It's not a good day for Caduceus.
But considering that his soul was shattered a few weeks ago, it's a miracle that he didn't commit suicide. Caduceus is a doctor. Not the brightest one around, but he's still a devoted doctor, really to do everything for his patients.
His cutie mark probably has something to do with that, for he can't find peace when he knows that somepony, somewhere, is in pain.

But, right now, Caduceus isn't a pony any more. He's not even a doctor. He's just a machine, only acting, never thinking.
They say that not a single soul get through the Factory, and that's true. It doesn't matter if you are a victim, an executioner, or just a witness. Fillies being broken and ground alive is a sight that breaks your soul and shatters your sanity.
You could say that Caduceus was the most unlucky pony in the world, because not only he was allowed to witness such horror, but he was also denied a swift death. When the Rainbow Factory's manager ordered for him to be thrown outside, the Doctor Atmosphere interfered, and pointed at the manager's own wounds.
From this day, Caduceus was forced to tend the crazy pegasus' wounds, unable to forget the horror, and yet unable to kill himself. He has to heal. It was his only purpose, the only thing keeping him alive, and yet still destroying his sanity.

Therefore, he's not surprised when a strange blue box appears in the middle of the room. He's not surprised when an earth pony jumps out of it, and quickly looks around. However, he's surprised when the supposed hallucination starts talking to him.
“Hello there, good boy! I'm looking for a friend, and she said she was visiting the Rainbow Factory, so I'm here! Would you believe it, I'm piloting a ship able to travel through space and time, and yet, I had trouble entering in this place! It's like someone doesn't want ponies running around here! And yet, you're not supposed to have any jamming technology here, so what's happening? Tell everything to the Doctor, I'm the highest authority around!”
Faced with that sudden barrage of questions, statements, and shocking revelations, Caduceus' brain quickly gives up, his old social habit taking the lead.
“Hello. I don't think I know your name?”
“I'm the Doctor.”
“Doctor Caduceus.”
“Oh, another doctor? Nice to meet you. SO! Where's the boss in charge of that place? I'm looking for someone.”
“A friend of you?”
“Ummm, no, but she's a nice companion. Easy going, even if she's a little clumsy. The other day, she accidentally pressed a button on the TARDIS, and we crashed on a planet, who was in fact a giant graveyard. Well, at first, it looked like one, but in fact we discovered that it was inhabited by weeping pegasuses, but that's beside the point.”
Caduceus' brain, still considered as 'dead', manages to give him an important advice. 'If you don't understand, just nod when he's done talking'.
He nods.
“Well, you're nodding. That's nice and all, but I really need to see your boss, like, right now, because, you see, I just remembered that jamming device you're using here, and that means trouble.” Luckily, while the Doctor is speaking, Caduceus' brain is slowly assimilating the fact that there's an intruder in the factory. “Because, yeah, I saw a similar magnetic signature back on the planet-”
“DOCTOR!”
“Yeah?”
“You're in danger. I'm not working here! I'm a prisoner!”
“Prisoner? Usually, prisoner are covered with chains and stuff.”
“That's because I'm the only prisoner!”
“Now there's something going on here, right? You don't keep prisoners in factories, you keep them in jails. So what's going on?”
There's just too much to explain. The younger doctor can't figure where to start, while the older doctor is staring at his face.
“W-well...”
“Haa, forget it. Just show me.”
“Excuse me?”
“Show me the way around.”
“What?”
“That thing. It's called a door. It leads to a brand new world. We open it, and we pass.”
“But we can't-”
“I'm the Doctor, I can.”
Leaving the confused doctor behind, the Doctor leaves the room.

In the meanwhile, Derpy was horrified.
She saw ponies being sifted and ground into horrible lifeforms, but she managed to shrug it off, because it was the doing of some horrible alien species. But that brutality she was witnessing right now wasn't the doing of an alien. It was the doing of a famous an renowned pegasus, the one they called the Fastest Flier in Equestria. And the whole thing was rendered more horrible by the fact that the renowned pegasus was mercilessly torturing a filly.
That's right. Rainbow Dash wasn't interrogating some political prisoner, or some criminal. She was torturing an innocent filly, just for the fun, and according to the demented smile on her face, she was having a lot of fun.
She was actually biting the fillies' feathers, and taking them off, one by one, triggering a pained scream each time.
“I'm sorry! I'm sorry!”
“Not enough, Scootaloo. You'll never be sorry enough to compensate the fact that you failed me.”
“I'm sorry! I'm sorry! I'm sorry!”
With a cruel laugh, the blue pegasus get an mouthful of Scootaloo's feathers, and starts pulling, half-tearing the young pegasus' wing, and causing her a great pain. There's a loud 'CCRRRCK' noise, and Scootaloo suddenly stop crying, only to scream.
Satisfied with Scootaloo's pain, Rainbow Dash drops her on the floor, in front of Derpy, walks to the door, and orders the guard to 'bring the patchguy here'. Then, she closes the door again, walks to Derpy, and sits in front of her, still smiling maniacally.
“So, Derpy Hooves, am I right? You've been caught trying to trespass. That's not very smart, not at all.”
Derpy tries to answer, but, from the corner of her eye, she still can sees the tortured filly.
“Oh, that? Don't bother about that, the doctor will patch her up.”
“The Doctor?”
Derpy's heart jumps when hearing that name. After all, there's still the Doctor! He'll fix everything!
But as soon as she stares at Rainbow's eyes, she understands that even the Doctor can't fix that one. Derpy wasn't the brightest pony around, but she traveled a lot. She's able to recognize evil when she sees it, but Rainbow Dash isn't evil.
Because in evil, you find malice, hate, and a large part of self-interest. No mercy, no empathy, in short, nothing like that. But Rainbow Dash' eyes says a different story. She's not doing those things by sadism, or because she was ordered to. She's torturing Scootaloo by pure hate.
Even Derpy can understands that, despite her clumsiness, her relative lack of intelligence, and her oblivious nature.
“Yes, the doctor. He patches ponies here. Hey, garbage, you should thank him. It's because of him that you're still alive.” Says Rainbow, while kicking the crying filly.
“Why are you doing this?”
“Because she deserves it. Right, garbage?”
Derpy tries to move, to instinctly protect the filly. But a loud metallic noise reminds her that she's tied to the wall, and therefore, can't do anything to help Scootaloo.

“Hey.”
Without even looking at the guard, the Doctor starts talking, still not minding the fact that the guard is threatening him with a taser.
“Hello there. Would you believe it, it was actually kind of difficult to find my way in. Now, where's my psychic paper? Ha, here, I'm the Professor … Tennant, from the University of... Arkham.”
The guard puts his taser away.
“Greetings Professor. How may I help?”
“Lead me to the second highest authority around.”
“Doctor Atmosphere, then?”
“How many doctors around?”
“With Atmosphere and the prisoner, two.”
“Guess that means three, then. Show me the way.”

And while the Doctor goes to meet the Doctor Atmosphere, the Doctor Caduceus enters in Rainbow Dash's office, and quickly dies a little more when he sees the crying filly in front of him. He tries to say something to comfort her, but he can't lie.
“All right! So, while the doctor is patching the failure, you and I are going to talk!” Rainbow Dash jumps in front of Derpy, and keeps on talking. “You're not from Cloudsdale, what you doing? Trying to find our secret? That's not every nice! NOT AT ALL.”
The pegasus' smile grows wider as she observes Derpy, expecting some kind of answer.
“I-I was just curious...”
“CURIOUS? I remember the last time a pegasus was 'curious' around here. We torn his wings off, and we dropped him in the Everfree Forest. He screamed for a while before something finally finished his misery. So, let me ask you again, are you curious?”
Derpy hesitate for a while, and finally decides to be frank.
“I was with someone. A doctor.”
Unknown to Rainbow Dash, Caduceus quickly turns his head when hearing that, causing Scootaloo to moans in pain.
“A doctor? Well, he's right there. Hey, you, say hello to the mare.”
“I mean... the Doctor.”
Rainbow Dash freezes, staring at Derpy for a while, and suddenly leaves the office.
“Keep an eye on them. If they try to move, beat them to death.”
The guards nod, and the pegasus quickly moves away.
“Why are you doing this?” The question is asked to the unicorn doctor.
“What do you mean?” He's avoiding her stare.
“Helping that pegasus.”
“I'm not helping her.” Caduceus answers instantly, without even thinking.
“You are.”
“I'm only doing what I'm supposed to do. Healing the wounded. Now, don't worry, filly, everything will be all right.”

“Who are you? And what are you doing here?”
“Hello, I'm the Doctor. Don't mind me, I'm just trying to understand what's that big machine for.”
“What? Guards! Stop him!”
“Oi, don't do that! Now, where did I put that paper?” The Doctor takes his psychic paper, waves it in front of Atmosphere, and quickly pulls it back to wherever it was. “Now that we are friends, since you're in charge of that place, maybe you could explain to me what's that machine?”
Atmosphere smiles, obviously calmed down.
“I always wanted someone to ask me that! Well, you see, it's genius! The filly is thrown here, after his limbs are-”
“That's great, that's genius, but wait just a bit, and explain the filly bit.”
“It's simple, really! Through a subrooting program in the sequential matr-”
“Oi! I'm the one using all the technological words!”
“It turns failures into rainbow.”
“Oh. That's not nice.”
“Of course not. But at least, they are being useful.”
Being too happy with himself, Atmosphere doesn't notice the look on the Doctor's face. Even the guards, being as emotionless and soulless as they are, notices it, and slowly backs away from the earth pony.
“So what you're saying is that everything you're considering as a failure is shoved down his throat, right?”
“Precisely!”
“Well, I'm not sure I like that, but you have a bigger problem here.”
“Uh? Like what?”
“Like this.”
Jumping near the machine, the Doctor takes his sonic screwdriver, clumsily try to hold it between his hooves for a while, before sighing and biting it. Then, he points it toward the machine, and turns it on.
There's a loud, guttural moan, making almost everypony in the room jumps.
“What's that?”
“Holy crap I shitted my pants!”
But the Doctor doesn't answer. Instead of that, he stares at Atmosphere, staring at the pegasus' maniac smile.