"... at the forefront of our fandom’s writing scene ... Masterpiece." —PCaRG
"... really enjoyable ..." —City of Doors
"...worthy of high praise." —PaulAsaran
"Lots of wonderful world-building, great action, well-developed characters and an engaging story." —Hoopy McGee

Steel Song is a lot of things. Earth pony. Uncle. Professional bodyguard.

Retired.

So when he receives a mysterious package from Princess Luna a few weeks after the changeling invasion, he's understandably apprehensive. More-so when he presents himself before the Royal Diarchs to find that not only do they desire him to come out of retirement, but to take command of a most unusual position...

A position that may have more significance than any of them suspect. Because strange thefts are occurring on the Equestrian Railway, thefts that nopony can explain. Thefts that may have far more sinister intentions than their seemingly innocent nature may convey.

Intentions sinister enough to shift the balance of power in Equestria forever.

Book I of The Dusk Guard Saga.
Epic Fantasy
Has a collection of Side Stories as well, the first of which is here.
Now with a TV Tropes page!
"This is 100% Approved by Twilight's Library!"
Added to Twilight's Library 11/26/2013
Added to Canterlot's Finest 12/01/2013

This story is a sequel to Days of Wasp and Spider

Believed dead by their creators, the ponies that will become Celestia and Luna have broken their mental conditioning and escaped into the wilderness. Here they plan the revolution that will free all ponykind, knowing that it is only a matter of time before their ruse is discovered.

Back in their underground arcologies, the ponies' erstwhile masters deal with the consequences of the escape, all the while unaware that something lurking at the bottom of space-time wants them all dead.

A Soot-Covered World, book 2.
Canon species only/no humans.
This story has nothing to do with the Holocaust.
Art by InLucidReverie, used with permission.

Three hundred years after the fall of Princess Luna, Equestria teeters on the brink of disaster. Bitter political infighting and power-hungry nobles threaten to tear the country apart in a bloody civil war, while in the south old enemies prepare to reclaim their ancient homeland from the ponies.

As Princess Celestia desperately strives to hold together her splintered nation, she sends a young pony on a quest to the northern lands that border Equestria in order to plead for aid against the threat of Grypha. This unlikely messenger is Rye Strudel, the flightless, magicless, half-breed son of a guard and a baker. Rye must do the impossible and unite the thanes of the north... for if he cannot, there may be no home to come back to.

Isolated from her friends and taken prisoner in the middle of a war, Twilight must deal with the very real dangers of being percieved as an enemy as well as the nightmares of her arrival on 'Earth'. Can she overcome her own fears and the fears of her captors? Will the wayward unicorn's assistance be a boon or a curse to the 'humans?' Most importantly, will she ever find her way home?

"In short, it's a story of friendship and plasma rifles, with the emphasis on the friendship. The characters are well written, the XCOM setting is fleshed out very well, and the story is compelling. If you love XCOM, you'll love the story, but even if you've never heard of it, it's more than worth giving the first 3 chapters a read.

There's excellent action later on, but the real strength lies in the collision between the friendly and naive world of Twilight Sparkle and the desperate world of humans fighting a losing war for survival and willing to do anything to turn the tide."

--Arzoo

(XCOM/FiM crossover)
(Cover art commissioned by a friend and created by the magnificent FoxInShadow!)
(Original cover art by the amazing Carnelian can be viewed here!)
(Gore tag for blood and some violence)
(Many thanks to the studius OminousTen, Arzoo, xXFluttershyForeverXx and finally Setokaiva for giving my rambles a once-over)
(Now with it's own TV Tropes page! Get to tropin' folks!)

SF (canon species only; no humans) Ponies were magically and genetically engineered to be the perfect servitor race. They are powerful, adaptable, intelligent and completely under the control of their creators. A laboratory accident frees one such pony from her mental chains, but how can one mare save herself and the rest of her kind if she doesn't even know she's a slave?
This is not the Equestria you know and these are not your little ponies... not yet, anyway.

Tags: Adventure, Diamond Dogs, Gryphons, NO HUMANS (did I mention that already?)
Other tags: historical, mind control, Clarke's 3rd Law, excessive use of high energy physics, before they were famous.
Detailed review by PaulAsaran.
Cover art by endrome , used with permission.
Russian translation (partial -- 'unofficially' completed in the comments)
A Soot-Covered World, book 1.