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T
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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.

Chapters (36)
T

A horrible Cataclysm has turned all of Equestria into a Wasteland of barren ash and twilight desolation. The Sun and the Moon have been destroyed. Everypony has died--including Princesses Luna and Celestia. But one pony miraculously survives; she is a lone wanderer, the last of her kind, surrounded by menacing creatures that hate her. She navigates the Wastes in an airship and scavenges off the blighted landscape to keep herself alive.

Then one day she meets an old companion who grants her a gift, the chance to go back in time to the warm and sunny days of Ponyville, where her dead friends live in happiness. How far will the last pony venture into this joyous age of Equestria, even if she fully knows that there is no way to change the horrible fate of everypony she loves?

2013 Edition: Smaller Chapters, Better Grammar, and a Few New Scenes

(A shout-out to Vimbert, pre-reader and gentlecolt)

Chapters (52)
T

A visitor arrives in Equestria, bearing a wealth of knowledge and a troubled past. The Mane 6 are quick to befriend the stranger, who helps them to discover what they truly value in life, and how to achieve it.

But learning to overcome their fears and achieve their desires comes at a steep price, paid by their innocence.

Chapters (16)
T

Twilight's life is in danger as a secret organization aims to take the life of Celestia and Luna. After discovering the remains of the vampire Alucard, Twilight is the new leader of an old organization called Hellsing, originally established during the great war by Luna before she became Nightmare Moon. Now Twilight, the Elements of Harmony, and Alucard must face and defeat those who want the lives of the Princesses.

Chapters (5)
T

NOTE: There may be spoilers in the comments. Read them at your own risk!

A mysterious viral outbreak grips Equestria, threatening the very life of the country. In an effort to stop the infection, Princess Celestia orders all individual settlements within Equestria to be quarantined. Can Twilight Sparkle, along with the other Elements of Harmony, figure out the cause of this horrific virus and put a stop to it? More importantly - can they survive?

Rated M for Violence, Adult Content and Language.

Chapters (23)
E

Twilight Sparkle and her friends must save Princess Celestia before Equestria is doomed...forever.

Chapters (11)
E

Inception inspired Pony time!

Princess Celestia has been trapped within her dreams. Princess Luna requires the help of Twilight Sparkle to rescue her sister from whoever has trapped her inside her mind, but as they go deeper into dream layers the more they risk losing their memories and even their own identities.

Chapters (6)
E

In the 31st Century, humankind has spread to thousands of planets in the Inner Sphere. Once united under the glorious banner of the Star League, the Successor States and their noble houses now fight bitter wars over the scraps of empire. When a JumpShip carrying a special task force from the Federated Suns suffers a catastrophic misjump, the occupants find themselves stranded above a strange, beautiful world at once alien and eerily familiar.

Meanwhile, in the peaceful realm of Equestria, Ponyville’s resident bookworm , Twilight Sparkle, has stumbled upon hints of a secret buried for centuries. A secret that may lay bare long-forgotten aspects of Pony history and culture.

Our story begins on the planet Valexa, where the beleaguered Militia has launched a last-ditch effort to call for help against overwhelming odds.

Written with those who are not familiar with the BattleTech/MechWarrior universe in mind.

Chapters (19)