Time Lords and Terror

Regeneration can sometimes be a... dodgy process

Time Lords and Terror is a Crossover fanfic between Doctor Who and My Little Pony: Friendship Is Magic.

After witnessing a series of strange events Twilight Sparkle and friends search for answers, only to find themselves entangled in a war between two ancient races and a plot that could end all existence. Luckily, our heroes find help in the form of an eccentric brown pony with an impossible blue box.

It can be found in its entirety here.

Followed by a two sequels, Mines of Dragon Mountain and Atmos-Fear.

Tropes used in Time Lords and Terror include:

Adaptational Badass: Who would have thought anything based on My Little Pony G1 villains could be so damn dangerous?!
Arc Words: Méchant Loup French for Bad Wolf.
Badass Adorable: Zecora, Twilight, Applejack, Rainbow Dash, and Rarity all kick a fair amount of ass.
Badass Boast: a fairly subdued but effective one from The Doctor.

"I'm The Doctor, and these (MLP Mane Cast...and Zecora) Are my friends. And we are going to stop you. Understood?"

Badass Bookworm: Twilight Sparkle, oh so much.
Berserk Button: Twilight has a couple of these throughout the story.
- Typically involving a Berserk Button called 'The Doctor'.
But for Me It Was Tuesday:

"Ooh...waking up in a strange hospital room, no idea where or when I am, the taste of embalming fluid on my tongue...must be Wednesday."

Casual Danger Dialogue: Twilight Sparkle has this memorable exchange with The S'Müz.

Twilight: "You must be The S'Müz."
S'Müz: We are...beyond you.
Twilight: "Quite."

Chick Magnet: Ten has a reputation for it, but it's taken up a level here when almost everypony has a Ship Tease with him.
Clarke's Third Law: Magic? PKE? Sounds the same to me!
- Any sufficiently analyzed magic is indistinguishable from science!!
Continuity Nod: When the Doctor wakes up in chapter two, he comments that his situation (he tastes embalming fluid, he's in a random, unknown hospital, and has no idea where he is) is just like his eighth regeneration. When he regenerated into his eighth form, he had just died from a botched operation to save his life and was presumed dead, and was placed in the hospital Morgue.
The Cuckoolander Was Right: Pinkie Pie is the first to catch onto the Doctor's train of thought, much to his surprise.
Cute Bruiser: Zecora especially gets this during her first encounter with the Carrionites. Applejack and Rainbow Dash also qualify.
Eldritch Abomination: The S’Müz is referred to directly as such.
Flat What: There's the requisite 'What? What?! ...What.' from the Doctor when he finds out he's a pony.
Heel Face Turn: Draggle, the only Carrionite to actually see the S’Müz for the indiscriminate Ultimate Evil that it is.
Heroic Sacrifice: Zecora. She gets better.
- Also, the Hervoken Commander. He doesn't get better.
Hoist by His Own Petard: Hydia is the first victim of The S’Müz. Also, the S’Müz is defeated when the ponies use their Elements of Harmony to absorb both the PKE it stole and the PKE that makes up its body and disperse it into Equestria.
Humans Are Ugly / I Was Quite a Looker: While not technically human, The Doctor insists he was fairly good-looking as a bald ape.
Magitek: Twilight's computers run on magic crystals.

The Doctor: "Not magic instead of technology, but magic as technology. Brilliant!"

My God, What Have I Done?: Each of the Mane 6, after The Doctor steps in on Twilight's Punctuated Pounding on Draggle. He doesn't want any of them to become like him.
Nerves of Steel: Rarity takes being thrust into a life-or-death adventure surprisingly well.
- Fitting, Rarity has displayed grace under pressure in the show being a fashion designer and all.
- Arguably all the ponies take being pitched against a Lovecraftian Horror quite well.
Not What It Looks Like: Twilight and the Doctor get into this situation due to a mishap involving Twilight's Element of Harmony.
No-Holds-Barred Beatdown: Twilight gives a horrific one to Draggle, ignoring her frantic pleas to stop. It takes The Doctor's intervention to keep Twilight from killing her.
Oh Crap: An oh-so-very satisfying one from The S’Müz.
- Also one from Reeka when the Hervoken Commander destabilizes her singularity attack and causes a small thermonuclear explosion that kills them both.
- Pretty safe to assume that every reader pretty much went Oh Crap when the Doctor was Killed Mid-Sentence. He gets better, though.
  - Not to mention a smaller one when learning (through here or the fan fic itself) that the S’Müz is in simplest terms a Cthulu-Smooze.
The Ophelia: Discussed by Rarity. When her friends show up out of nowhere in a strange blue box with an even stranger stallion to drag her away from the business proposition of a lifetime because Equestria is in terrible danger, her first reaction is to assume that she's simply going insane.

"I always thought losing my mind would be a little more... dramatic."

Really Nine Hundred And Five...ish Years Old: The Doctor naturally, much to Twilight's surprise.
Reverse Polarity: Name-dropped, natch. Later used to destroy the Life Energy-gobbling S’Müz by pulling the energy back out through the Elements of Harmony.
Sequel Hook/And the Adventure Continues...: After the S’Müz is vanquished and everything's back to something approaching normal, the Doctor offers to take the girls on further adventures in the TARDIS... which they gladly accept once they realize the implications of having access to a time machine.
Shout-Out: A double whammy for both Whovians and Bronies alike!
- The main villains are Carrionites (as seen in The Shakespeare Code), and they're named for the witches from the G1 My Little Pony movie.
  - The Hervoken are an even more obscure reference. They and their war with the Carrionites originate in the Tenth Doctor novel Forever Autumn.
- The S’Müz is a Darker and Edgier take on the Smooze.
- Applejack calls The Doctor "Professor", much like another companion he used to have.
- Word of God states that this incarnation of the S’Müz is based off Sovereign. Compare the speech pattern of the S’Müz to Sovereign here.
Summoning Artifact: The Hervoken charm cube.
- 'This thing reads like stereo instructions...'
Ultimate Evil: Again, The S’Müz. It has no reason to destroy the multiverse beyond spite, it's simply offended by the rest of reality.
Villainous Breakdown: The S’Müz pretty much freaks when the ponies start stealing its PKE.
- Hydia has a minor one when Draggle confronts her about how summoning the S’Müz is a blindingly stupid idea.
Villains Want Mercy: Hydia pretends to do this as a distraction so she can summon the S’Müz.
- The S’Müz begs and pleads with the Mane Cast to stop destroying it. They don't.
  - Draggle frantically pleads with Twilight to stop pummeling her to near death. When The Doctor steps in and saves her, Twilight is horrified at what she almost did.
Walking Wasteland: The S’Müz consumes passive life like bacteria and plants just by being there and kills higher lifeforms with a touch.
Younger Than They Look: Draggle is about a century old, but is practically a newborn by Carrionite standards. This is only relevant when she is transformed into a unicorn foal after having her body and mind destroyed by The S’Müz possessing her.