(Post-Mass Effect 3)(FemShep)
When the Reapers were defeated, the galaxy believed that Shepard and Anderson were both lost in the final battle. However, the two long-time friends were also known for not letting death stand in their way.

Waking up, in the middle of a desert, on an uncharted planet they both embark on their strangest mission yet. Attempting to find their way back to the Human Alliance, a place called Canterlot may hold the answers they seek. But first, they had to get there while trying not to draw too much attention to themselves.

Too bad for Anderson since massive explosions and collateral damage followed Shepard wherever she went, without fail.

Crossover of My Little Pony and Mass Effect.
Cover image credit goes to: CSImadmax at http://csimadmax.deviantart.com/
Chapters 1 - 6 proofread by: http://www.fimfiction.net/user/GermanDash (Pre-March 2021 update)

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).