"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 two sequels, Mines of Dragon Mountain and The Nightmare Engine.
Apocalypse How: The S'Müz can cause a Class X-5 as it can destroy one reality and move on and destroy another. As a last ditch effort, the Doctor can detonate the Tardis to cause a Class X-4 which would destroy the current universe but would also kill the S'Müz, thus keeping other realities safe.
Badass Adorable: Zecora, Twilight, Applejack, Rainbow Dash, and Rarity all kick a fair amount of ass.
Pony!Doctor probably also counts
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's bookworm nature comes out in full force while working with the Doctor to save the world.
Back from the Dead: Thanks to the Elements of Harmony destroying the S'Müz, the ponies that were killed through out the story get resurrected, including Zecora and the Doctor.
Beyond the Impossible: A storm in the first chapter was "outright contradictory to all known magical laws." Trying to quantify the impossible event that happened over her head makes Twilight shout AAAAAARRRGH!!!!
Bigger on the Inside: Initially Twilight tries to rationalize it but when she steps inside the TARDIS she's amazed.
Bizarre Alien Biology: The Doctor has two hearts even in pony form. He also has the ability to vomit up certain poisons.
Borrowed Catchphrase: When explaining her plan to defeat The S'Muz, Twilight uses the Doctor's trademark of speaking at rapid-fire, and tops the speech with "Allons-y!" It helps that at this point, the Doctor is temporarily dead.
Brick Joke: That book of Twilight's the Doctor accidentally teleported into the sun; it's spoken of in chapter 2 and The Doctor returns it in the finale. Twilight makes it explode so it won't embarrass her any where.
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. There is a scene in the third chapter where Pinkie Pie lists off what makes him attractive to the Mane Six
For Applejack it's his strength and charisma
For Twilight it's his boundless knowledge and endless line of questions
More specifically the magic readings that Twilight gets are nonsensical because she doesn't understand (or doesn't know) the "science" behind it. The Doctor on the other hand...
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.
Cute Bruiser: Zecora especially gets this during her first encounter with the Carrionites; all three are wiped out thanks to her manticore dust and staff. Applejack and Rainbow Dash also qualify.
Deus Exit Machina: At the start of the story, the princesses are patching holes in the universe that would cause its heat death if left unattended. This means they are unable to help with the current crisis and the Mane Six are the only ones who can help The Doctor. Justified, the holes are a by-product of the villain's entry into the pony universe.
Eureka Moment: In the penultimate chapter, both the Doctor and Twilight (albeit at separate times) realize how to defeat the S'Müz (using the Sonic Screwdriver to reverse the polarity of the Elements of Harmony). With the Doctor, it's when Rainbow mentions how life is being pulled out of everything around them. For Twilight, it's when the same pony mentions how the current situation sucks.
Twilight and the Doctor get into this situation due to a mishap involving Twilight's Element of Harmony.
A second time, when Draggle reincarnates as a foal and is held by Twilight, everyone assumes The Doctor is the father.
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.
Noodle Incident: Sometime in the past The Doctor had some adventure with Princesses Celestia and Luna. By the end of it, the latter had developed a crush on him. Because of the Timey-Wimey Ball involved, The Doctor himself doesn't know what happened and is looking forward to it.
Learning (through here or the fanfic 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."
Rule of Symbolism: Parental sacrifice of the most good-hearted of a damned species, that is to say, Hydia's slaying of Draggle, brings forth resurrection for both the world at hand and the sacrificed child. This is, in fact, an aversion of the Messianic Archetype trope, as Hydia had evil intentions and resurrection was not at all part of The Plan.
Sensory Overload: Used to explain why Fluttershy's so withdrawn. She's really good at picking up body language, and there's so much of it per pony she can barely stand it. It's also how The Stare works; she can basically overwhelm any creature with "I AM YOUR OVERLORD." signals.
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!
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.