Equestria is growing, and magical savant Twilight Sparkle is disgusted by the crime and corruption this change has brought. Her life is changed forever when she discovers the Death Note, a notebook with inexplicable and deadly powers. She uses this book to pass judgement on those she deems unworthy of life, aiming to create a perfect world free of crime. But when the two Princesses put their best pony on the case, a mysterious detective known only as L, a psychological game of cat and mouse erupts between the two.
Comments contain spoilers. Artwork by blu-red, opening by Anon3mous. Now with its own TV Tropes page.

Twilight and the other Elements of Harmony have saved the land of Equestria from Nightmare Moon, Discord, and the Changeling army, but now they face perhaps their biggest challenge yet. A challenge that lurks behind smiling faces and friendly eyes. A challenge that threatens to overtake the entirety of Equestria and enslave its inhabitants. But the ponies won’t face this threat alone. Help comes in the form of the most unlikely of companions: four teenagers, a hawk, and a blue centaur.

Weeping Angels are invading Ponyville. Who better to fight them than Derpy and the Doctor.

When Ponyville is invaded by weeping angels, there are only two ponies that can fight them. Derpy Hooves and Doctor Whooves. Watch as the Duo, along with the mane 6 fight off hoards of these stone monsters. And remember, don't blink, not even once, blink and you're dead.

Traveling between parallel universes is impossible, especially during the process of regeneration, but the Tenth Doctor doesn't have time to question the facts. He's just been thrust through a tear in the fabric of reality, gotten a new body, and landed on a planet called Equestria. Specifically, he's landed in the worst possible place in all Equestria – somewhere that's ready to unleash a “big ol' storm of chaos”.

That's just the beginning of the Doctor's strange new lease on life: there's a whole host of mysteries to explore. Who is Derpy Hooves, the gray pegasus who understands more about him than even she knows how to explain? How does Princess Celestia already know him? And what's the truth behind the Order?

Above all, the Doctor needs to discover if this new universe can heal the wounds he suffered in the last. Only one thing is certain: there's an awful lot of running left to do.

(Warning: For those of you who haven't watched up to the Doctor Who episode 'The End of Time'... spoilers. Also, this story begins between Seasons 2 and 3 of FiM, and things start to... diverge from there.)

Side stories can be found at The Merely Mundane Tales (of a Mad-Pony in a Box).

Twilight Sparkle finds a book in the library.

Twilight Sparkle reads aforementioned book.

Twilight Sparkle's life is thrown upside down, her view of her teacher shattered, and her friends pitted against each other.

Everything will return to normal.

One of these statements is false.

'Unseen and unheard: They must never know'.

That's the motto of the CMAA, the Cutie Mark Allocation Agency. Nopony knows who they are or what they do, but they're vital to the workings of Equestrian society.

This is the story of two of these unsung heroes of the pony world, who selflessly sacrifice their time and energy for those blasted mysterious cutie marks that the ponies seem to like so much.

(Thanks to Zemious for the excellent cover picture for this story!)

I'd heard about the TV show My Little Pony: Friendship is Magic from my college roommate who is way too into the show. Disturbingly so, actually, but good gravy I would never watch the darned thing! What am I, five? I've got better things to do with my time than watch a silly little girl's show. However, that didn't stop... something from transporting me into the world of the show, so here I am... in Equestria... trying to get home. This is gonna be interesting.

Special thanks to GuyFace, Jack Kellar, Storm Shaker, Spiffy McSquee, and Goober Trooper for helping me with this one!

After Twilight discovers a dusty old book detailing trans-dimensional portals used by denizens of ancient Equestria, she learns that one of these portals is right outside Ponyville. But something went wrong with the spell. Instead of a being from a different dimension, she summoned a pegasus who seems more confused by this than her. When she tries to send him back to where he came from, she gets hauled along for the ride. Turns out the portals match their users to the universe they are entering. How will Twilight handle being human?

Set between The Regal Sisters and Discord and Time.

In the two weeks that Twilight and her friends have been travelling with The Doctor, they have been to many different places, and had many adventures. These are just a few. Come and see what life is like for a pony, travelling throughout all of time and space.