This story is a sequel to My Little Background Pony: Friendship is Magic
After the Summer Sun Celebration, the Doctor has been living as Time Turner and is enjoying his new life as a resident of Ponyville. He's got a good job, great friends, and life seems peaceful.
But it doesn't last. Ponies have gone missing lately, and it seems the perpetrators are not normal by any means. Can Time Turner, Derpy Hooves, Bon Bon, Vinyl Scratch, Lyra Heartstrings, and Octavia find out what's going on and, more importantly, put a stop to it?
Extra character tag: Bon Bon
Chapters (8)
I recently saw the Doctor Whoove's and Assistant episodes on youtube--DerpyXDoctor stories are so cute. Please continue this, I'd like to know what happens next!
From what I could imagine, it would be that weird mutated Lazarous from the Lazarous experiment Episode.
3506825
That sounds just about right. In any event, I expect that AJ and Twi have company:
Oh, my. This is getting scarier and weirder by the second....just like Who!!
Me likey!!
Lol, But seriously this is an amazing story. Keep up the great work.
And cue the pant stains.
3516408
Unfortunately for them they don't wear pants....LOL!!!!!
Wonder what the Krillitanes would think of Discord and his mismatched appearance? Probably justify their ideals, to some level.
Wow.
This is crazy, this is almost exactly like my story, "The Background!"
Except I haven't written more than one chapter....
Oh, well, always nice to meet another whovian!
\Keep Smiling!
And I hope you saturday is awesome!
(Day of The Doctor ftw!!!!24.media.tumblr.com/18a45f8698e750c2541a9c400240985d/tumblr_mqid1cTTOs1rhasruo1_500.png )
-SS
Spoilers indeed. STM said the whole narrative will change and he does not disappoint!!!! GFNM!!!!!!!
3529139 Ummmmmmmm. STM?
GFNM? 
Could someone please explain to me what the hay you're talking about?
3529284 Stephen MOFFAT said that he'd change the basic premise and he did....that's because Gallifrey falls no more. (All thirteen Doctors freeze Gallifrey in time to make it look as if it had been destroyed. Rassillon and his mob are dead while the noncombatants are playing a longish game of statues while waiting for Twelve to find them.)
will you be making more stories involving the alternate 6?
3555100 As soon as I can figure out what the next story will be.
Which will take a while.
so does this mean that ,even though we get cameos of the 6, we wont see twilight?
so if these six took care of NMM why is twilight even here
i feel like you cheated a but lol the Krillitanes are a catch all villain that can literally be used in any situation. how were we to guess that
3520864 theyd probably worship him. cus he can do pretty much anything and everything
lol you know somethings wrong with the doctor when his own species refers to him as a "Madman"
3572347 Well, in a world where the Doctor has always been a pony, I have to take a few creative liberties on monster designs.
3529322
"The best trick the Doctor ever pulled, was convincing himself and the entire universe, that Gallifrey had fallen"
but anyway you know what surprises me...is that no one had ever been surprised that gallifreyins have the technology to revive the dead.....they revived the master, rassilon and countless other famous time lords during the war and that was without using time travel
3555256 What about the Alternate 6 encountering the Daleks? Or the Cyber... what the hell would Cybermen be called in this 'verse? Either that or have a special where the Doctor regenerates and the Alternate 6 have to deal with the fact that Time Turner now looks a hell of a lot different.
3583670 In time.
3587684 Either that or The Canterlot Wedding, Alternate 6 version.
I'm doubting they already have pinkie pie she's too... Tricky to catch
Pants...pants... Sounds familiar...
... OH YEAH!!! 
I sawlyra in pants
No more jigsaw ponies? Wait til they meet discord lol. Seriously them vs discord think about it.
3555256 them vs discord!!!! Then make it after he shows up, vinyl saying, what was that about you promising no jigsaw ponies a few weeks ago? I'd definitely read that.
3572321 because.
In my mind I see a pony with a scorpion tail (I think from fallout equestria?) Huh
Ever since you wrote that his circumstances are the same as the Third Doctor's, I've been reading his lines in Jon Pertwee's voice (I wonder: if I went back and started again, would I read his "allons-y" in Jon's voice as well?). It helps, in that regard, that I'm going through Classic Who at this time and I'm currently in his third season (just finished watching "Day of the Daleks," in fact). Also, though I probably could have mentioned this in the previous story's final chapter instead of the first of this one, I didn't even notice that the EUP balance was off until you said "except for Derpy, who could fly" or whatever it was.
Either way, continuing onwards.
...Okay, now my voice for the Doctor is fluctuating between Ten and Three. Both for the reasons mentioned in my last comment and the fact that Ten is the Doctor I know best (my first Doctor, and the face I associate with him the most).
Is it the krilotaines?
I KNEW IT!!!!!!!! Hahaha
4710265 4710286 Honestly, I didn't think anyone would get that.
Have a prize: five moustaches!
3583670 I think the Cybermen might be called Cyberpoines or something to that effect.
3555256 do more please this is great!
Hmm...
Seeing as the circumstances surrounding the Doctor's appearance in Equestria are almost exactly the same as 3's exile, except, y'know, Equestria, nor Earth, I'm going with the idea that this is an alternate 3rd Doctor, where 3 is much younger, and y'know, a pony.
Krillotaines.
6232568 Have you read the previous story? It goes into more detail. And yes, this Doctor's backstory was meant to recall to the Second/Third Doctor's regeneration.
Dear 4494092 her apprenticeship would have ended eventually. And you also have to account for the fact that they meet in the cannon universes.
Sincerely
Songdrawn
Delivered
Dear author
shameless quotes aside.
You are a very good writer. So I don't fear for a loss of good story's now.
Thanks
Songdrawn
Delivered
7244034
Celestia was probably just being thorough and making several contingency plans. There were probably like, 5 other groups she thought could wield the elements; in this universe, the Doctor was just faster.
6232584, 4710265
It's spelled Krillitanes, not krillotanes.
Good story, though.
Oh! And also, 3506825
Lazarus, not Lazarous