"Derpy? Derpy, where are you?" the Doctor cried out, searching for his newest companion.
Quickly, he pulled his sonic screwdriver out of his collar and used it to scan the area. Checking the results, it registered only two life forms in the area. The Doctor looked up at the castle.
Two life forms in there? That can only mean one thing...
With that thought in mind, the Doctor started galloping off the the castle. If anypony could help him get to the bottom of whatever was going on, it was those two life forms.
Meanwhile...
Derpy woke up somewhere cold and hard. This was a new feeling for the mailmare. Had somepony replaced her bed with something uncomfortable while she was away? Add in the pain in her right hind leg, and it was no wonder she didn't feel very rested.
Opening her eyes didn't reveal much to her. For a few moments, she blinked rapidly, trying to see if her eyes were really open. The darkness of the room she found herself in was absolute, and she couldn't see an inch in front of her face. She wondered why it was so dark. Did Luna forget the stars and moon tonight?
She tried getting up, only to bump her head on the incredibly low ceiling. The bump was all she needed to clear her memories. The events of the last two days rushed back to her, and she started to panic. What had happened? Last thing she knew, she was standing right beside the Doctor! How did she get here.
Derpy blindly felt around, and her fears were confirmed. She was, in fact, in a small box. It reminded her almost of being trapped in a coffin, but she quickly snuffed that thought. Negative thinking wouldn't help her now.
She felt her right hind leg with her left, searching for the source of the pain. After a few moments, she found it. What felt like a manacle was tightly attached to her limb.
Manacles were good, right? If she were trapped in a box and her captors weren't going to open some time, they wouldn't need the manacle. She'd be trapped in a box and would have no means of escape. The fact that she did have a manacle meant it was going to be opened sometime, and they didn't want her escaping when that time came.
Which meant there was still a chance. She only had to wait.
Derpy took a deep breath and closed her eyes, hoping she was right.
The castle stood directly in front of the Doctor. Even in his worried state, he had to admit, it was quite beautiful. Stained glass windows, towering spires, and beautiful arches all came together to create what was less a building and more a work of art.
The Doctor made his way to the large front door, ignoring the complete lack of guards. They only caused problems for him anyway. Authority figures and the Doctor didn't get along well.
As the Doctor opened the well-oiled front door, a question ran through his mind. Why was he spared from whatever took the ponies and Derpy from the city? The two life forms he suspected to be the princesses were understandable- they had a considerable amount of power and could probably resist whatever was snatching ponies up. But why him? He may be an alien, but he wasn't much more powerful than the next stallion.
He made his way through the familiar halls of the castle. He had explored them many times before, and if things went well he'd likely explore them again. He was familiar enough with his surroundings that he let his mind wander as he walked. he had to try to figure out what was happening.
One- The halls of the castle are clean. That means whatever happened must have happened recently. The princesses have much more important things to think about than cleaning.
Two- The princesses and I haven't been affected. Is it perhaps because we aren't basic ponies? No, that can't be right, the few griffins and other races that live in the city are gone as well...
Three- Ponies are disappearing into thin air. Perhaps a teleportation beam? Magic, maybe.
Four- I'm about to walk into a door.
The Doctor snapped out of his thoughts just in time to avoid crashing into the large, ornate doors to the princess' court. He reached a hoof to the handle only to find it locked. That's odd, he thought. Usually these doors are unlocked and open for the public. No matter!
The Doctor whipped out his trusty sonic screwdriver and pointed it at the door. The silence was broken by the whirring sound of the device, followed by a small click as the door was unlocked. He quickly stepped inside and closed the door behind him.
The hall was beautifully crafted, with stained glass windows with depictions of the princesses, lifelike statues, and two thrones at the end of the room. What caught his eye, however, were the two Alicorns standing in the middle of the room.
The smaller, blue one was pacing back and forth, obviously lost in thought. The larger white one was looking at the collection of stained-glass windows, a look of extreme sadness on her face. Neither noticed the lone traveler enter the room.
"I've found no trace of them anywhere in the kingdom, sister. I fear we may not see them again."
When Celestia spoke, Luna stopped her pacing. "Surely they are still here in the kingdom somewhere, sister. They cannot have vanished!"
"Are you sure? 'Cause I see an empty city just outside that says otherwise."
The two princesses turned, startled, to face the owner of the new voice. The Doctor stepped closed and put away his sonic screwdriver.
"I just watched my friend vanish into thin air. In my professional opinion, which I respect, I think it's quite likely they're gone."
The Doctor trotted closer to the stunned princesses and shook both of their hooves. "Hello, I'm the Doctor. I'm here to help!"
Derpy sat in her box, desperately trying not to worry about whether or not she'd have enough air to survive until she had a chance to escape. Surely whoever put her here would want to keep her alive long enough to do whatever it was they wanted to do to her.
As she was thinking about that, she heard a noise from whatever was outside of her box. "Hello!?" she shouted, trying to get the newcomer's attention. "Please, help! I'm stuck in here! Help!"
She could hear footsteps approaching her prison, and the sound of nearby locks being undone. A calm voice spoke to her from the other side. "Calm down, my friend. I am here to get you out."
Derpy let out a sigh of relief. Rescue! Hopefully she could get out of here and find the Doctor. She was quickly regretting her decision to travel with him.
The front of her box was opened, and she was blinded by the light streaming in. She let out a small gasp and rubbed her eyes, happy to be able to stretch her limbs. "Oh, thank you so much!" she started to say before being able to see who freed her. The words were lost when she got a good look at her saviour.
The creature in front of her was most definitely not a pony. It stood on two legs and was wearing a suit of tight black leather. Its black, insect-like face was what was most surprising about it. It had two large black eyes that took up most of its face. Its large mouth was lined with razor-sharp teeth and two of what could only be described as mandibles were jutting out of it.
"Hello, my pony friend," it said in its calm, smooth voice. "You and I have much work to do."
Derpy screamed and jumped out of the box, but quickly lost her footing when the shackle on her right hind leg was pulled taut. The creature reached down and grabbed her around the midsection with one arm and unlocked her binding with the other. It pulled her up and placed her over its shoulder, ignoring her thrashing and screaming.
Derpy stopped hitting at the creature long enough to examine her surroundings. The entire room was made of some sort of silvery metal, and many more silvery boxes like the one she was just in lined the floor. She hoped there weren't any other trapped ponies in them.
The creature walked towards a silver door Derpy hadn't noticed. When they got close, it slid open all on its own and they entered into a hallway of some sort. On one side, a long window spanned the length of the hall. The right side of the hallway was mostly smooth, interrupted ever once in a while by some silver doors.
Derpy looked out of the window, and her jaw dropped. Floating outside in the night sky was a green and blue orb. After a few minutes of amazed gaping, she realized it was her own planet. She was in a spaceship.
She started to panic again. How will I get out if I'm in space I can't escape if I have nowhere to go! she thought. She started to hyperventilate, but managed to calm herself down after a moment. This was no different than being in the Doctor's TARDIS, right?
Except she wasn't on her own when in the TARDIS.
The creature holding her captive turned right, into one of the magic doors that opened on their own. The hallway they turned into had walls that were covered in buttons and blinking lights. An idea started forming in Derpy's mind. One of these buttons had to be important, right?
Feigning acceptance of her fate, she went limp. After a few more moments, she could feel that her captive had been lulled into a false sense of security and had lessened his grip. With a sudden burst of energy, she flapped her wings and flew out of its grip.
The creature snarled and reached for a silvery box on its side. Derpy flew down the hall, pressing as many of the buttons she could reach. If there was one thing she was good at, it was making trouble.
Alarms started to blare and the creature raised its silver box to point at her. A beam of some sort of magic energy flew out of the tip, but she was quick enough that she wasn't hit. The energy hit the console behind her, which exploded in a shower of sparks that singed her tail.
She flew out of the hallway and around the corner, aiming to put as much distance as possible between her and the bug-man. Diving into another side room, she ducked and hid behind the nearest object she could find, aiming to make herself as small as possible.
After a few moments, she could hear the footfalls of the bug-man getting closer and closer. They stopped as the door opened, and she held her breath. For five of the longest seconds of her life, the creature surveyed the room, trying to find her. When it left, she let go of her breath.
Slowly, she rose from her hiding spot and inspected the room she found herself in. Long, clear tubes filled with a bubble blue liquid lined the walls, and she went to inspect one.
The item could more accurately be called a 'vat' of liquid. Something dark was floating in it, but the liquid wasn't clear enough to be able to see. She pushed her face up to the glass to get a better view.
Thunk
The mare jumped back in surprise and just barely managed to stifle a scream as the pony inside the vat pressed herself against the glass. A unicorn mare with wires attached on her body looked out at Derpy, saying something the grey pegasus couldn't hear.
Derpy ran up to the glass, mouthing the words don't worry, I'll get out out before tentatively peeking out the doorway. She didn't have to look at any of the other vats to figure out that that was where the missing townsponies had gone.
Looking left and right revealed that that bug-man wasn't waiting for her in the hall, and she quickly flew out. She didn't know where to go, but she knew she had to do something.
She had to contact the Doctor.