In the Rainbow Factory...

"Ow... what happened? Dashie?"
Pinkie Pie rubbed her head and saw a small scorch mark on her shoulder from the tazer. She looked up and saw Applejack bucking the cage wall. Her muzzle and ropes were on the cage floor. She looked at Rarity, who was sitting in the corner, her hair a frazzled mess, her makeup smeared all over her face, and her horn broken. She looked around for Fluttershy but couldn't find her. After looking around for a few more seconds, she saw Fluttershy hanging above the Pegasus Device.

"So... I see you're finally awake. And I expected you to be the first one to wake up." Rainbow Dash said from. All three ponies looked up and saw Dash had landed on top of the cage.

"Let us go!" Applejack yelled. Rainbow Dash made a clicking sound and hovered above.

"You really think I would after your betrayals? No. Never. You knew how I would react after your whole Mare-Do-Well act."
Applejack was about to protest again then realized she was right.

"It... it's true. We all knew it. But..." Rarity buried her head in her hooves, smearing her makeup even more than it already was.

"Help!" Fluttershy cried. She had finally woke up and realized what was happening.

"What is Fluttershy doing up there?" Applejack asked, pointing and biting her lip.

"Oh. She's the first one up. Which reminds me... YOU CAN BRING HER IN NOW!"
Two pegasi pushed a cage in.

"Girls!" Twilight cried, grabbing the bars.

"Twilight!" The three ponies in the cage cried. They ran towards the side of the cage and watched as the pegasi pushed her until she was directly across from them but was slightly angled to face the device as well.

"Fluttershy!" Twilight cried and tried to force the bars apart, failing miserably.

"Aaaaaaand that's not going to work." Rainbow Dash said.

"Rainbow! Please! Don't do this!" Fluttershy tried to yell. She cried and pulled on the shackles around her hooves. She tried to flap her wings, but they were being pulled back by a separate pair of shackles.

"What are you going to do to her!?" Twilight shouted.

"Oh. Well, you'll see. And then it'll be the annoying one's turn."
"Whaaaaaaaat? I'm not annoying!"
Everypony turned towards her.

"Okay. I can sometimes be annoying."
Rainbow Dash rolled her eyes and flew over to a control panel, pressing a few buttons and powering the machine up.

"Just so you know, what you're about to see will not happen to all of you. Each of you may be killed in the same or different way than another."

"Are you going to give us a lecture?" Applejack said.

"I'm not Twilight. And no, I'm not."
Rainbow Dash smiled and pushed a final button before the shackles jerked. The one around Fluttershy's wings pulled and so did the one on her back left hoof. Fluttershy began to cry even more and screamed as one of her wings was torn off her back. Blood began to pour out and it trickled down Fluttershy's body.

"STOP! PLEASE!!!" she screamed. But it didn't.'

The shackle tore Fluttershy's other wing off. As it pulled back, the skin and some flesh peeled off since it wasn't a clean snap. Fluttershy screamed and nearly passed out. Rainbow paused for a bit as one of the pegasi below injected something to keep her wide awake and alert to the torture. The smell of blood had already begun to spread out around the huge room. The pegasus flew back down and Rainbow continued. The left shackle jerked very suddenly and Fluttershy's back left hoof was torn right off. Fluttershy gritted her teeth. Her throat already hurt, and her head too. She couldn't sustain the pain any longer. But whatever that pegasus had injected into her was keeping her from passing out.

P-please. L-let this b-be over a-alread-dy.

The shackles on her right back hoof and front left hoof started pulling away from each other and both hooves began to tear off. Blood poured out of each wound. Fluttershy was losing every sense due to blood loss. Both shackles jerked and tore both hooves out. Fluttershy let out a small squeak, the only sound she could muster up. Now she was hanging by her front right hoof. The shackle opened and dropped the timid pegasus into the machine. It grinded her up, splattering blood and flesh everywhere. The pain was beyond what Fluttershy had just felt. It was enough to make her make the loudest scream anypony had ever heard from her. As the last bits of Fluttershy disappeared into the machine, yellow and red spectra spewed through the tubes and into its coagulated parts.

The four ponies below stared, their mouths agape. They all instantly began to furiously yell and pound at the cage bars.

Dr. Atmosphere flew over to the cage Pinkie was in and was able to confuse Pinkie. He injected something into her body to temporarily numb her so he could get her out.

"Hold the others back while I get this one!" Atmosphere yelled. Two pegasi in the room flew over and went inside, quickly pinning Applejack and Rarity to the floor. The one holding Applejack struggled a bit but managed.

"Alright. Put her on there and we'll begin. But first... Glaze? Do you have it all ready?"
"Yes." Glaze said. She rolled over the cart of sharp tools to the table similar to the one from Cupcakes (the fanfic). Pinkie Pie screamed as she was being strapped down.

"SHUT UP, or you're death will be long and painful."
Pinkie Pie gave Dash a look of anguish and nodded. Dash rubbed her hooves together.

"Alright. So should we start with the cutie mark? Or with the hair?"