Chapter 21- Dark Secrets

(Moonlight Shadow)

We split up shortly after we met up in the generator room. So far everything was going according to Johnny's plan. I won't lie the appearance of these two new ponies in armor didn't sit well with me. One was a civilian who had no place being involved with any of this. The other one was Celestia's adopted daughter. True, she was a trained agent, but Celestia would have kittens if she knew that Sweetie Drops was here. Worse yet, there was no way that we could let her know right now, not in the middle of this operation. And then there were the bugs. The living power armor. No matter what, news of those needed to be kept tightly under wraps. And then there was the kissing. Blast it Johnny, why? I was starting to feel…

The ding of the elevator woke me from my thoughts. I was using magic to make me invisible. The doors opened to the hallway outside of the office of Dr. Brass. I stared at the door to his outer office for several minutes, my thoughts churning. I didn't know what to believe at this point. Was Dr. Brass a part of this? Or was he being deceived like the rest of us? I had to know. I respected Dr. Brass. I trusted him, believed in him. Could he really have been deceiving us this whole time? I didn't know. But by Tartarus I intended to find out.

I had been inside here before, so I quietly teleported myself inside the outer office. The same secretary was still seated behind he desk, busily typing away on some type of typewriter that was connected to a ponvidio display somehow. I used a simple sleeping spell to render her unconscious. The I locked the door to the outer office, making sure that no pony else would wander in.

I teleported into the inner office. The lights were out, and the office was quiet. Dr. Brass must be elsewhere, perhaps doing his experiments once more. I was fine with that, I wasn't quite ready to confront the pony himself. Not until I was satisfied with either his guilt or his innocence.

I dropped my spell and made my way around his desk. Out of habit I lit up my horn and made sure there weren't and booby traps on it. Once I was satisfied, I began my search.

The first thing I noticed was that despite it's size, Dr. Brass's desk was quite spartan. One would almost say unused. I opened the first drawer, and got my first surprise. Inside it were several pictures in frames. The sort that usually sit on top of a desk. There was one of a jovial looking mare, his wife if I remember. The second was a two part frame, with older faded pictures in them, a stallion and a mare, his parents no doubt. The final one was a family picture. It was set in a park somewhere, the ponies from the two part frame were sitting on a checkered quilt serving food to two young colts, twins. I could just make out the cutie mark on the one on the left. It was Dr Brass's. The one on the right must have been his brother. It was a really heartwarming photo, just one more reason I wanted to believe in his innocence.

Beneath the photo's was the usual assortment of pens and pencils. Notepads and sticky notes. I used an old Watch trick, taking a pencil, I gently rubbed it across the surface of the top sheets of the sticky note pad, and the others. Each had revealed a message that had been on the page before it. The sticky note pad had 'meeting with Luna, 7pm' on it. The notepad had 'It has come to my attention that several discrepancies in our inventory have been noted during our last audit. From this point forward, the heads of all depar', then the writing trailed off the page. So Dr. Brass had noticed that things had been going missing. That was a point in his favor regarding his potential innocence.

I looked through the other drawers. There was a place in one where file folders used to hang, but it was bare. Just as the other drawers were. This desk was just for show. I used my magic to scan the rest of the office. There were no hidden safes in the walls, but there was a hidden passageway concealed beneath a section of floor tiles, I was making my way toward it when a voice called out from behind me.

“I wouldn't go in there Miss Shadow. I very much doubt you'll like what you find.”

I turned, silhouetted by the light from the desk, I made out the metallic gleam glinting off the limbs of the pony before me. It was that pony from before, that assistant of Dr. Brass. “Mercy. Merciful Solace.”

“Ah, you remember me. I'm glad. So few ponies know my name before their demise.”

“Demise? Really? It seems to me some pony is getting rather ahead of herself,” I say smiling at the unicorn advancing toward me. “And isn't it a bit extreme to be threatening me? After all, this office, this building, it all belongs to Luna, technically we have the same boss. Now I am in here on Luna's behalf, so before this goes any further I have just one thing to ask you. Who's side are YOU on?”

“Oh I think Miss Shadow, that we both know the answer to that.” She says leaping into the air aiming a kick directly at my head.

(Johnny)

Shortly after joining up with Bonny and Lyra, Moonlight took one set of keys, and left to go check Dr. Brass's office. Meanwhile the rest of us made our way to the elevator, and using a master key, made our way to the first sub-basement.

I didn't know what to expect when the doors opened up, but it wasn't what I saw. We exited the elevator into a large open room. Bonny and Lyra were stealthed, and I was using an invisibility spell. Bonny did a quick scan of the room and reported that we were the only ones here, so we dropped our stealth and had a look around.

Along the walls of the room were huge tanks reaching almost to the ceiling. I read the names on them aloud as I passed them. “Mirror Pool Water. Changeling Blood. Source A-1, Source B-1, Source C-1, Source D-1, Source E-1, Source F-1,” then the sequence repeated but the numbers had changed, 'A-2, B-2,' and so on. The back of the room was divided into two sections. Each was a cube shaped room with a single door each. The one on the left had a door plate that read 'Orientation Room'. The one on the right was labeled 'Primary Source Room. Authorized Personnel Only!'

We made our way to the first room, the 'Orientation Room'. I open the door and trotted inside, Bonny and Lyra close behind me. I had absolutely no idea what I was looking at. Well, I mean it sort of looked like a reclining chair. Sort of. It was green and black and the texture of the surface looked like the hide of an alligator or some scaled lizard. Coming up from the back like a stinger on a scorpion, exactly like a stinger on a scorpion, was a curved tendril of carapace, that ended in some sort of clawed cap. It was exactly the right size to fit over the head of a pony. I was just reaching forward to touch it when behind me Bonny screamed and fell to the floor clutching her head.

“K-Kill it! Kill it, kill it, kill it!” She yelled, still clutching her head.

“J-Johnny… D-do what she s-said.” Lindana stammers, detaching herself from Bonny's head. “There are f-fragments in her head. F-f-fragments of m-memories. J-Johnny please! You h-have to k-k-kill that thing!”

For a moment I just gaped at Bonny, I had never seen her like this, it's like her mind was gone. She was wailing like a lost soul. Then my brain finally kicked me in the plot. I whirled around and cut loose with my Creeping Death spell. The same one I last used on the Butcher's goons so long ago.

It was still as potent as always, but as I watched the chair thing dissolve, something flashed in my mind. It was like a memory, but a memory I didn't have. Someone else's memory? Something similar to this chair, but metal? An argument. A pony in a lab coat… During? No, not During, but similar. And Celestia… she was there she was yelling at the other pony… then she pulled a lever and… and… nothing.

I shook myself out of whatever it was I was seeing, and focused my attention back on Bon Bon and Lindana. Bonny had quieted down, Lyra was stroking her mane and making soothing noises, and Lindana was looking up at me.

“Thank you Johnny. That was… very painful. For both of us. Bon Bon is almost back to normal, she'll be able to speak to you soon.”

I wasn't in the mood to wait when my best friend had just undergone something that traumatic.

“What was it Lindana? What was that… thing? And why did Bonny react that way to seeing it?”

“Johnny, I don't have all the answers, but I'll tell you what I can. When Bon Bon saw that… that horrible thing, it triggered long buried memories. Well, not really memories, more like the remains of memories. Fragments. Pieces of memories that were long ago destroyed. I'll tell you all that made sense. The first piece was of a filly. Judging by her coat and mane, it must have been Bon Bon, but it was before she was called that. Before she was called Sweetie Drops. Her name was… was… ugh, I can't remember. Anyway she was playing in a park, then the next fragment she was flying over the ground, but not willingly. She was crying, being carried by something. The next fragment she was in a dark place. There was green and black on the walls. Then, there was that thing. That thing that you killed. Just now. And a creature. It was a changeling! Little Bon Bon was being strapped into the chair. And that changeling was telling her horrible things! And the chair… the chair made her believe them! And-”

“ENOUGH!” Bonny yelled forcing herself upright. “Stop Lindana. Just stop talking about it!”

“It's okay Bonny, it's okay.” Lyra said gently as she took Bonny by the hoof. “Johnny totally destroyed that thing. It's gone. Forever! Let's just go outside okay? You don't have to think about it anymore. It's all over and done.”

Bon Bon allowed Lyra to guide her out of the doorway. “Y-yes, your right.” Bonny says in a shaking voice. “It's all over. All… over.”

I turned back to the remains of whatever that chair thing was. 'Orientation room' indeed. If there wasn't a need for secrecy I'd blow this whole floor to ashes. I looked down at the pile of dust which was all that remained of their mind control device. I kicked once, scattering the ashes, and made my way outside.

Bonny seemed to have recovered enough to put on a brave face. I cupped her muzzle in my hoof for a moment, and offered her the best smile I was able to give. I wanted to tell her to wait here while I checked the other room, but I knew what she would say, so I didn't make less of her courage by asking.

I trotted over to the entrance to the second door. I had no idea what a 'primary source' was, but anything that was labeled restricted sounded like someplace I really wanted to check out. It took only a moment to find the right key, and we made our way inside. What I saw next made me stop in my tracks.

There were ponies in this room. Seven of them. Along the far wall there were six vertical tubes. Each tube contained a pony, and each was filled with a strange liquid. On a small plaque atop each tube was a letter A-F. Off by itself on a side wall there was one more tube with a pony inside. This tube had no letter, but I recognized the pony inside immediately.

“Dr. Brass.” I whispered.

Just what was going on here?

“Johnny,” Bon Bon said at my side. Now that we are so close, Lindana is picking up faint life signs from the ponies in these tubes. They're all alive Johnny. These tubes are keeping them alive, but in some kind of sleeping state. At least that's the way it seems to Lindana.”

“Can we get them out? Wake them up?” I ask, looking at the control panel next to Dr Brass's tube.

“Lindana says she thinks so. She said there was something crudely similar to this in Celestia's vault. She's sending me what she thinks should be the 'wake up' cycle, but she isn't one hundred percent sure. Do we want to risk it?”

I stared for a moment at the pony in the tube before me. Do I gamble? Do I risk a ponies life for the answers I needed? I knew that Duskwind wouldn't. But he wasn't here right now.

“Do it.” I said, not daring to blink.

Lindana inputs a sequence of commands on the control panel in front of me. I pay close attention as she does, in case I ever need to remember how to do this. I watch as the fluid drains away through a grate in the bottom of the tank. A moment later the front of the tube hisses open, as the occupant coughs and sputters, spitting out the remaining fluid in his mouth.

He rubs his eyes, and blinks for a moment, adjusting to the light. Then he sees us.

“Who, who are you? D-did my brother send you? Are you here to finally kill me?” He says, his voice resigned, and not at all afraid.

I step in front of him.

“Sir, I have no idea who your brother is, but we are not here to kill you. If anything, we are probably here to save you. Depending of course, on what you have to tell us in the next few minutes.”

“Save me? Save me!” He says, his face becoming animated. “Oh thank Celestia! Oh thank you sweet Celestia!”

“Trust me, she's not all that sweet,” I say deadpan. “Now I don't mean to press, but we are on a rather tight timetable. I assume that I have the pleasure of addressing Dr. Brass. The REAL Dr. Brass. Now I need you to tell me as concisely as possible, exactly what in Tartarus is going on in this place!” I say, my voice raising of it's own accord.

“Yes. Of course… of course. Where to begin? Well, to start with, the pony that has been posing as me? He's my brother. My twin brother. Brass Buttons. But let me tell this from the start. Yes, that would be best I think.

My brother and I were born in Appleloosa, to strict but loving parents.”

“Doctor, I hate to rush you, but we are really pressed for time. Cliff notes please.” I say, trying to sound tolerant.

“Alright, alright. The short version. My brother's talent led him to become a tailor. At first, I wasn't sure what my cutie mark meant. But I found that I always had the need to understand things. To get down to the 'brass tacks' as it were. This led me to my interest in steam powered locomotives, and later to my development of the M.I.S.P. engine. When I heard of what Luna was planning to do here in Whinnyappleous, I knew that this was where I had to come. Luna was building the future, and I knew I could be an important part of that.

I managed to gain an audience with her, and showed her my invention. She was very impressed, and we discussed the many ways that it could be applied to improve the lives of her subjects. She formed her own company, Night Industries, and issued patents under my name for everything I could develop. For awhile things were going very well. But a side effect of all of my accomplishments, was my popularity. I kept having to be pulled away from my work to make all of these silly public appearances. I was a celebrity, when all I wanted to be was a scientist.

That's when I had my idea. I secretly contacted my brother, and persuaded him to come to Whinnyappleous. My idea was that I would pay him a generous salary to do nothing but stand in for me at public functions. We cover up his cutie mark with a replica of my own, and who would know the difference?
And it worked out perfectly. He was the face of Dr. Brass. Friendly, kind, and always happy to speak to the public. Meanwhile I was free to pursue my work undisturbed.

That was, until three years ago. One night I was pulling an all nighter in my lab, when I was struck from behind. I woke up in one of my own suspension tubes, that I was developing for exploring deep space. A pony stepped before me. It was my brother. He smugly told me his plan. To keep me here, out of sight of everypony, and replace me as Dr. Brass. The fame had gone to his head. He ranted at me at how unfair it was, that since he was my twin, that he deserved the same fame and glory that I had. The fool. He could've had all of that anyway. I never wanted it! But he wouldn't listen. He activated the controls, and I was out.

It was six months later that he woke me up to gloat once more. But this time he wasn't alone. He had another pony with him, a geneticist. This time his ranting was more delusional. Now he had plans to take over the city. They were going to plant spies in all the levels of Luna's government, from the Watch, all the way to the nobility. Then when the time was right, he was going to loose an army on Whinnyappleous, and take over the city in one fell swoop. He then started bragging about eventually taking over all of Equestria, but by then I was laughing openly at him. I called them both delusional. Mad fools that were living in some dreamland. They would be caught before they ever got close to their goals. My brother just laughed at me, and shut me down once more. But then, three months later when he woke me again, I found I couldn't laugh at him anymore. He showed me a device. He said he acquired it from a changeling hive. He said their queen forbid it's use anymore, and they were willing to sell it to Dr Brass for 'research purposes'. I had heard about this terrible thing from Princess Celestia. It was a mind control device. I gazed upon the repugnant thing in horror. Brass Buttons was serious. He really intended to take over the city. And with this device he could. But that wasn't the truly horrifying thing. No, that came later. When his partner showed me his contribution to my brother's plans. He had been ponynapping innocent ponies off of the street. He had found a way to combine different strands of pony d.n.a. together. He was creating ponies. But not normal ponies. No. He was creating horrible freaks of nature. Trying to combine strains of pegasus, unicorn, and earth pony d.n.a. Things that could not be done. For, as I'm sure you know, if say, a pegasus and a unicorn, were to have a baby, the baby would either be one or the other. Never once has there been a pegasus with a unicorn's horn. The three different magics are incompatible with each other. One or the other will always be dominant. The only exception to this is the alicorn. And even then that only occurs under certain circumstances which causes a pony to reach an ascended state, or if one or both of it's parents were an alicorn.

All this is commonly known. But this fool choose to ignore all common sense. He's desperately trying to 'breed' alicorns. With science! I've seen horrors. Horrors I tell you! This pony must be stopped. My brother as well. We have to get out of here and warn the Princess!”

I thought about everything he said. And he was right, we needed to warn the Princess. Just not the one he was thinking of. “From what you have told me, there is no way we can be sure of any of Luna's ponies. We have no way to know which ones have been compromised. What we need to do is get you out of the city altogether and get you to Princess Celestia as fast as we can.”

I helped him to his hooves, and we made our way to the other tanks that I had passed by when I recognized him. This time I took the time to look inside. There were two of each race of ponies inside. Two pegasi, two unicorns and two earth ponies. My jaw dropped open in shock. I recognized two of them.

“That one, that one right there!” I said pointing to one of the earth ponies. “That's Babs Seed, the missing pony we have been looking for! And this one,” I said pointing at one of the others, “That's Cocoa Butter! My secretary's sister! The one that had gone missing, so long ago! Dr. Brass why are these six ponies in here?” I asked, a growing horror forming inside of me as one possibility occurred.

“This is what my brother kept bragging about. This is the core of his army. His 'source material'. In his deranged state he decided that the best stock to use for his experiments were ponies that had the same d.n.a. as the six hero's that wielded the elements of harmony. He sent out his minions into the city to capture any pony closely related to them by blood. Sadly, ponies go missing in this city all the time, so no one found it overly odd that these six specifically had been ponynapped.”

My mind was a churning mixture of joy and anger. Finding these ponies alive after all this time was fortune beyond measure. Ori would be overjoyed to know that her sister was still alive. But what Dr. Brass had said still filled me with rage. He was right. Nopony noticed that these six were gone. Except that it was my business to notice such things. That was one of the reasons Celestia put me in this city in the first place. But no, I didn't notice. I never connected the dots. Not even when two of those dots had been staring me right in the face the whole time.

“We've got to get these ponies free.” I said turning to Lindana and Bon Bon. She gave me a quick nod, and began inputting the same sequence of commands she used to revive Dr. Brass. It took us a few moments to get everypony upright and lucid. Once they were all coherent, I explained to them what happened to them, and my plans to get them to safety.

"We need to get you all out of the city, without being noticed, and to Celestia as fast as we can. She'll be able to keep you all safe until we can root out all of the spies that the fake Dr. Brass has planted all over the city.

Bon Bon, Lyra, I need you two to escort these ponies to safety, but first I need you to make a side trip to Ori's apartment and collect our ponies there. The way things are now, no place in the city may be safe. Have Ori send a message to Celestia explaining what is going on, and have her take a candle with her to let Celestia know where she can meet you after you get out of the city. After you pick up our friends you need to make your way to the 113th street undertrain station. There you will find a black and while piebald earth pony in a tattered coat, with a cutie mark that resembles a hoof with a bit stuck to it, who goes by the name of 'Easy Money'. Yes, this is all a facade, no, do NOT ask him about any of it. Just tell him that Johnny Appleseed wants him to get all of you safely out of the city undetected. If he has any questions introduce Cocoa Butter and tell him that she's the 'mission from Maud'. He'll understand. Once out of the city, you all need to get to Celestia as fast as you can, she'll get you all to safety.”

“Should I even ask what YOU intend to do Johnny?” Bon Bon asks.

“Me? I intend to borrow a page out of YOUR playbook Bonny. I'm going to go down there, 'horn a blazing' and take the rest of this place apart!”

Author's Notes:

And we finally find out some of what's really been going on. Cocoa Butter is alive! Dr. Brass isn't the evil mastermind, and we now know who ponynapped Bab's Seed.
Originally this story was a one chapter one shot, which several people had written me and wanted me to expand. I had originally planned an epilogue explaining what had happened to Cocoa, but kept it to myself all this time when I decided to keep going with the story.
Now don't think for a second that all the cats are out of the bag. Oh, no. There are many more revelations yet to be made. All the way down to the last epilogue.
But as for next chapter, prepare for some action!