumbling stopped, and everything was quiet. Scootaloo opened her eyes in surprise and stared at the motionless giant in front of her. She couldn't believe it, she just commanded a massive monster. "Sit?" With a loud thud and yet another earthquake it sat down in front of her. Scootaloo sat down as well in complete disbelief. "That actually worked?! You can understand me?" The behemoth didn't respond and tilted its head. "Do you talk? You know.... Words. 'Blah Blah Blah' like that? Can you do that? Blah blah blah?"
The giant stared at her for a moment, before speaking what sounded like deep grunts. "Argharolllgaroghall"
Scootaloo flinched but tried to be supportive, like a true friend. "...well... You get the idea anyway." She lifted up a small stone in her hooves. "This is called a rock. Rock." She tried to copy how Miss Cheerilee would teach the young foals how to speak.
The cyclops looked at her for a moment, got up, and ran into the Everfree at a speed that was very unsettling. Scootaloo wondered a few moments why it had left, then suddenly it returned carrying a boulder the size of the tree house. "ROAGHK!"
"Very.... Good...." Scootaloo couldn't believe what she had just seen. How could something be that strong. After taking a moment to recover she tried to continue her lesson. She pointed at one of the orchard trees of the Apple’s farm. "And that is a tree."
Before she could even react the giant walked over to the tree she pointed out and pulled it out of the ground. "TREEEH!"
'And that was destruction of property.' Scootaloo switched into panic mode."WOW! WHAT ARE YOU DOING PUT IT BACK! Apple Jack would kill me if she found out you did that!" And with that the cyclops put the tree back in its hole rather confused. "I think that's enough of our lesson... Can you at least understand me and answer with a nod for yes and a shake for no?" It nodded back in reply. Excitement filled her tiny body. She had so many questions that she wanted to ask, but so few of them could be answered with only yes or no. Suddenly she remembered her wish.
"Are you my Daddy?" He nodded again. Scootaloo jumped in the air in celebration. "I am so going to rub this in Diamond Tiara's face! This is the best thing that has ever happened to me! I should tell every pony about you! ...No... They'll panic. The ponies of Ponyville always freak out whenever something they don't understand happens. Like when we met Zecora. Okay you stay here and don't get seen. I'm going to school." Scootaloo pointed at the tree house for emphasis before she started walking towards her scooter and school. Unfortunately her hoof steps had a thundering echo. This was going to be a long day...

Chapter 3: Under the... lake? (Edited)

Author's Note

I can't believe how much support this story has gotten so quickly. Its barely 2 days old and already has ~~33~~ 34 likes and 0 dislikes! Who are you awesome people and why are you here?!
Well thanks so much and I hope I can keep entertaining you all. And please comment, I don't care about what; lore, corrections, suggestions, why you like it, why you hate it. Just comment.
Again thanks so much and enjoy.

Chapter 3: Under the... lake? (Edited)

"This little Sea Slug has come along and glued together all the crazy ideas I've had since the war... it doesn't just heal damaged cells, it... resurrects them... I can bend the double helix... black can be reborn white, tall, short, weak, strong..."
―Brigid Tenenbaum

Scootaloo was on edge. Somehow nopony had seen her new massive daddy; even with his earthquake inducing trot. They were nearing the school and it was inevitable that they would bump into somepony. Suddenly she heard the sound of rustling behind them. Her eyes grew wide and her heart threatened to beat out of her chest.
"Somepony is coming! Quick hide behind a tree or something!" She commanded, staring at the nearing source of rustling bushes and grass. Several rapid tremors followed by silence told her that her Daddy had done what she asked; she just hoped that whoever the pony was that they somehow couldn't feel or hear the ground shake. Her heart thumped faster and faster as the rustling drew near, until finally a squirrel jumped out of the foliage. Scootaloo let out a deep breath she didn't know she was holding. She took a moment to steady her shaky legs and calm herself. 'Be brave, like Rainbow Dash.' She told herself silently. She turned to face the direction her thundering daddy had gone and immediately facehoofed.Sitting behind a thin tiny sapling of a tree in complete view of the world was her big daddy.
"That isn't hiding!" She yelled at him. 'This could not be any worse. The big lug is as subtle as the 's' in subtle.' She thought to herself, while the towering cyclops peeked out from behind the tree confused; as if the little 2 inch wide trunk could actually block his vision. Scootaloo knew it was time; she had to convince the tan giant to not go to school with her. "Okay... I got to go to School." She spoke loud, clear, and slowly pointing towards the school for emphasis. "You, go hide and make sure that nopony can see you. I'll come out later when school ends. Okay?" He nodded yes, and Scootaloo sighed with relief before walking towards the school. Unfortunately after only a few feet her foot steps had a thundering echo. She facehoofed again and looked back at the giant. "No, you stay. I go." She pointed to a big nearby bush which he climbed into, it hid him pretty well, but she could still see his glowing yellow eye. "Stay." Scootaloo slowly backed away still looking at him until she reached the school. Finally confident he would stay safe and put she went inside to the horrors of school.

Alpha peered from his bush into the school windows; inside he could see many Little Sisters sitting in desks in front of a teacher. Now his Little Sister's actions started making sense. However, he didn't understand why she hadn't told him that the building was a Little Wonders Educational Facility, or why it wasn't properly marked. Although why she had pointed out things for him to get, but then got angry that he had gotten them still confused him greatly. Almost as much as why she had tried to get him to talk. Didn't she know that he could only speak in deep grunts, growls, moans, and roars as designed by Dr. Suchong. It was luck that he was able to make that hard 'T' sound for tree. Now that he thought about it, he was surprised by the amount of trees the ponies here had just left out in the open. Didn't they realize how easy it would be to sabotage them and destroy their source of oxygen. He shook his head confused, these ponies were so strange. He looked back up to watch his Little Sister learn reassuring himself that she was safe.
Now normally he wouldn't disobey an order from his Little Sister, however, since her safety takes priority over her orders he headed back out to the forest he recovered her in. It felt strange to him to see so many tall trees unguarded, and with strange wildlife living freely. Lost in his thoughts Alpha nearly walked straight into a large stream of water, but managed to catch himself and not fall in. The third part of Alpha's programing kicked in. 'Repair and maintain Rapture.' He had, at least as far as his programing was concerned, discovered a massive leak probably due to a hull breach. Although judging from the amount of water pouring out he concluded that the breach would be too large for him to close off alone, it did however give him a direction. 'I simply have to follow up the river to the breach and I'll find Adam slugs in no time.' With time being something he did not have very much of he thundered up beside the river causing several seismographs nearby to detect a small anomalous earthquake in an area that otherwise had no fault lines.
Eventually Alpha made it to the large Saddle Lake and trotted straight in believing he had made it to the sea. He marched towards the deepest area of the lake. His footsteps finally stopped causing the ground to shake. As he walked about he combed the lake bed for large black slugs, unfortunately before he could find any something else found him. Alpha had just found a small cloth bag with a loop on the end when he noticed the twenty or so creatures swimming around him. They were strange fish like equines with colorful patterned scales instead of fur and a multitude of fins and sails across their bodies resembling hair. They had surrounded him and were floating about gracefully at various depths pointing rusted tridents at him, which was very different from him walking on the seafloor due to his great weight. He didn't know exactly what was going on, but he assumed that they wanted him to leave. They had left a small gap in their formation away from where he wanted to go, and they hadn't attacked him yet despite their numbers advantage. They were most likely attempting to herd him through the hole in their formation and away from his goal. Alpha however wanted no part in their plan. 'I don't have time for this.' He lifted up his right hoof and focused on using a particular plasmid. Suddenly the water surrounding Alpha became charged with high voltage electricity which caused varying effects to the sea pony guards. Those that were particularly close to Alpha suffered from cardiac arrest while those further away felt excruciating pain and muscle spasms. Although Alpha was at ground zero the attack didn’t faze him. He was far tougher than the sea ponies, and despite a few muscle spasms he shrugged it off. Their reaction was almost instant as they fled away from him in every direction, it was almost as chaotic and fast as when there was a half price sale on Adam. 'Didn't like that shock jockey did you.... No wait... Electro bolt...' The feeling of blood running out his muzzle and yet another headache stopped his thoughts. 'I have to find an adam slug these headaches may be my body failing me already.' He left the wounded and dying sea creatures that remained and continued his search.
Nearly four hours later Alpha finally found a large black slug, ironically enough near a undersea stone village he assumed the sea ponies lived in. It took him some effort to remove the slug off its rock without killing it but he eventually accomplished his task and placed it in his sack. His mission accomplished Alpha went on his way to return to his Little Sister.

Scootaloo had never been more glad to get out of school. She was going to make sure nothing bad had happened to the giant cyclops and show him to Sweetie Belle and Applebloom. She had been resisting the urge to run back to the big tan giant and instead walked calmly to keep the surprise for her best friends. Unfortunately the only thing that could possibly ruin her mood turned out to be right behind her.
"Hey blank flanks move out of the way and let ponies with actual parents through." Diamond Tiara commanded like the brat she was.
Scootaloo stopped and faced the little snob and her side kick Silver Spoon her teeth grinding. That was a low blow even by Diamond Tiara's standards. She would have let it go if Tiara had just been insulting her, but the fact that Tiara had insulted Sweetie Belle for having busy parents and Apple Bloom for what happened to her’s was just wrong. She tried to think of a comeback. "Hey I have a dad!" Scootaloo caught Applebloom flinching slightly. Horse apples she just insulted Bloom and not defended her, definitely not Scootaloo's proudest moment.
Diamond Tiara didn't seem to care about any of that though and continued being a smug rotten brat. "Oh yeah? Well then why don't I see you with him more often? Is he embarrassed that you’re just a blank flank?" Thankfully before Scootaloo could teach that rotten filly a lesson the ground began to shake and the rhythmic thumping began to grow louder heralding only one thing. Scootaloo smiled smugly as Diamond Tiara and Silver Spoon's expressions evolved from confusion, to disbelief, to terror as their eyes grew wide and their hooves quaked frozen in place. Finally a large shadow fell over Scootaloo and her friends while a yellow light targeted Diamond Tiara and Silver Spoon. Pointing up and behind her Scootaloo proudly proclaimed to her friends and enemies. "This is my Dad."
Diamond Tiara and Silver Spoon stood there for a moment before running away as fast as they could leaving a couple small dust clouds in their wake. Scootaloo took a deep breath of the justice that still hung in the air, before turning to try to calm down her friends. Unfortunately they seemed to have had a similar idea to Tiara and Spoon. 'I probably should have told them about him... I didn’t really think this one through.' Scootaloo looked up at the giant. "Hey. Thanks for scaring those bullies off, but can you be a little less scary around my friends?" He tilted his head to the side confused. She facehoofed again and decided that explaining how to be less scary wasn't going to work. "So... How was your day?" Scootaloo asked trying to end the awkwardness of the situation.
The massive cyclops brought out a filthy moss covered object she thought may have once been a bag. He unstrapped it from around his neck and placed it on the ground. Just when she thought it couldn't be any weirder he pulled out of the bag a massive slimy black thing and placed it in front of her. Scootaloo looked between the black thing and her big daddy, absolutely confused. However, he didn't offer any answers and just leaned in looking at her expectantly. Still with no idea what was going on she poked the black blob with her right hoof a couple of times only to watch as two black eyestalks shot out and it slowly start to crawl away. She looked back up at the tan cyclops her ears splayed back. "Was I supposed to do something with that.... Or were you just showing it to me?"
His shoulders and head fell instantly making him appear sad. Scootaloo didn't know what had happened but it was very strange to see him express any emotion besides confusion. Before she could even attempt to comfort him though the massive stallion broke out into a coughing fit his yellow eye flashing red with each cough. Without warning he punched a nearby pine tree into splinters. Scootaloo watched as the behemoth took his anger out on the tree, she wasn't sure if it was something she had done that caused it but it was terrifying.
He eventually calmed down and looked at her with his glowing yellow eye. Before he could even do anything something fast and multi colored slammed into his side.

Chapter 4: Subject Alpha VS Rainbow Dash

Something has gone wrong. We don't seem to have an archived copy of that chapter.

Chapter 5: Disarming the situation

Author's Note

http://youtu.be/wQKKj_qeOBQ
Sorry for the short chapter, but I decided I need to give you guys something after I've been gone so long. Next few chapters will be longer and far more entertaining.

Chapter 5: Disarming the situation

"A man chooses. A slave obeys."
―Andrew Ryan

A tense stand off began between the six most powerful and legendary heroes in all of Equestria and Subject Alpha. For what felt like several minutes the only sound that broke the silence of the stare down was a deep growl emanating from the tan behemoth.
Eventually though Twilight broke the tense silence. "Rainbow Dash, are you okay?"
The usually talkative cyan pegasus was still watching her life flash before her eyes. "What!? Uhh...Y-yeah." She shook herself out of her trance, and slowly got up wincing as she put pressure on her back leg that had been pinned to the ground. "I've had worse crashes.... Just not many..."
Nodding, Twilight turned her attention to the orange and purple foal being pressed against the metal and leather titan. "Scootaloo, how about you? Has it hurt you?"
Scootaloo shook her head. "Nah, my dad would never hurt me." Everypony's eyes nearly popped out of their heads.
"Scoots... You mind running that by me again?" Rainbow dash asked after picking her jaw up from the ground.
"Well... Last night I saw a shooting star... And... I don't have a family.... So.... I wished I had a dad, then he fell out of the sky, and saved me from timberwolves.... And yeah..." Scootaloo explained.
Twilight facehoofed. "Scootaloo that doesn't make any sense!"
"Well neither does Pinkie Pie, but nopony questions her!" The filly retorted.
Twilight gave a silent touché, and tried to think of what to do next. "Can you get him to calm down and come with us to my castle? I don't want to freak any pony else out, and I want to do some tests on...him."
Subject Alpha pressed the small Pegasus even tighter against his chest. "I don't think he wants to..." Scootaloo replied.
A few moments of silence passed as a plan formed in the purple alicorn's head. "Fluttershy. Can you try to calm him down?"
The yellow Pegasus gave a look of 'why me' before nodding. "S-sure... I'll try." She answered, and very slowly walked towards the giant. She stopped a few feet short of the towering beast and spoke in a kind, gentle voice. "Hello, Scootaloo's daddy. If you would be so kind... Could you come with us. That is, if you wa-" the rest of her words were cut short when Subject Alpha placed Scootaloo down and brought his helmet right up to her face. Every pony watched in terror not knowing what to do, and then Fluttershy did the unthinkable. She gave him the stare. For several tense seconds everypony held their breath.
"DING!"
Subject Alpha's helmet changed from red to bright green. His form visibly relaxed and he stood up tall tilting his head questionably at Fluttershy.
Pinkie broke the awkward silence that followed. "Did it work!?"
"I-i think so..." Fluttershy replied hesitantly. "Uh... Could you, follow me Mr. Scootaloo's dad, If you don't mind?" Subject Alpha nodded, and the very awkward trip to Twilight's castle went off without a hitch.

Phials by Flimflam bros.

Presents

"Stare Down"
Control your enemies and get them to work for you. Make eye contact and even the most powerful of beasts will be under your control. Maintain eye contact for prolonged control.

"Why let Unicorns have all the fun?"

Chapter 6: Desperate Measures (Edited)

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Chapter 7: Subject Alpha Vs Big Sister (Edited)

Author's Note

Suggested music

Chapter 7: Subject Alpha Vs Big Sister (Edited)

"Big Sisters are the new gatekeepers of Rapture: Born from Little Sisters, they don costumes much like their former protectors--the Big Daddy. However, these lithe, broken, mysterious creatures are worlds different from the hulking beasts that inspired their design..."
―Unknown

'PROTECT LITTLE SISTER' Subject Alpha 9-2's mental programing commanded with indelible authority. He brought his attention back to what he believed was a Rogue Big Daddy before him; hoping that his Little Sister would do as he said and find some place safe to hide. With a single thought his 50 Cal machine gun extended out from his armored saddle loaded with Armor Piercing ammo, and brought up his drill just in time to block a two foot needle from stabbing into his face. Quickly countering Alpha opened fire with his machine gun only to watch his enemy disappear in a puff of purple smoke before the bullets even hit. For a moment the Big Daddy froze in place as his mind tried to make sense of what just happened. Unfortunately one moment was all the Rogue Daddy needed. A ball of fire slammed into Subject Alpha's left side and sent him rolling across the muddy ground. Quickly getting up and throwing his body to his left Alpha managed to avoid the next volley of fire and locate his opponent high in a pine tree. He returned fire with his machine gun. In turn the mad Rogue avoided the stream of bullets by jumping from tree to tree with ease. The Rogue suddenly flipped the tables by firing balls of fire while it jumped around in the trees surrounding Subject Alpha. Nowhere near as fast as the Rogue, Subject Alpha was unable to dodge the firestorm, and was pounded by blast after blast of incinerate. Although the small balls of fire would normally be more annoying than dangerous to Alpha the sheer number of blasts that hit were taking their toll.
Thoroughly pissed, Subject Alpha timed the Rogue's next round, raised his right hoof, and with proper leading launched his drill. The drill head flew through the air with its coiling retractable cable trailing behind before burying itself several inches into the Rogue's back right thigh. Alpha then retracted the cable and pulled with all his might, slamming the Rogue straight into the ground. The drill bit dislodged itself from the Rogue Daddy due to the force of the impact, and Alpha knew just what to do with it. Returning the drill back to his right hoof Alpha leaped into the air intent on smashing the drill into the Rogue. With a perfect back flip the Rogue gave another screech and charged him again.
Blocking the needle with his drill again, Alpha moved in close and delivered a headbutt. Although the Rogue was sent sliding several feet both of their helmets rung for several seconds. ‘Definitely not my brightest idea.' Although it was annoying to him, it was a downright excruciating for the rogue daddy. It was holding its helmeted head screaming in pain, and he could have sworn the rogue had an unsettling vibrating effect similar to a tuning fork. Alpha span his drill up and attempted to thrust it into the rogue’s midsection, but yet again the flexible rogue jumped out of the way. However, this time Subject Alpha was ready and launched his drill into the rogue's back, pulled it back to him and then bucked the rogue off his drill. The force of his buck managed to launch the rogue daddy twenty feet straight into a tree. Wanting to give the thin rogue a taste of its own fiery medicine, Alpha launched his own fire burst of incinerate. Acting quickly the rogue backflipped onto the tree it was against, and while upside down blocked his attack by telekinetically making a shield out of nearby rocks. The rogue then aimed the burning pile of rocks back at him.
It only took Alpha a second to realize the inevitable. 'Well... Shit.' With the force of a car slamming into him at 20 miles an hour, Subject Alpha was flung back 30 feet and landed on sharp rocks. Upon impact with the ground Alpha's drill accidentally launched, slammed into a rather large boulder of granite, and shattered into several dozen pieces. It took Subject Alpha several seconds to process the fact that his high tech drill had just been turned into a glorified brass knuckle.

Issue: Hydraulic Fluids / Gases within drill cause subject to become unreliable. unstable.
--Launching option to be removed from drill in All future models.
-Dr. Suchong (Creator of the Big Daddy), December, 31, 1958

'Oh Buck!' Alpha got up as quickly as he could and what remained of his drill retracted back. However when he faced where the rogue daddy had been it was nowhere to be found. He turned around searching for the give away red glowing visor, but he couldn’t locate it. Subject Alpha tried to keep aware of any sign of an attack, but by the time he heard the sound of a distorted screech it was already too late. The rogue daddy dropped in from above; the massive needle attached to its left hoof ready to skewer him. To Alpha the world moved in slow motion, but no matter how slow everything became he was still the slowest one there. He could only watch as the needle came closer and closer. With the full force of the rogue behind it the needle entered his stomach just under his front right hoof, and lanced him. The rogue grabbed his neck to hold him close, and while twisting the needle inside of him began to literally drain the life out of his body. Subject Alpha screamed in agony as his strength, and his Adam was drained from him. He felt so weak, so quickly, and his mind struggled to think of a way out of what had to be one of the worst hugs in history. 'Protect Little Sister.' Even in his final moments his mental programing commanded him to win. Suddenly the rogue's reaction to being headbutted came to his mind. "Well I'm dead anyways."
Alpha slowly brought his head back with all the strength he could muster, and brought his face down on the rogue daddy's head.
"Ding!"
The Rogue pulled its life sucking needle out of him and grabbed its helmet in an attempt to block out the noise. Alpha rushed forward now able to use what little strength remained in him to push the rogue into a tree.
"Ding!!"
The rogue's helmet slammed against the tree and caused the rouge to give an endless twisted scream. Backing up slightly Alpha activated what was left of his drill. The rogue charged at him in a blind fury. Alpha delivered an uppercut to the rogue with every ounce of his strength left..
"Ding!"
The rogue flew backwards and slammed the back of its helmet against the tree again.
"Dong!"
The rogue daddy collapsed at the base of the tree, and its visor turned off. Staring at his unconscious foe, Alpha prepared to finish it off. His machine gun extended, once more loaded with armor piercing rounds. At this range he could not miss. The barrel of the gatling span up.
"Wait! What are you doing!?" A particular foal yelled out.
Alpha slowly put his machine gun away, and stared at his Little Sister, who should have been very far away.
"What is with you and trying to kill ponies!?" Scootaloo yelled at Alpha.
'Because they are trying to kill me as well, also dead ponies can't hurt you.' Alpha thought to himself.
Scootaloo grabbed Subject Alpha's helmet and peered in with adorable puppy dog eyes. "Please... Dad... No more killing... I have no idea what happened tonight, but please. There is no reason to kill anypony."
'You are absolutely adorable, but sadly I must follow my programming and if I must kill then I will--'
'Serve Little Sister!'
'Et tu Programae?' Alpha slowly and carefully nodded. 'fine I won't kill anyone tomorrow... I wish I could stay longer...'
"Thank you!" Scootaloo squealed with joy and hugged Alpha's helmet. "Oh I almost forgot!" Scootaloo stopped hugging Alpha and picked up some rocks. The little filly then threw the rocks at Alpha as hard as she could. "What were you trying to do with me earlier! Some ritual sacrifice or something!? No more needles! Okay?! I hate needles!" When Scootaloo ran out of rocks, she punched and kicked him, and when she got too tired she cried. Alpha didn't react to her rocks or punches, but lifted her up and gave her a big gentle hug when she cried. When Scootaloo finally calmed down he placed her back on the ground.
"Thanks." Scootaloo said calmly before giving Alpha's hoof a hug. After a few moments Scootaloo realized that there was still a unconscious armored pony next to them. "Uh... So do you think you can carry that back with us?" Alpha gave a shrugging nod, began unwinding what was left of his drill and started tying the unconscious thin pony with the tow wire.

The walk back to the crystal castle was long, painful, and tiring. Alpha knew his time was coming, at least he was able to protect his little sister one last time. He walked inside the castle with the guards giving him dirty looks, but still giving him his space. Suddenly there were those six mares again, it felt like he was missing so much. Like he was blinking and suddenly minutes would pass, and their voices seemed so far away.
The rainbow colored mare led Scootaloo away, but before he could follow the white unicorn stopped him.
"You’re hurt..." She gestured to the blood trail behind him. "Please let us help you." She spoke with a kind reassuring voice, but he knew he could not be helped.
"Please darling, would you kindly take your helmet off?"
Alpha paused for a moment. 'Something she just said doesn't sit right with me.' He thought. Slowly he sat on his haunches and slowly grabbed his helmet and gave it a sharp turn. The sharp hiss of releasing pressurized gas. Slowly Alpha lifted the bulbous metal helmet of an Alpha Big Daddy off his head and revealed a messy sweat plastered orange coat, a rats nest of a long auburn mane, bright glowing yellow soulless eyes, and a muzzle covered in blood.
'Would You Kindly?'
Subject Alpha suddenly felt the world spin around him. He vomited blood before the mares and he passed out knowing this was his end.

Would You Kindly: Would You Kindly?

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Chapter 8: Examination

Author's Note

Sorry this took so long.
Warning unedited.

Chapter 8: Examination

"One does not undertake an experiment knowing one has failed "
―Rosalind Lutece

Rarity sat down in her throne and rubbed her face not knowing what to do. For some reason the giant tan suited pony, that Scootaloo believed was her "dad", had decided to wake up in the middle of the night, break down nearly every door in the castle, and took Scootaloo. The worse part though was that nopony could seem to find the orange filly and her giant friend. Doors could be repaired, but if anything happened to Scootaloo Dash would be devastated. Just as she thought about her the cyan and rainbow Pegasus flew into the throne room and made a quick landing. All of the old bearers of Harmony looked to Dash for news.
"Nothing... I found nothing..." The usually brash Pegasus was on the Virge of tears as she spoke. "I tracked them to the Everfree but then the trail went cold. I don't know what to do girls..." Rainbow Dash buried her face in her hooves, and a heavy silence filled the room. Everypony watched as their friend suffer and felt completely helpless.
"Hi girls! We're back!" Scootaloo cheerfully announced breaking the silence. The orange and purple filly was covered in mud, came riding in atop her "dad", with a odd tan form bundled in wire beside her and a giant smile on her face. Scootaloo jumped down from the massive pony's back and was immediately hugged by a teary eyed Rainbow Dash.
"I'm so glad you're okay!" While the rest of her friends were still recovering from the shock of the filly's sudden return, Rainbow Dash asked the one question on everyponys' mind. "What happened?"
Scootaloo looked around to all the curious faces staring at her, cleared her throat, and began. "Well... I'm not sure exactly why it happened, but here's what happened. I went to sleep tonight on top of my dad, because he's nice and warm, but for some reason in the middle of the night he wakes up, and stands up so fast he launches me across the room. I don't know what, but something must have spooked him, because before I could even realize what is going on, he picks me up and starts charging through doors. I'm yelling at him to stop, but he just doesn't listen and carries me into the Everfree forest." Scootaloo then sat on her haunches and began emphasizing her words with her front hooves. "Then things get weird. He takes me to a bog and suddenly just set me down on a rock. Now I'm thinking 'Maybe he just wants to show me this place, or somthing', but then he takes off without me and starts searching for a weird giant needle in the mud. Well when he finds it he pins me down and tries to inject me with it! That was scary, but just before he stabs me with the needle a weird talking box falls from the sky and lands like ten feet away from us. He let's me go, I don't know what's going on, I still don't know what was going on, but when I looked up to see where the box fell from, I see a weird tear thing in the sky. Suddenly Boooooooooosh!!! it explodes into water, and soaks everything." Scootaloo spreaded her front hooves out wide to demonstrate the explosion. "Then were the water lands this thing suddenly appears." Scootaloo gestured to the Big Sister tied up on Alpha's back. "And it and Dad get into an Epic fight, but in the end Dad won and we brought it back here. And that's what happened." Scootaloo smiled and folded her front hooves her tale complete.
Everypony stared at the filly not sure of what to make of her tale, except for Rarity who stared at the wobbly legged Big Daddy and the blood trail following it. Rarity quickly formed a plan and spoke before anypony else. "That's quite the tale Scootaloo. Uh... Dash can you go clean her up, please." The cyan Pegasus nodded and the two of them left the thrown room. As soon as Scootaloo left Rarity slowly approached the behemoth, getting between it and where Scootaloo left with Rainbow Dash. "Your hurt..." The alabaster unicorn tried to reason with the Big Daddy gesturing to the blood trail behind it. "Please, let us help you." The tan giant turned his bulbous near featureless helmeted head to look at it's blood, and then turned back to the mare in front of it. Rarity didn't know what it was thinking, but she knew that nopony was going to be able to help it if it didn't get out of that suit. "Please darling, would you kindly take your helmet off?" For a moment the giant pony remained completely motionless, and Rarity grew worried that it would not allow anypony to help. Slowly it sat onto its haunches and brought its front hooves to its helmet. Rarity silently thanked Celestia and watched as it quickly twisted its head. Slowly the metal bulbous helmet came off revealing a startling sight.
The Big Daddy was a large orange stallion, with a dark auburn mane. Both his mane, and coat were very unkept long rats nests. As horrifying as his mane and coat were, his eyes were far more unsettling that is if you could call them eyes. Where the stallion's eyes should have been were two yellow lifeless glowing bottomless pits. There was no distinction between the whites of his eyes, pupils, or irises, only yellow. His muzzle was more concerning health wise though. It was a mixture of orange fur, brown dried blood, and red fresh blood, that poured from his nose and mouth. All in all Rarity was terrified of what she saw but glad she had the stallion remove its helmet. The silent moment of observation of the pony underneath the mask suddenly came to an end when the stallion vomited a horrid mixture of sick and blood. Rarity just managed to dodge out of the splash zone when the great stallion keeled over, sending his forgotten unconscious prisoner skidding across the smooth floor.
What little medical know-how the fashionista had, kicked in. She rushed over to the Stallion and with both her hooves applied pressure to the gapping wound on the stallion's side. "Somepony get a doctor!" The reserved unicorn shouted.

Less than ten minutes after he had collapsed the Big Daddy, and Big Sister had been loaded onto separate reinforced metal gurneys and rolled into the castle's infirmary. Doctor Suture looked over Alpha thinking of how this was the stranges procedure he had ever preformed. He had been called to the newest Princesses castle in the middle of the night alongside Nurse Redheart, with no idea what was in store for him. The light blue unicorn wiped sweat, and stray strands of his white mane away from his dull blue eyes. Now here he was beginning what could possibly turn into a operation, with a screwdriver, as he had to remove a pony from a suit not designed to be removed from. Giving one final twist the large metal saddle made a solid thud against the gurney, finally free from the rest of the suit. Sighing Suture placed the screwdriver on a small table beside him, and gave a glance at his cutie mark, a green cross.
He silently remembered the promise he made to help everyone, pony or otherwise, no matter the challenge and turned his attention to the four guards standing guard around his other patient. "Hey, you four! If you would do something useful, by helping me lift this heavy thing, instead of stupidly standing around a restrained sedated like a bunch of idiots, that would be great." He deadpanned. The guards all glared at him in frustration just as tired, but gathered around the stallion's gurney with the Doctor. "Redheart, when we get this thing off of him I want you to take my place and get him out of this thing." The tired nurse
Together the five stallions lifted a four hundred pound peice of Rapture machinery to an empty gurney. The gurney managed to hold the advanced saddle's weight, but made some very concerning groans of protest. The five stallions took a moment to catch their breaths. Twilight had wanted to study all the equipment they took off those two, and had insisted that instead of piling it all on the floor, that it was taken to her study. Dr. Suture though, was just glad he wasn't the one who had to wheel it all over to the princess.
"By Celestia!..." Redheart exclaimed, interrupting their panting. Suture walked over to the mare to see what sort of unseen injury had disturbed her so greatly. What he saw made him freeze in his tracks, where the stallion's navel should have been at the center of his belly, was a vast multitude of tubes, wires, cables of all various sizes, and colors. Each tube and wire was in some way connected into the Big Daddy's lower torso, pumping various fluids into a system between the stallion, and small machines hidden inside the suit. It all reminded him of a foal attached to a placenta by its umbelical cord. "Doctor, what should we do?" Nurse Redheart brought him back from his reverie. Shaking his head he Suture got back to the task at hand. He tried to think through what the situation required of him, while also passing his unsureness off as him educating Redheart. "We can't remove any of the equipment attached to him, obviously, as we don't know what the purpose of each part is... I want you to take a blood sample, hook him up threw the helmet hole to a monitor and I.V, and then give him a transfusion of O negative. He's lost a lot of blood. I'll treat his wound, scan his body for anything else, and take bone, and horn marrow samples. Then let's put him back inside this thing, don't want to accidentally disconnect something." Nurse Redheart gave a quick nod, and the two set to work.
The two medical professionals encountered no issues as they worked, however the monitor reported the stallion's brain activity slowly dropping, until Dr. Suture scanned the unconscious stallion's body. Suture took a double take, and did another magical scan. Redheart took notice of this and prepared for the doctor to list injuries for her to treat. "Gallbladder, Appendix, Tonsils, Adenoids, Prostate, Right Kidney, Spleen, Testicles..." The doctor mumbled out barely loud enough to be heard. "Doctor? Is something wrong with all of those organs?" She asked, hoping that she had just misinterpreted that the large stallion had massive organ damage. "Yes. They are gone. They have all been surgically removed. This stallion has been under the knife many, many times." He replied matter of factly, hiding his shock while, Redheart's jaw dropped.
Everything else went without a hitch, and they moved onto their next payment. The guards stood at the ready as the restraints on the Big Sister were removed, just in case she somehow woke up early. Suture messed with its helmet for a few seconds, before finally figuring out how to remove it. However as soon as he saw the muzzle underneath the doctor froze. "She's just a filly..." He spoke in shock trying to confirm what he was seeing. Underneath the mask was a very light grey mare with a black mane, who could be no older than sixteen although her legs were abnormally long. She was at the cusp of marehood, her face still pudgy like a filly, but deffinately with a more mature form. "I have daughter that's older than her." The doctor spoke quietly feeling a heaviness in his heart. Fortunately removing the mare from her suit was easy as she wasn't attached to her suit like the stallion.
Upon removal they discovered that she was a Pegasus, her wings had been restrained against her body with belts, and that her open wounds from fighting Alpha had already miraculously healed. Finally Dr. Suture scanned her, fearful of what had been done to the tall young mare. Redheart watched as Suture backed away from the gurney, sat down, his face nearly turn green, and his eyes grow wide. She stared at the mare and wondered what had been done to her. After a moment of fighting his gag reflex the doctor finally spoke. "Well nurse... Her legs are extremely weak, having grown rapidly to math the height of princess Luna, which explains those braces... And... I need you to bring the ultrasound over." Redheart stared at him completely in shock. "She's with foal?!" Suture nearly shook his head slowly, and was silent as Redheart set the ultrasound up. When Suture activated the advanced device he didn't bring the probe to the mares uterus, but instead much higher up the Big Sister's torso. Redheart, and the guards watched the monitor of the ultrasound in horror as a low resolution image of a living fat snake like creature inside the Big Sister's stomach appeared. Suture and Redheart both silently wondered, just what kind of monsters would do these things to ponies.

Twilight sat with Scootaloo in the infirmary the next day, they couldn't hide her "dad's" absence from the filly for very long. Scootaloo was sitting at the foot of the massive stallion's make shift bed, and watching him like it would make him better faster. "Is he going to be okay?" Scootaloo asked the violet Alicorn not removing her gaze from the Big Daddy. Twilight had to take a moment of silence to think. "I don't know Scootaloo..." She answered truthfully. "The Doctors did everything they could, and hes stable now.... But we aren't sure what's wrong with him yet..." Scootaloo was silent for a few seconds... "He has to be alright Twilight..." The orange and purple filly choked out as tears began to flow. "He has to..."
For several hours Twilight watched as Scootaloo curled up against the massive stallion, waiting for the test results to come back, and to make sure that nothing happened to the filly. The alicorn got lost in her thoughts and paced the room trying to figure out why somepony would do such terrible things to Alpha and the Big Sister. The sound of struggling and panicked breathing brought Twilight back to reality as the grey mare woke up. The purple Alicorn quickly faced the struggling gangly pegasus, and charged a spell. "Stop!" Twilight commanded trying to channel her inner Luna. The grey mare had broken her front hooves rerestraints and looked up at the Alicorn with her wings opened wide. The mare's yellow sonless eyes locked on Twilight and for several long tense seconds nothing happened. Neither made moved a muscle, until the pegasus noticed her wings. Twilight watched in confusion as the Pegasus suddenly turned to look at her right wing, and acted like it was the very first time she had found it. She grabbed, stretched, and flexed her wings in absolute astonishment. A huge genuine smile formed on the mare's face as she turned back to twilight. "I'm an angel." Suddenly blood poured from the pegasus's nose, and she collapsed back on her bed.

Chapter 9: While the cat's away

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