Author’s Note: The story from now on will be in third person. Hope you all enjoy it! I’ll be modifying it as I read over once more tonight - if you see any glaring errors, please feel free to post them in the thread on Ponychan!

The group had moved away from the main scene of the crime into a room adjacent to where the murder had taken place. The sound of rain echoed on the cheap tin roof, still coming down hard and fast. A leak had formed near the corner of the room leaving, the cheap plaster on the walls sodden. Sniffing, the Doctor could still smell the blood from the other room, but mixed in with the smell of the rotting plaster giving it a more earthy scent. Looking between his companions, he couldn’t help but feel like he should avoid time travel for the rest of his time in Equestria; he couldn’t tell who was a new friend, who was an old friend, or even who could potentially one day, he thought, looking at the commander, become an enemy.

Something about the pegasus didn’t feel right. He noticed that whenever the pony turned to talk to him, it was always using his right eye. The Doctor could see the left one, it looked fine, moving with the other in perfect synchronisation... Something just felt odd.

“So let me get this straight, Doctor,” Duke said, breaking the silence “You think that somepony here has an ancient artifact from a dead race, capable of spying on anypony and is using it to clean the streets? Why not report the criminals, why kill them?”

“That, I don’t know.” The Doctor replied, “The problem with The Lens is that it requires a great deal of concentration to use, but more so to actually kill with it, and the user would have to be, well... I’m sorry to say this, but the user would have to be a Time Lord.”

“One of your people?”

“Yes. Part of me has a bad feeling that it might even be someone I know...”

“But if they can see what is happening, why not...”

Duke was interrupted by one of Avian’s coworkers, who had tapped him on the shoulder, a parcel between her lips. Duke glared, and the young mare backed away slightly, before flicking her eyes over to the Doctor, who raised a hoof and took the package. Tiny copperplate handwriting on the surface simply read “Doctor”, with a simplified drawing of the Doctor’s cutie mark underneath. Puzzled, the Doctor turned back to the assistant,

“Who gave you this?” he asked, paying attention to her expression. Slowly, seemingly somewhat disturbed, she explained that a blue stallion with a bright yellow mane had given it to her. He had then pointed at something behind her, and when she had turned back, he was gone.

“What do you think? A lead?” Avian asked, looking over his spectacles at the still wrapped parcel.

“Only one way we’ll find out, I guess.” The Doctor responded, keeping his eyes focused on the brown package whilst he awkwardly tried to open it.

“Allow me, it’ll be a tad easier,” Avian began, his horn glowing. The box raised and began to open, revealing a strange yet familiar instrument, similar to a wrist watch, yet elongated along one surface.

“Is that... Is that the lens?” Duke asked, staring at the device rotating in front of them.

He saw the Doctor’s face light up as he worked out what it was, and cracked a slight smile, guessing he had been right...

“That, my good commander,” The Doctor started, slipping a hoof through the hole of the device and tightening it, “Is a brand new sonic screwdriver. But I’m a little worried that you don’t recognise it...”

“I’ve seen you use something like that, but it wasn’t so similar to a watch... It was more like a pencil.”

“Which probably means that at some point, I break this. That’s an incredible shame... It’s marvellous!” he coos, lost in the wonder of his new toy.

The Doctor then raised the device in front of him, pressing the much larger and hoof friendly button with his nose, pointing it at the silhouette of a colt on the wall. Pulling away, he stares at the screwdriver, waiting for it to indicate results.

“Hmm, there are a lot of readings here that I don’t recognise, but I do see the energy signature of the Lens... and something else?”

He pressed the button again after adjusting the settings, causing specks of red light to appear on the wall holding the charred remains. The specks soon began to connect with each other, forming symbols on the wall, ending again with a crude drawing of the Doctor’s mark.

“Ah, yes, the symbols,” Avian gasped, before levitating a notebook over to him.

“Commander, I assume that is the reason you were looking for... Wait, what?”

“Yes, one of the girls from the lab was able to find them when she had to cover for my assistant. It’s a unique protein biomarker, found at a few sites so far...”

The commander snorts, looking at the floor. The Doctor opened his mouth to speak before remembering the story about the foalphile. His features start to soften, realising that the winged white stallion obviously felt terrible about the affair.

“I would have done the same, Duke.”

“That doesn’t make it alright. Anyway, Avian, you were explaining?”

“Ah, yes,” the scientist started again, “Well, when Malditof was reading the crime scene, she found a novel and unique protein, one that not even her Majesty’s royal science division could identify. Elsie and Emmess had a look, but they weren’t really able to pick anything up either, it’s most odd. We do have a rendering of the protein itself back in the laboratory if that would help? Do you have any idea what it says? It’s quite obviously a message for you, after all?”

“That sounds like a good idea, I’d like to meet Malditof, Elsie and Emmess” the Doctor mused, smiling broadly after his made the connection between their names, “Just one thing that’s been bothering me...” he trails off, before turning to Duke and pressing the button on his sonic. Part of the commander was illuminated, the illusion created by his ornate silver armour fading away, white fur replaced by Duke’s natural dark gray colouring. The device still whirring, he pointed the light at Duke’s face, the healthy right eye stared back; his left one scared and sewn shut. A little shocked, the Doctor deactivated the screwdriver.

“You’re not who you say you are.”

“Doctor, trust me, I am.”

“YOU’RE USING A SHIMMER!” the Doctor exclaimed loudly, backing away.

“Doctor, all of the guard do. It’s a part of the uniform, relax.” Avian chipped in, “Princess Celestia wanted all of her guards to look the same, so that it would be difficult for an individual to be targeted or singled out whilst on duty.”

“You even gave her the idea of calling it shimmer magic, if the story is true.” Duke added, hoof on his chin, “How long have you actually been here, Doctor?”

“...I think this would be my third day since breaking through. Also, would you please stop telling me about things I haven’t done yet? It takes away the surprise.”

“I’m sorry, but you practically ordered me to give you... what did you call them? Ah, yes, spoilers.” Duke replied. He looked at Avian, the two aging colts giving each other a brief stare, daring each other to crack a smile, “It’s completely necessary this time.”

“Oh, alright... In that case, explain to me who this princess is?”

“Ha, now that is one thing that you said we can’t tell you about. You’ll have to wait.”

The Doctor gave a brief pout before relaxing his face, mildly shocked that he was the type to pout when upset. Duke and Avian stared at each other again, before leading the Doctor back out into the cobbled streets outside of the building. Peeking through the door as he passed, the Doctor was able to quickly read the message written on the wall in the slowly fading red light. Very interesting indeed.

“So, what can you tell me? Do any of my... old enemies raise their heads?” he asked, raising his voice over the sound of the rain striking the cobbles and Duke’s armour. The others didn’t seem to hear him, Duke taking the lead and Avian behind him, a floppy hat keeping the rain off of his head. Stopping for a second, the Doctor pushed his hair back out of his eyes, the wetness holding it back on his head. He decided to descend into thought as he started walking again, following Duke, thinking about the meaning of the message that had been left on the wall.

The Lens was a very powerful communication tool, not too dissimilar to the communication cubes that replaced it in that it could breach different times, allowing for messages to be passed anywhere, anywhen. He had no doubt that the person, sorry, pony using it, was a Time Lord.

The idea of someone else having survived the time war thrilled the Doctor, but he was very unsure as to how to let his companions know that he could read the message left on the wall. It was an old and very obscure form of ancient Gallifreyan, one beyond even his understanding, that the TARDIS had thankfully been able to translate for him.

Whoever it was, they needed help. The Lens had picked up on their distress, and had found individuals in the same amount of pain... but why had it been killing? This was the most confusing part, to kill with the device would take an enormous amount of energy, he couldn’t be sure how many others had been murdered with it until he had seen the pictures of other crime scenes that would undoubtedly be at the laboratory he was being lead to.

Looking down, he began to muse at how easily he was moving around on four legs now. It had taken a little while, but he was quite pleased with the result. In the occasional glow of streetlights, the Doctor could see the blood of the poor children washing off of his hooves, his stomach lurching slightly as rage and disgust danced together inside. The cobbles had become much more uniform now, and they were beginning to reach an incline, water readily flowing downhill from the most breathtaking castle the Doctor had ever seen.

“How on Earth is that still standing?” He asked, looking at how it had been built into the mountain. Avian heard him this time, the old unicorn dropping instep.

“A lot of it was built using magic.” he responded, motioning with a hoof.

“I... see. So why haven’t the high winds and rain caused it to fall off? More to the point, why isn’t there more havoc from this storm? It almost feels fake.”

“Ah, well, lower parts of the city below have flooded... unfortunately, but we’ll be able to get them fixed up in no time. As for the weather itself, pegasi have an interesting affinity for clouds and the weather, they’re able to walk on clouds, as well as influence their location. We had been going through an extreme drought when the weather teams finally found this storm front plaguing a village down on the plains. The castle itself is protected by her Majesty’s magic.”

“So they towed it here? The storm?”

“Yes. We even had a very famous display team looking for cloud to use. I’d say we’ve got another week of rain left to make up for the dry spell.”

The three of them finally made it to the entrance to the castle, passing through an elegant stone gate. The look of the castle from the inside was just as impressive as from the outside, huge turrets attached to the keep, several smaller but no less impressive buildings also in the courtyard, not reaching as high as many of other conical topped towers. Passing from cover back into the rain, Duke yells, explaining that the first task is to report in to Princess Celestia.

“Once we’ve been debriefed, we can go to the lab.”

“Wait, so you work directly for the Princess?”

“Princesses” Duke corrected.

“Yes, well, anyway, I thought you were a police officer?”

“I was once. I started out in the city guard. When I was about twenty-five, I was chosen to join the Royal Protectorate. I was a captain when my...” the stallion trails off for a moment before snapping back to reality, “commanding officer was killed by a dragon. I was chosen to ascend to his post and now I command all of her Majesty’s forces. This case however, is of personal interest.”

“Yes,” Avian chimed in, slightly bitter, “The protectorate have this annoying ability to pop up whenever they please. They’re very fond of internal work, when they’re not acting as bodyguards to Celestia and Luna.”

“Avian, my old friend, you’re still hung up about Snapshot commandeering your team without asking? The Praetor of the science division was fine with it, I don’t see why you’re still so bothered.”

“Yes, well, you have a very insubordinate subordinate, Duke.”

“I’m sorry, but what is a praetor and who is Snapshot?” The Doctor asked, as they passed through the two huge solid oak doors at the entrance to the keep. Shaking his mane out, the Doctor sprayed two nearby white pegasus guards with water, gaining him a look of light disgust from them, before they were waved away by Duke.

“A captain within the protectorate and my second in command in regards to the personal protection of the royal family - I should probably mention that the two of you don’t see eye to eye. Thankfully, he’s away on an assignment in Appleloosa. The Praetor is typically the head of a chapter of the Guard, such as the science division. We don’t have a praetor in the protectorate for historical reasons. There was a traitor around a hundred years ago, her post was never re-filled. I run the protectorate myself because of this.”

The Doctor became aware of how voices were echoing in the strangely quiet entrance to the keep. When he had visited medieval castles like this before, they had often had busy little market stalls, at least in the courtyard, if not the occasional little shop within the larger castle buildings themselves - obviously the storm had been causing more trouble than they had been letting on. Listening to Duke, he couldn’t help but also notice the sound of their hooves against the polished stone; part of him missed having fingers, but he did like the sound that his new appendages made.

The group stopped outside of a huge set of gold-inlaid oak doors, a pair of pegasi stood on guard in front of it. Duke nodded and they stepped aside, opening the doors using huge golden rings held between their teeth. The Doctor looks around into a beautifully ornate hall, lush red carpet running from the threshold of the door up to a huge golden throne. Despite the rain falling outside and the heavy cloud cover, light was filtering through the stained glass windows in a way that lead the Doctor to believe was artificial. Clearly impressed, he wandered up to one of them, trying to look for the light source.

“Ahem,” Duke cleared his throat, “Doctor, this way please?”

Turning back, the Doctor could see another, far taller pony sat on the huge golden throne, she had the warmest smile, and the purest of pure white fur, outlined eyes watching him with the wonder of a mother assessing her child, multi-coloured hair moving of it’s own accord as if held on a breeze.

He felt his jaw open slightly, he’d never seen a being so beautiful, even in his hundreds of years of life, yet so... alone. It was her eyes that had given it away, on the surface, she looked warm and inviting, the sort of ruler that any race could hope for, but he could tell from her eyes that she was as ancient as him, potentially with similar regrets yet putting on a brave face for her people.

“Your Majesty, I would like to present to you, The Doctor. Doctor, this is Princess Celestia, ruler of Canterlot and of Equestria.”

Celestia’s warm smile didn’t move at all, causing the Doctor to wonder if she had met him before, like everyone else so far. He saw Duke and Avian bow deeply to her, but didn’t follow suit, unsure as to how he should feel in the presence of the towering alicorn.

“You never do bow to me... I can see you wondering.” she eventually said, a warm, gentle and melodic voice flushing the Doctor with what almost could be described as pleasure. She seemed able to read him quite easily, continuing her speech, “This is not the first time I have met you, but I feel that it may be the first time you have met me? Regardless, it is an honour to finally have the upper hoof, so to speak! Welcome to our world, I hope Sir Duke and Avian have taken care of you.” she laughed. Even her laugh oozed grace and kindness, a ruler genuinely interested in the plight of her subjects, regardless of the sorrow she was hiding within.

“Thank you, your Majesty... May I call you Celestia?” The Doctor replied, eventually settling for what he felt was a respectful nod towards her, rather than a full bow. Duke twitched slightly, obviously not too fond of the idea of being informal towards his queen, or princess, as the case may be. The Doctor wondered whether bringing up her title would be a wise idea, but chose to save the conversation for later, should he get time alone with her.

“You certainly may, my friend. I will have to let my little sister know that you have graced us with your presence once more! Luna does have quite the crush on you, but of course, you couldn’t possibly know that yet.”

The Doctor laughed, “Well, I’ll do my best to be a gentleman.”

“You always do. Now, Sir Duke,” Celestia started again, ignoring Duke’s cringe at the use of his title, “Has there been any update on the situation in the city? Has the Doctor been able to shed any light on what could be happening?”

Duke gave his full brief, starting with how he had obtained the Doctor from Brassy Bridges, through to an assessment of the scene in the old blacksmiths shop, before letting Avian take over to explain the scientific aspect of the investigation. Avian eventually got to the point that the Doctor had determined an outside influence was killing the killers and expressed his desire to get down to the lab. Celestia paid attention throughout, looking visibly distressed when the scene regarding the two young foals had been described to her, and slightly confused when the Doctor had been unable to give a meaning to the symbols etched on the wall, other than that they were from a member of his species also trapped on Equestria.

“Is there anything you can do?” She eventually asked, still looking upset.

“Well, I could probably at least work out who has the Lens, if not track them down using the psychic residue and that fascinating protein left at the scene.”

“Then I must beg of you Doctor, please, please help us bring the murderer to justice. You may use any ponies and resources that you may require. If needs demand it, I can get several very high level magic users to assist you...”

“That’s just the thing, your Majesty. I’m not sure if I should,” The Doctor interrupted, warranting another snort from Duke, “If the lens holder hadn’t eliminated this murderer, and assumably those responsible for other killings in the city, the one who killed the children would have been free to carry on. The only thing that I could possibly hope for is to obtain the lens. I mean no offense by this, but I doubt you have the power to kill with it on your own, so it would make sense to let your security services look after the device as a warning system. In return, I want the Time Lord released to me. I am the last of my species, aside of the lens holder, and I may be able to return them to my original universe. If they are doing this maliciously, I know of ways to deal with them; seal them away permanently.”

“What do you think, Sir Duke?” Celestia asks, looking at her knight.

“Well, he hasn’t steered us wrong yet. I say we give him a shot, Ma’am.”

“You have a deal, Doctor. Now, I must speak with Sir Duke in private, we have things to discuss regarding other matters... specifically repairs from the storm. It would seem that the weather teams took their orders a little too seriously.” she said, cocking an eyebrow, the smile still not leaving her face.

Avian bowed, and the Doctor nodded once more before leaving, heading towards the science division’s area of the castle and into the basement levels to find the main lab. Celestia sighed as the doors were closed,

"Was any fury recovered from the crime scene?"

"Yes, your Majesty. The science team found a vial in the scientist's personal effects shortly after I was sent to retrieve the Doctor."

"I see. I think we need to find someone external to deal with this threat - even with the dealers behind bars it is still getting into the city. Have Chameleon notified." Celestia said, a look of determination upon her face...

Next Chapter: Downpour - Chapter 3 Estimated time remaining: 16 Minutes