Courier: this was quick! Well thing about two partners you've got then ending in your head but now that the build up is established it's time for the end to begin.

Disclaimer: I own nothing apart from the brilliant ideas too great for Hasbro to handle

Doctor Whooves

The End part 2

Ponyville, Sugercube Corner 1002 CR

"I'm The Doctor and I'm you're only hope" he answered as he adjusted his tie. He stood slightly taller than Applejack and sported a navy blue blazer, with a light grey shirt, waist coat and matching tie.

"Who?" Applejack replied raising an eyebrow before helping Twilight up.

"The Doctor and if that Cyberpony is following us then that door won't hold it. We need to move" The Doctor informed before walking ahead.

"Cyber what? Listen here Jackass I want to know everything right now! Especially what you've done to Twilight" Applejack yelled making the stallion look to Applejack.

"I'm fine Applejack but I would also like to know everything especially what that thing was and why it called its self Cup Cake?" Twilight asked still slightly shaken by the experience.

"I'll explain everything but we need to get somewhere safe" The Doctor replied checking for other Cyberponies.

"We could go to my library" Twilight offered but The Doctor shook his head.

"No bad idea, the Cyberponies are using teleport circuits implanted in the floor boards. Best place to be is outside" the Doctor informed looking out for any Cyberponies only to creep out passing ponies.

"But I don't have floor boards the floor is 5 meters of solid oak" Twilight replied making The Doctor smile.

"Oh okay then, lead the way" The Doctor added before Twilight headed for the Golden Oak library Applejack gave The Doctor a stern look.

"You first" Applejack insisted as The Doctor went ahead of her he too giving he farm pony a look of equal intensity.

Golden Oak Library

"Spike! Spiiiike!" Twilight called out as the three entered Twilights home with The Doctor jumping up and down.

"Ooh this is quality oak, I like this place" The Doctor complimented before scanning the building for Cyberpony tech.

"Now can you explain yourself?" Applejack demanded as Spike walked in.

"What is it Twilight and whose that?" Spike asked before Twilight picked him up and sat him down.

"Spike takes notes at everything The Doctor says" Twilight ordered handing the dragon a notepad and pen.

"Somepony's edgy today" Spike retorted as he prepared to note everything the mysterious stallion said down.

"Wouldn't it be better to note things yourself?" The Doctor asked Twilight who perked up a bit confused by the question.

"Well Spike here is my assistant and I get him to take notes when I need to focus on other things. Personally I'd be lost without him" Twilight explained before looking at Spike who was happily noting things down most likely his description.

"Well you where saying?" Applejack rudely asked as The Doctor looked to the fillies with his age old eyes.

"*sigh* where to start? Twilight what you saw was a cyberpony a cold calculating machine from Gaia's sister planet Terra. Unlike here they focused on scientific advancements rather than magic and eventually they began to implant themselves with cybernetics allowing them to live longer think faster, and store more memory. Perfectly normal for a technologically advanced civilisation but eventually they came to a point where their biggest flaw was their emotions. So they removed them causing the entire population to become logical and calculating. So they started thinking like machines adding more and more implants eventual turning themselves into a pure mechanical race with the only pony part of their body remaining being the brain" The Doctor explained as Spike took notes with the occasional 'wow' every now and then.

"So these Cyberponies are those inhabitants coming here?" Applejack asked with The Doctor shaking his head.

"no the original Cyberponies from Terra where destroyed after a group of ponies that had no implants detonated a megaspell in the planets core destroying it along with everything on it" The Doctor continued with spike raising his hand "yes…uhh" the Doctor acknowledged the dragon however unable to recall his name.

"Spike and what's a megaspell" the little dragon asked with Twilight giving him a proud look as it was a brilliant question.

"a Megaspell is an normal spell amplified to insane proportions there are different verities of a Megaspell but the most famous is designed to wipe out everything in a 500 mile radius" The Doctor answered shocking the unicorn yet also intriguing her but he wasn't done explaining "however despite the planets destruction smaller creature known as Cybermites where bound to bit of the destroyed world which eventually came her as meteorites. Overtime they studied you and grew as a intelligence before deciding to do to you what they did to themselves. That's how a cyber invasion starts, first the odd pony, then a dozen, then a hundred, a thousand, then 100 of thousands. Which makes me come to the hardest part of this explanation, when that Cyberponies stated it was Mrs Cake it wasn't lying, that was really Mrs Cake, or what's left of her." After learning the truth Twilight cupped her mouth in gasp, spike dropped his pen and Applejack looked at the Doctor with fear in her eyes.

"You can't be serious, Mrs cake wouldn't try to harm Twilight" Applejack added standing up but The Doctor remained calm and explained further.

"When a pony is converted they lose all sense of one's self. They remember who they were but can't act on it as their emotions are inhibited, doing that topped with linking the brain their primary processing core renders them slaves trapped in cage of steel that they can't feel" The Doctor finished as Applejack sat down feeling devastated for Mrs Cake.

"What about Mr Cake and the twins?" Twilight asked.

"Carrot Cake was taken with his wife. The twins were left behind as their age makes them incompatible till they reach an older age. That's why you faced the cyberpony first I was getting the kids out. Their being taken care of by an old acquaintance of mine" The Doctor answered before a thought popped into his head "speaking of you meeting it first, you where looking for someone, who exactly? Come to think of it you recognised me and not in the 'I passed you in the street' way".

"To hay with that! Is their anyway to reverse what's been done to the Cakes?" Applejack yelled with The Doctor shaking his head in shame.

"Afraid not, the conversion process isn't as simple as sticking a few implants like they were originally. They only need the brain so in order to make a new Cyberpony they remove it and wire it into the metal body incinerating the remains. I'm afraid anypony who is converted is pretty much dead" The Doctor replied.

"So how do we stop them? The Elements of Harmony?" Twilight asked making The Doctor think.

"I've read about those, you're two of the current bearers correct?" he asked earning a nod from the unicorn "well the elements aren't weapons, so I doubt they would be able to affect them, the best bet to stop them is for me to disable their emotional inhibitors".

"What would that do?" Spike asked no longer writing notes.

"Well i did say that anypony converted is pretty much dead but that's not entirely true. The brain is still intact so by extension that includes their mind and soul all being suppressed by the EI, so if it were to be deactivated theoretically every cyberpony would remember who they were…" The Doctor then grew quite as he knew what would happen if a cyberpony where to realise what it had become.

"So they would be free?" Spike added feeling slightly optimistic.

"In a way but imagine how you would act if you realised what you had become. It would drive you insane and concerning the cybercore it would overload with emotion and most likely explode if every cyberpony had a reaction like that" The Doctor described before walking to the door.

"They would really be dead" Applejack added looking at The Doctor.

"Better dead than trapped as a Cyberpony. I promise you both that I will end this" opening the door The Doctor left the library with Twilight needing to explain the newspaper so she quickly followed.

"Where's she going?" Spike asked after watching his best friend leaves him behind with Applejack lowering her hat.

"She wants to help, it's in her nature to help others but it's in mine to help my friends. Spike stay here for your own safety. Lock the doors and don't let no pony in. also send a letter to the princess. Better to raise the alarm than let this gloss over and take us by surprise" Applejack ordered spike before leaving to follow Twilight and The Doctor leaving the baby dragon alone but not before she made a quick detour.

"Doctor, Wait up!" Twilight yelled as she caught up surprise at his trotting speed.

"Go home Twilight" The Doctor responded bluntly but Twilight had a sense of duty to Equestria she wouldn't abandon.

"But you'll need help" Twilight insisted but The Doctor stopped to look at Twilight directly.

"Spike's a baby, right? I think he'll need his mother know more than ever" The Doctor replied making Twilight blush madly.

"Whoa whoa whoa, I'm not Spikes mother!" she assured while being heavily embarrassed.

"Well he looks to you as one, even though he doesn't say it. Anyway I don't need your help" The Doctor commented before continuing to walk off.

"You can't do this alone!" Twilight yelled hoping for the stallion to change his mind.

"Sure I can, I've done so before" The Doctor added before a newspaper was shoved in his face with Twilight's magic.

"Just look at this first then" again looking back at Twilight The Doctor took the paper and read the head line.

"So?" The Doctor asked not concerned.

"It's tomorrow's newspaper" Twilight revealed still not worrying the Stallion.

"You do know that papers are printed a day before issue right?" he asked making Twilight facehoof herself.

"I got that paper three days ago" suddenly intrigued The Doctor took a closer look at the paper taking in a deep breath before licking the pages grossing Twilight out.

"This Paper is a least a week old. Interesting" The Doctor said before putting on a pair of glasses as he gave another look over the paper "and it's covered in Artron energy emissions curiouser and curiouser".

"Artron energy? What's that?" Twilight asked with The Doctor giving a quick glance at her.

"Sciency word for Time Magic. Means who ever gave you this paper is a time traveller. But it wasn't me".

"what do you mean it wasn't you. You're not a unicorn you can't use time spells" Twilight questioned making the stallion raise an eyebrow.

"As you may have guessed I'm not from around here nor am I from Terra. I come from another planet called Gallifrey and we have mastered the art of time travel on a magical and scientific level. In fact we pioneered it. But like I said this doesn't prove much other than somepony was trying to get your attention" as The Doctor said that Twilight remembered she also got that letter earlier today.

"This also came in the mail today" Twilight added handing The Doctor the blue envelope before he let out a sigh.

"of course…" quickly looking over the note he quickly licked it also "slightly younger than the paper yes both have traces of Artron energy of similar intensity and…in my writing, perfect" The Doctor added with a bit of sarcasm at the end "ok forget what I said, it was definitely me who sent you that paper and this letter or future me, the me that knows how this ends and judging by the what's written here that's not good".

"What do you mean? It's perfectly detailed to lead me to where I met you" Twilight asked as The Doctor removed his glasses.

"exactly, I don't have the attention span to write something this detailed and complex which means this message is a build up of multiple outcomes" The Doctor deduced only confusing Twilight further and The Doctor easily saw that on her face "I'll try an simplify it. Time is a strange thing it's never the same no matter how you look at it. Originally judging by this letter being addressed to you means that we meet up regardless but the order in which we meet is a deciding factor in the outcome".

"What outcome?" Twilight asked unsure of his meaning.

"Meaning who wins and who loses. The paper is important as well, you would have never looked into the missing ponies until you saw this, tomorrow when we originally met but something went wrong something so serious I had to change events and send this back 5 days before we met with this letter a day before so we would meet today…it's a trial and error bootstrap paradox" The Doctor stated again confusing the mare.

"What?"

"Oh come on Twilight you're a smart mare, a bootstrap paradox is a loop in the time stream when a future event causes a past event. We meet tomorrow something happens, the 15,000 become their army and win or we do but the damage is too severe so we send this information back to change it but with each time we repeat this battle we restart the cycle by altering the data." Before Twilight could respond The Doctor continued his rant "let me elaborate, I personally would never write a note this complex, i haven't got the attention span for it but if I had something to work with like a previously written note, all I would have to do is add to it making it more detailed and judging by this note it's been rewritten about 4 times".

"so we've lost for times?" Twilight finally got a word in but it was in vain.

"not entirely, like I said we either win or lose the point is we deemed it necessary to change the past but when we find the perfect ending we just copy the note we have and send it back sealing the paradox similar to trial and error hence the trial and error bootstrap paradox" just from his explanation Twilight could tell The Doctor was vastly more intelligent topped with his experience Twilight could definitely learn a lot from this stallion.

"so how do we know if we're going to win?" Twilight asked making the stallion smile.

"we don't, this could be the perfect solution or we change the past again. But we won't know till we play our hand and I'm pretty confident" The Doctor finished before pulling out his strange device and Twilight was relieved and a little bit sad to see Applejack had caught up.

"Applejack, I'm glad you came along but wouldn't it be better to make sure your family is safe" Applejack stood with her hat down as a small tear fell to the ground.

"It's too late for that Twilight. I decided to help a while ago but I left for the farm to warn them to stay in the barn since it's built on solid ground but when I got there Big Mac and AppleBloom were gone" Applejack revealed making Twilight gasp in horror and The Doctor looking down fearing the worst.

"What about granny smith?" Twilight asked as her friend hadn't mentioned her grandmother.

"She's in bed, I found her unconscious on the floor" Applejack replied before the doctor explained why without prompt.

"It's not a guarantee but Cyberponies don't usually convert somepony if they see less than 70% percent compatibility in a donor. It can be connected too hundreds of factors primarily age, intelligence and magical potential and they rarely find somepony 100% percent compatible" he added making Twilight think about what that cyberpony said to her back at the bakery "I would say she was lucky that the Cybermen need younger minds for processing power but they'll come back for her during the invasion most likely to assimilate her memories and past experiences".

"So what about the others have you seen them?" Twilight asked making the doctor concerned.

"Others? what others?" The Doctor asked in an urgent tone before smacking his head "OH! How come I didn't see it before? They've been around for years, at least a hundred meaning they witnessed the return of nightmare moon and saw the elements as threat and have tried to separate you. Have one of you gone missing recently?" The Doctor asked making both mares look at each other.

"Fluttershy, she didn't show up to the pool party we where having this morning and after Twilight informed us of the disappearances we aimed to look for her so we'd have all the elements ready" but then the realisation hit Applejack hard "If they saw us as a threat then that means…".

"Fluttershy, famous veterinarian lives in a cottage not too far from here. Easy pickings compared to Twilight in her solid oak house and you up early and out in the fields working the farm" The Doctor deduced with Twilight thinking about the others.

"Rarity, would have asked around having to enter buildings".

"Making her an easy target, only tricky part was getting the colourful one. Lured her in with a puppet and surrounded her I suppose but I haven't seen her lately" The Doctor added as he again scanned around.

"Then stop talking about it and find them!" Applejack ordered earning a stern look from The Doctor.

"Whatcha think I'm doing? Putting up a cabinet" he replied as he looked at the readings.

"Actually Doctor what are you doing?" Twilight asked as the Doctor closed his extended device.

"well when I arrived I found out that the Cyberponies were around so to find them I popped back a day to have longer search time but instead I came across the cake Twins alone in the bakery, before I investigated further I got the kids to safety and when I got back a had barely enough time to scan before you came in and attracted Mrs Cake" The Doctor began to explain before being interrupted.

"What do you mean attracted?" the unicorn asked.

"I said before the three main categories the Cyberponies look for is Youth, intelligence and MP, magical potential. And you've got a lot of power Twilight, so much so you're like a BEACON to them. What did cake say your compatibility level was?" The Doctor asked.

"100%" Twilight recalled perfectly.

"they've got you in their sights now and they'll aim to capture you and aim for a perfect conversion essentially making you their primary cybercore or CyberQueen of you prefer but luckily after it scanned you, I hit that cyberpony with an EMB" The Doctor continued and yet again being interrupted.

"An EM what now?" Applejack asked more confused than Twilight.

"*sigh* an electromagnetic bomb, designed to short circuit the Cyberponies motor systems rendering them immobile but I'm very good with technology top of my class in fact next to math, and I implanted and electrical based virus into the EMB meaning when the device frozen Mrs Cake it implanted a virus into her electrical systems" as The Doctor began to buzz with excitement he continued to rand as Twilight barely followed and Applejack was completely lost "what does this virus do? You ask? Well it hacks into the communication system of a unit allowing me to track its signal via radio coordinates" he finished taking out his device and checking the data again.

"So you can find them?" Twilight asked with the Doctor giving her a smile.

"No need I already know where they are" he admitted making both mares slightly angry.

"WHAT!" they both shouted in unison.

"Since when!" Applejack demanded pulling at The Doctors tie.

"since about 5 minutes ago but I couldn't believe the results" he added before turning to Twilight "what's the weather forecast for today?" he asked with Twilight looking to the sky and back to The Doctor finally lost but Applejack let go seeing the flaw that The Doctor saw letting him give off a big smile.

"It's sunny all day today" Twilight said unable to figure out what the Doctor was getting at.

"But you've figured it out haven't you Applejack?" he asked as Applejack stared at the Doctor finally able to think like he did for a brief moment anyway.

"heavy rainfall, I prepped the other week for it but it never came" Applejack revealed and The Doctor span around.

"and clear skies all round but I also noticed something else, it's far too warm even for the middle of summer, Celestia's too precise" The Doctor stopped and looked at the two mares "so what stops rainfall and can generate enough heat to rival that of a sun?" he stated before looking up followed by Applejack and Twilight both mares eyes widening in shock.

"By Celestia!" Applejack exclaimed followed closely by Twilight.

"No way, there's no way that can be there. It's not possible for us to miss it!" Twilight questioned unable to fathom what she was seeing. Hovering over ponyville was a large silver craft, large enough to encompass two large cities.

"And yet there it is, right under our snouts…well above them if you want to get technical" The Doctor added before he smiled "now we're in trouble".

Next Time:

It's only the beginning: Part 1