This story is a sequel to The God Empress of Ponykind

One thousand years ago, Luna, Warmistress of Equestria and sister of Empress Celestia, fell to the powers of Chaos and plunged Equestria into a brutal civil war. The Traitors were defeated, but not before Luna made the ultimate sacrifice and was sealed away in the Immaterium with only the soul of a slain Primarch to keep her company. For a millennium she has been locked away, waiting for a chance to return to her home and her sister.

Now, she has been freed from the Immaterium, and as she takes her first steps in a new Equestria, one ruled by the powers of Harmony, only one question remains:

Does Equestria still need the services of a Warmistress?

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Princess Celestia: Goddess of the Sun, ruler of Equestria, beloved Princess of ponies. She is loved by all, and loves all in return. A calm and wise ruler, she sits on the throne in Canterlot, maintaining peace and harmony throughout the land.

What most don't know is that her past is much darker: She was once a commander of legions, a warrior and scientist of unmatched skill. Thousands of monsters and abominations fell to her forces, slain in the name of an old leader, one entombed within his own throne. Free of her old form, free of the powers of Chaos, she was cast into a new realm, in a new form, with a new lease on life.

She is the God Emperor, Eternal Ruler of Equestria and Lord of the Imperium of Man.

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In 2185, during his campaign against the Collectors, Commander Shepard discovered a previously unknown species whose origins predated any other race in the modern galaxy. Following a daring rescue from their ancient sanctuary, the Equestrian Herd was brought back into the galaxy where, for the first time in eons, they must walk their own path.

Knowing full well the terrible threat that lingers on the edge of the galaxy, the leader of this newly freed race fights to secure her people’s future while attempting to prepare for the storm on the horizon.

This is her story.
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The long awaited Sequel to Mass Effect 2: The Equestrian Equation This is a reader directed story. Your choices will shape events.
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Also, this series has its own TVTropes page now! (Special thanks to user CrowMagnon for setting it up).