A/N So this takes place between in the middle of Season 3, near the end, so Twilight's still a unicorn and there's still a golden oak library. So just needed to clarify that :). Now enjoy the story ~Ivy Shadow.

Rainbow Dash flew through Ponyville, doing flips and twirls through the air, leaving a small rainbow behind. Ponies stopped to point at her and watch in awe. It was nothing new, but that didn't make it any less beautiful. She then saw a familiar purple face right in front of her, but it was too late to turn away. They crashed into each other, and fell into a bush.

"Sorry, Twilight."

"Oh, it's fine! I was just looking for you!" the purple unicorn exclaimed.

"But why? Are we going to organize the library—again?"

"No, we're gonna go play a game, you'll like it. And it's not 'organize all the books in the library'."

"So where are we playing the game?"

"At the library, c'mon let's go!" Twilight used the magic to drag Rainbow along.

"I can fly, you know."

"This is faster!"

Twilight seemed a bit off to Rainbow, but she didn't push it.

"Hi Rarity! Hi Applejack!" Twilight called to her friends as they passed Carousel Boutique. Rarity appeared to be busy convincing Applejack to put a dress on.

"Can you get 'er to quit trying to coat me in poison?" Applejack asked.

"Dresses are not poison, they are graceful and beautiful," Rarity protested.

The argument continued, but their voices faded away as Twilight galloped on.

"Hey Pinkie, Fluttershy!" Twilight exclaimed as they passed Sugar Cube Corner, where Fluttershy and Pinkie were sharing a bit of cake.

"Hiya Twilight, Rainbow!" Pinkie exclaimed, for once not elaborating and going on and on, probably because of the cake she was stuffing into her mouth.

"Hi Twilight and Rainbow," Fluttershy said quietly, just loudly enough that Twilight and Rainbow could hear her.

Twilight continued running through Ponyville, her magic still pulling Rainbow along. They quickly arrived at the library, and Twilight finally put Rainbow down. "Come on in!"

"So what are we going to play?"

"Scientists!" Twilight exclaimed, pushing the door open and sprinting to a bookcase. She pulled a book, and a trapdoor opened, revealing stairs to a basement.

"You have a basement?"

"First pony I've ever shown it to, only discovered it a week or so ago!" Twilight galloped down the stairs, and Rainbow zoomed after her.

"What's the machine for?" Rainbow asked, eying a circular machine, with bits sticking out in the middle.

"Well, we are playing scientist...you're the guinea pig!"

"The what?"

"That means you get in the machine and I'm the scientist!"

"Oh," Rainbow didn't exactly want to this, but she didn't want to disappoint her friend either. She willingly flew into the middle of the machine, and Twilight locked the six parts onto each limb: four legs, two wings. "So what experiment are we doing?"

"The science of friendship!"

Suddenly, Rainbow noticed that Twilight's right eye was twitching.

"Are you okay, Twilight?"

"Never better!" Now Twilight's ears were twitching.

"Twilight, you don't look so good, if you let me out I'll just take you to...the nice ponies...who will fix you..." Rainbow tried to word this very carefully, so as not to trigger Twilight in a dangerous fashion.

"It's fine, I'll just inject this serum into you, allowing me to make you unconscious, and soon I'll go break friendship down into a science!" Twilight squealed, levitating a light blue serum in a test tube.

"Twilight, have you gone insane!?" Rainbow Dash screamed, trying to escape the circular machine, attaching her to the rim at every limb, tightening a little every time she resisted.

"I'm not insane, I'm a scientist!"

"A mad scientist," Rainbow muttered.

Twilight raced over, the serum being levitated by magic, and slowly poured into a needle right in front of Rainbow.

"Where's Spike?" Rainbow asked worriedly, thinking the little dragon could knock some sense back into her friend.

"I killed him!" Twilight exclaimed, stabbing the needle into Rainbow's neck.

Rainbow screamed in agony, the 2 inch needle still injecting the serum.

"Now, we learn."

And suddenly, everything went black.

-={+}=-

"Hey Pinkie, wanna go play a game?" Twilight asked Pinkie, doing her best not to twitch, but the occasional twitch still twitched.

"Ooh, what game?"

After Twilight had made Rainbow unconscious, she had quickly decided that she should get at least one more friend. She randomly picked from a red hair from Rainbow's mane for Pinkie, an orange one for Applejack, a yellow one for Fluttershy, and a violet one for Rarity. The red one had been chosen, so Pinkie it was. Twilight had then thrown away the hairs, thinking she wouldn't still need them.

"A fun little game, you'll like it!"

"Alright, let's go! I'm so excited!"

So Twilight led Pinkie back to the library, and back down to the basement.

"We're gonna play scientist, so go ahead and get on the machine, cause you're the guinea pig!"

Pinkie boinged over to the machine, this one similar to Rainbow's, except that there were only four places for limbs, as Pinkie did not have wings.

"Now I'll just inject you with this serum..." Twilight muttered to herself, taking another needle and pouring the serum into it.

"Twilight, are you okay, you look like you ate one too many cupcakes."

"I'm fine!" Twilight started to twitch again: ears, eyes, head. "Now lemme just inject you with this..."

And that was when Pinkie screamed, and Rainbow woke up.

"AAAAAAAH! Pinkie? Twilight? TWILIGHT ARE YOU OUT OF YOUR FUCKING MIND!?"

"No, I'm just studying the science of friendship!" Twilight was still twitching, and it was getting more and more unnerving. "I don't think I have enough friends here, I should go get Applejack, Rarity, and Fluttershy!"

"NO!" Rainbow screamed. Pinkie would have screamed again, but she still hadn't awoken from unconsciousness. Twilight ignored the scream, almost skipping out of the basement, to get her last three friends.

-={+}=-

After some more persuading, and enthusiasm, Twilight was walking back to the library with her other three friends in tow.

"Have you seen Pinkie Pie and Rainbow Dash?" Fluttershy asked quietly.

"Oh, they're already there," Twilight assured them as they approached the door. She heard Rainbow screaming and quickly turned around. "Just give me a second." With that she ran inside, grabbed the serum, and injected it into Rainbow again, who screamed louder than before. Luckily, none of her friends bothered to chase after the noise. She glanced at Pinkie, the pink mare still bleeding and unconscious. She sprinted up the stairs and out the door.

"Alright, let's go!" Twilight let every pony inside and led them down the stairs.

"I didn't know ya had a cellar? Is it a cider cellar?" Applejack asked.

"No, it's a just a normal basement," Twilight said, trying to resist the twitches. "So, we're all playing scientist, I'm the scientist, so just get on the machines."

Fluttershy, Rarity, and Applejack got onto their respective machines, and Twilight used her magic to lock them onto the machines. She then levitated a metal cap that appeared to be a giant thimble, and placed it over Rarity's horn, locking it down. She then slapped Rainbow and Pinkie awake, which took way too long in her opinion.

"Now that everyone's awake, I can explain!" Twilight squealed, no longer resisting the creepy twitches.

"SHE KILLED SPIKE SHE'S NOT STABLE!" Rainbow screamed.

"SHE WHAT!?" Pinkie, Rarity, and Applejack screamed.

"Why would you do that?" Fluttershy asked, sniffing as tears fell down her yellow cheeks.

"Well, he was getting in the way, and I didn't need him anymore. Besides, now I have a body to do experiments on!"

"TWILIGHT! GET YOURSELF TOGETHER!" Rarity screamed, as politely as she could while still being pissed.

"WHAT DO YOU WANT WITH US!" Pinkie shrieked.

"I told you: I'm studying the science of friendship, because friendship is science! Right now, your machines are all hooked up to one main machine, which tells me your current feelings towards each other. Now I'm going to perform the first test: the test of death."

"DEATH! ARE YOU OUT OF YOUR FUCKING MIND!" Applejack screamed.

"I'm going to pull five hairs out of Rainbow's mane: red for Pinkie, orange for Applejack, yellow for Fluttershy, blue for Rainbow herself, and violet for Rarity. Then I will choose one at random, and that pony will die, and I'll record your feelings about it!" Twilight was twitching even worse, and she took the five hairs out of Rainbow's mane, Rainbow wincing at each one. Twilight placed them on the table, closing her eyes, and choosing one at random. Each of the other five ponies in the room prayed that something would knock Twilight back into reality or she'd say it was a prank, but no such luck. Twilight chose a hair, and showed the five ponies her choice. It was the violet hair.

"Pity, I expected Rarity would have some very detailed expressions, but the rules are the rules, and the experiment wouldn't be fair if I didn't stick with the hair I'd chosen. Say good-bye, Rarity," Twilight levitated a nearby dagger, which none of the ponies had noticed, and it levitated over to Rarity, who tried to use her own magic to stop it. But the thimble like object on her horn stopped herself from using any magic. The dagger inched closer to Rarity's throat, and pierced it, before digging in deeper, until it stuck out the back of her neck. Rarity screamed in pain, blood dripping from the wound, before going limp, as Twilight had hit an artery.

"TWILIGHT DO YOU KNOW WHAT YOU JUST DID!" Fluttershy screamed, at a relatively normal volume, as opposed to her softer screams.

"And the data is coming in, great!" Twilight completely ignored all the screams, most of which were similar to, although louder than, Fluttershy's. "Rainbow Dash is extremely pissed and is doing her best to try to escape, to try to 'knock some sense into me'. Rainbow, I'm perfectly sane!" the way Twilight was twitching—worse than ever, each ear and eye individually in no particular pattern—didn't exactly help her case. It was very unnerving, and the other four ponies, the alive ones, all shuddered, at least as well as they could in the positions they were in. "Now, Fluttershy is scared she's next, Pinkie is really pissed at me, and is trying to think of a way to laugh me into sanity," as Twilight said sanity she did a bigger twitch, her entire body twitching as if she had been electrocuted. "And as for Applejack? She misses her crush...?" Applejack blushed before glaring at Twilight again. "And also wants revenge." Twilight screamed, levitating the knife out of Rarity's neck and breathing heavily. She suddenly dropped it and smiled creepily, her mouth now beginning to twitch as well. "So in short practically all of you which to enact revenge it sounds. So instead of showing mercy and friendship to your friend you'd rather kill be to bring Rarity's death to justice," Twilight did another full body twitch at each word she put emphasis on, and Fluttershy did a small gasp of fright.

"Twilight, if ya let us go, we won't hurt ya, promise," Applejack tried to compromise, but she was certain that it was impossible, and that was true. Twilight didn't even really hear her, she was writing things down on a clipboard, notes for her experiments of craziness.

"The second experiment is about pity," Twilight disposed of the violet hair and closed her eyes. She levitated a random hair and opened her eyes.

"Yellow. Fluttershy."

Fluttershy gasped and cried, "But...but my animals...who will take care of them?"

"Someone will, don't worry," Twilight was still as twitchy and crazy as ever, and her mane was getting split ends and it was twisted in some awkward ways. "And who said you were going to die? Anyway, here's the plan: I am going to get a thing, to hurt Fluttershy with, and I'll study your reaction to it. Now, Fluttershy, I'm going to set you free for a second, and if you try to leave, I'll go get Sweetie Belle, and show her this..." Twilight gestured to Rarity's limp body, still attached to the machine.

Fluttershy gasped.

"Anyway, Fluttershy will come into this little bubble, which my toy will be able to enter and exit, but you will not be able to exit. Only enter. Just to make it easier for Sweetie Belle to not have to see that." Twilight again pointed at Rarity's limp body before, gesturing to a bubble like object, and her head violently twitched. She quickly recovered and released Fluttershy, who collapsed onto the ground. She laid there for a few seconds before stumbling into the bubble weakly. Clearly, she was a little numb. Twilight then levitated a huge case from a dark corner, and opened it, smiling at all of the things inside. "I'll use the whiiiiiiiip," she announced creepily, and anypony would have sworn her head was slowly moving sideways, like something out of a horror movie. The whip was slowly levitated out of the case, and moved towards Fluttershy, slowly, as if taunting everyone in the room.

"TWILIGHT! DON'T DO IT! YOU LOOK LIKE YOU DID WHEN YOU WERE PANICKING OVER THAT FRIENDSHIP LESSON!" Rainbow was right. Twilight had the same hairstyle, the same creepy eyes, and even worse ideas.

"I have to do it. FOR SCIENCE!" and with that Twilight took the whip and lashed it across Fluttershy's face. The timid pony shrieked and sobbed in pain, and in her sadness through. Pinkie sobbed too, and Twilight took note of this on her lab sheet.

 "TWILIGHT WHY IN THE HAY WOULD YOU DO THAT!?" Applejack screamed.

"I told you, for science! Now, onto more important matters, THE RESULTS! Pinkie seems to care the most, Applejack the least clearly because she's not crying, Rainbow in the middle. Applejack and Rainbow want to get revenge though, and Pinkie wants to get save her. That's success for Pinkie, and failure for the other two."

"BUT APPLEJACK CRIES ON THE INSIDE TWILIGHT!" Pinkie yelled.

"She does? Were you crying on the inside Applejack?"

"DOES IT EVEN MATTER? WHAT SOIL HAS YOUR NOSE BEEN IN!?"

"So that's a no then. So Pinkie is currently the best friend, you two best try to keep up. Fluttershy, back to your station. Twilight's horn lit up as the same colored glow surrounded Fluttershy as she was levitated back to her little machine. Fluttershy was practically limp, but even though she was bleeding, she was still obviously breathing. Twilight levitated a bandage over Fluttershy's wound, so she wouldn't bleed to death, and looked back at her clipboard. "Ah, the next test: the test of sacrifice. This one is tough, and unfortunately, some of you are very likely to die. First, I will pick the groups of two, using the hairs." And with that Twilight randomly put the hairs into two different piles, two in each. "Rainbow Dash and Fluttershy. Pinkie Pie and Applejack," she read, the blue and yellow hairs in one pile, and the red and orange ones in the other.

"So what do we have to do to live?" Rainbow asked worriedly.

"It's simple. You will each be given a choice: sacrifice yourself for the other pony, or have them die instead of you. If you both choose sacrifice, you both live, if one chooses sacrifice and the other chooses to have the other die, the sacrifice one dies, and if you both choose to have the other die you both die. And you won't know the other pony's choice. Now, I will levitate the remote in front of each of you so you can vote with your muzzle." Twilight's horn lit up and four identical remotes with two buttons were levitated in front of each pony. "The green one is for sacrifice, the red one is for killing the other."

Each pony made their vote, Applejack and Rainbow taking longer to decide.

"And the votes are in! First, Rainbow Dash and Fluttershy. Fluttershy chose to sacrifice herself, and Rainbow, after a lot of thought..."

Fluttershy gulped.

"Rainbow sacrificed herself as well! They both get to live!"

Fluttershy and Rainbow sighed in relief.

"Now for Pinkie and Applejack. Pinkie, a surprise to nopony, sacrificed herself. She was unfortunately not particularly lucky, as Applejack voted for her to die. Pity, Applejack, killing Pinkie Pie."

"Applejack?" Pinkie's eyes filled with tears.

Applejack would have tears drip, but she did cry on the inside, "I'm sorry, Pinkie. Truly I am."

"Buh-bye, Pinkamena Diane Pie," and then Pinkie was electrocuted by her little circle machine, and she screamed, before going limp like Rarity.

"More of you lived than I thought, but now, another test. The test of honesty," Twilight looked right at Applejack, who gulped. "It's simple, really. Each of you has a secret, which is in these files," Twilight's horn lit up and some files flew in front of her, circling around her face. Each of the other three ponies glimpsed a sight of their own face in a file or two. "Now, if somepony was to know your secret, perhaps a specific pony...it would not go over well, now would it?" the other three ponies gulped. "You have two choices. Read the secret in your file aloud and be humiliated, or lie and risk the consequences that will come of it. I'll just pick a random file and begin," Twilight placed the files down and blindly chose one. "Rainbow Dash."

"Fuck," Rainbow Dash muttered as Twilight's horn lit up again and an open file was in front of her, easily readable. "I-I need reading glasses to read this."

"No, you don't. Read, or lie."

Rainbow Dash read the file to herself in her head first, The reason the barn fell over at the end of the most recent Apple Family Reunion (that Applejack planned) was that Rainbow Dash had made a huge hole in the back of the barn, making it more fragile than ever, and causing the bats hitting the barn to make it fall over easily. Rainbow Dash gulped, staring at the file, then glancing at Applejack. "Uhhhhhhhhhhhh...I really liked that kitten that Fluttershy showed me when I was getting a pet, but I was too embarrassed to admit it," Rainbow Dash lied. Applejack snorted in amusement, and Rainbow blushed, embarrassed at the lie.

"W-Will there be any c-consequences?" Fluttershy asked fearfully.

"All consequences shall be dealt after everyone reads or lies. Now, Fluttershy, here is your file."

Fluttershy gulped, as her file was levitated in front of her. Fluttershy has had a sexual fantasy about Rainbow Dash. Fluttershy gulped, looking at Rainbow Dash and blushing. Fluttershy was lesbian, and had had a crush on Rainbow Dash ever since she saved her from bullies in flight school. "I-I h-had a sexualfantasyaboutRainbowDash," Fluttershy said it really quickly, hoping nopony would notice, but Rainbow did.

"Y-You have!?" Rainbow seemed extremely surprised.

"Mmhmm," Fluttershy whispered, blushing in embarassment.

Is she actually lesbian? Well, so am I... Rainbow Dash thought to herself.

"Now for Applejack, the element of honesty. After that embarassment about her crush earlier, it may be surprising that this is even bigger."

Applejack read the file that had been levitated in front of her, The current Winona is Applejack's seventh dog, the other six died due to too much labor. Applejack looked at Fluttershy, I can't do that to 'er, but if I lie, it could be 'er or Rainbow that dies 'r worse. "Winona is mah seventh dog. The rest sadly passed on because I made 'em do more labor than they were capable o'. I'm mighty sorry, Fluttershy, I didn't mean to, I just over estimated 'em."

Fluttershy started crying, "Those poor dogs, they didn't even get a proper burial!"

"Well, now I'll say who lied and who read. Rainbow, you lied. Fluttershy, you read. Applejack, you also read. So now Rainbow will have to suffer the consequences. You must share the real secret, and one extra for good measure. Talk. Now," Twilight ordered.

"The real secret is...that...so remember that Apple Family Reunion you organized a little while ago Applejack?"

"Sure do."

"Well, you know how the barn fell down?"

"What are you gettin' at?"

"There was a hole in the back that I made, which is why the bats knocked it down so easily."

"How could you Rainbow!"

"It was an accident, and I couldn't bring myself to tell you!"

The two ponies glared at each other.

"Now, an extra secret."

"I-I-I-I," Rainbow stuttered, a secret in mind, although not one she wanted to share.

"Talk Rainbow," Twilight was levitating a spear, and she seemed to be smiling at the thought of stabbing somepony with it.

"I...I love wearing dresses."

Applejack burst out laughing, unable to put a word in.

Fluttershy was silent, quietly blushing.

"Now, the final test. Only two of you will have to take the test, because one of you will survive. It's a test of loyalty. It's the simplest of all the tests. Now, the worst friends will have to take the test, as a punishment. Applejack has done the worst, although she may be tied with Rainbow Dash now. Fluttershy, you must now wait, and hope your friends are loyal to you."

Everypony but Twilight gulped.

"The test, as I stated, is simple. Rainbow Dash and Applejack will each be presented with a knife. They must each choose a friend to kill, or to take her own life. And they cannot choose the same pony. Then, they must kill that friend, or herself. Applejack, whisper to me your choice, then Rainbow Dash, you must do the same. Now, Applejack, your choice?"

Applejack froze. Up until this point, she had made many terrible choices that had ended the lives of two of her friends. She didn't deserve to live anymore, and she knew what she had to do. Twilight got in a position where Applejack could whisper her choice to her, and she nodded.

"Rainbow Dash?"

Rainbow Dash didn't know. If she killed herself, Fluttershy would most certainly be sad, unless Applejack had picked her, which she doubted, and if she killed Fluttershy, she'd never forgive herself, but Applejack...? It's the best of three terrible choices. And Rainbow Dash whispered her choice to Twilight.

Twilight sighed, "Unfortunately, you both picked the same pony. I would like...Rainbow Dash, to choose again. Your new choice?"

Rainbow Dash gulped. Fluttershy, could she be strong for me? I can't kill her, she'll go to Heaven, or wherever dead ponies go, knowing her crush killed her. If I die, it'll be like a sacrifice. Because, I guess I do love her. "I know my new choice."

Twilight walked over, and Rainbow Dash whispered the choice to her. "Interesting, very interesting. Well, girls," Twilight's horn lit up and Rainbow Dash and Applejack were free from their circular machines. Rainbow Dash was about to fly away, but Twilight stopped her with magic, "The price will be more than it already is if you decide to that."

That stopped Rainbow.

"And now, your knives," Twilight levitated two knives to the two girls.

"Bye Fluttershy, Rainbow Dash," and with that, Applejack picked the knife up in her mouth and slit her throat. She fell limp, and silently bled to death.

Fluttershy and Rainbow Dash's eyes filled with tears.

"Fluttershy, I-I love you too," Rainbow Dash picked up the knife in her mouth and copied Applejack, slitting her throat, falling limp, and silent bleeding to death. Fluttershy started sobbing aloud, and Twilight freed her from the circular machine.

"Now, Fluttershy, before I allow you t—"

"SHUT UP TWILIGHT AND GIVE ME A MOMENT!" Fluttershy screamed at a normal scream volume. Twilight, no matter how crazy she was, was taken aback by the comment, and allowed Fluttershy to continue.

"Rarity, I'll try my best to continue your boutique. Pinkie Pie, your parties will be remembered by all. Applejack, I'll look after Winona the seventh. Rainbow Dash..." Fluttershy had to stop as she sniffed, "Rainbow Dash, I loved you, I love you, I will always love you."

"Aw, how sentimental. Now, before you leave, you need to read my conclusion," Twilight pointed at a spot on her clipboard. "That paragraph there."

Fluttershy sighed, like she didn't care anymore, "After multiple tests, this experiment has come to an unexpected conclusion. Sometimes ponies are selfish, sometimes not. But in the end, the simple conclusion, was that friendship can be measured using science. Simply put," Fluttershy stared at the end of the sentence, and Twilight glared at her.

"Read on."

Fluttershy sobbed through the last part as she fell to the ground in defeat, "Simply put, Friendship is science."

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A/N How'd you like it? If you want me to write another MLP grimdark let me know in the comments, I had a ton of fun writing this one. If you have any questions or anything, again, let me know in the comments.

~Ivy Shadow