You've got ponies in my Warhammer!
You've got Warhammer in my ponies!

It is the bright and prosperous future of the 41st Millennium. For ten thousand years, the God-Empress Celestia has sat immobile within her Golden Throne, watching over the countless billions of ponies that stretch from one side of the galaxy to the other. But the fragile peace of the Equestrium is assailed on all sides by the selfish, the spiteful, and the mad. Her Majesty's Most Holy Inquisition of the Ordo Harmonious stands eternally vigilant, ready to face down all that threatens the Equestrium with the full force of the Empress' compassion.

For young Inquisitor Twilight Sparkle, to study the mysteries of magic has been her life's goal. But now the time has come for her to discover something far more powerful than magic and save a galaxy standing the precipice of chaos. In the future, there is only friendship...and hatred is heresy.

Twilight Sparkle and Spike, both at home from a long day of adventure and relaxation, find themselves reading a new and mysterious book gifted from Princess Celestia, which may be comedy, tragedy or just a plain old spell book, but can the words twisted inside of the book send a dark spell out to attack the elements of harmony, or elements of a different kind?

Scootaloo's life was just beginning to take a turn for the better. Rainbow Dash had made her her for real little sister. She had friends and a home. But the very night this all began, she had a strange dream. The next day, before she can even get used to her new world, it blows up, all because of a strange key.
Now, it's up to her to save all of Equestria, and possibly all other worlds. At least she won't have to do it alone... right?

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A MLP:FiM/Kingdom Hearts crossover.

Spartans never die, they're just missing in action. This has never been more true for Jorge-052 as, after activating the slipspace drive that was supposed to kill him, he is instead flung into a strange world where war is but a distant memory. Will the aging soldier be able to adapt to this new peaceful planet? Or will his only salvation be found in finding a way back to his own chaotic universe?

(It's my first time, so be gentle)
Now featuring a TVTropes page by Sabo88

Princess Celestia has been the sole ruler of Equestria for more than a thousand years. Over those years, she gradually drifted apart from those ponies over whom she watched tirelessly. But now that Princess Luna has returned, and has begun to share the burdens of rule that Celestia has had to carry alone for so long, she is forced to come to grips with the isolation and loneliness that she has brought upon herself. Having kept herself distant from her subjects for so long, she turns to the pony whose friendly nature has already helped to save Equestria on multiple occasions for help and comfort.

This story is a sequel to Ascend

Congratulations, Twilight. With Celestia and Luna on their constitutionally mandated vacation, you're in charge of Equestria. The position of Regent is an honored and hallowed one. But maybe it's a bit early to congratulate you. After all, whether it's a nobility jealous of your ascension, or a military unhappy with Celestia's decisions; one thing's certain: your reign will be anything but peaceful.