My Little Timelord

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The Doctor and his lovely assistant, sharing a moment.

The mysterious Doctor Whoof and his wonky-eyed companion have vanquished the Dalek-Cybermen Alliance and saved the citizens of Ponyville from the wrath of their evil plot! But, as Ponyville rebuilds, ponykind finds itself under attack. Never before seen creatures are bleeding through from the darkness, their origins unknown and their intent indecipherable.

The Doctor and his companion have disappeared, and ponykind, scarred by war, must defend itself. From the ashes of that dark conflict a new order has arisen, tasked with protecting the future. Torchwood: outside the Monarchy, beyond the Royal Guard. Equestria’s fate hangs in the balance.

This fic was one of the first, and certainly is one of the most popular, Doctor Whoof and Derpy ship fics to ever be written. In true Doctor Who fashion, it features extra-terrestrial invasion, time travel, and a Torchwood offshoot.

The fiction may be found here.

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This My Little Pony Friendship Is Magic Fanfic provides examples of these tropes:

• Death Ray: The Daleks just wouldn't really be complete without them.
• Fandom Nod: At one point, Ditzy sees a younger version of herself and calls her younger self Dinky, and seems convinced she is hers and the Doctor's daughter.
• Spin-Off: Just like in the TV Show, Torchwood is established to combat any future alien attacks.