Both Link and Epona race to fight evil once again, however once they make it to the thing that is behind all the monsters that roam Hyrule, they get a big surprise. Once again, Equestria is threatened by evil and Link is once again called to the line of duty. Isn't he?
~~~
[NOTES]
I will add tags as I go along.
Cover image was made by Aeroflyte on DeviantArt, which can be found here, go check him out.
Now edited by these people: m2pt5 and Crescent Quills!
Based off of the Ocarina of Time timeline (which includes Majora's Mask), but takes a few aspects from Twilight Princess.
~~~

This story is a sequel to Why No One Messes With Luna

Shepard has done the impossible. Old foes have set aside their differences, new friends have come into the fold, and the galaxy is more united than ever before. But the Reapers care not for the new alliances they face; they will fall, as countless civilizations before them fell. It is inevitable.

There is still hope. The Crucible, source of unimaginable power, has been constructed by the allies. With this new source of hope in tow, the allied fleets break through the Earth blockade and attempt to use this newfound weapon in a last, desperate attempt to defeat the Reapers and save the galaxy as we know it. Fleets of all races, soldiers of every kind, are united in this final stand.

Equestria, too, has sent what they can to aid in this final battle. Or rather, who, they can.

The Reapers have no idea what they have unleashed.

Warning: This story contains spoilers for ME3 and takes place during the ending of the series. This story is less approachable than the previous stories and may be confusing to those who are unfamiliar with the ME3 ending

Coverart is by Ziom05, on DeviantArt, and can be found here.

Where the HELL am I? Last thing I knew me and my spotter were providing overwatch for a convoy but now I'm in a forest that was no where near my position. I know this because with all that green it would easily stand out in all the sand. Is there any possible way that I can get home or am I going to be stuck here with all these weird talking horse things?

The story is generally the same. A group of ponies go on a quest to stop an insane alicorn who had escaped banishment, learning about friendship along the way and mastering the Elements of Harmony. But the details...

It can be Trixie Lulamoon leading the Elements of Harmony against Corona.
Rainbow Dash could be Celestia's student and go to Ponyville.
Equestria could have a deep connection to three young people in its distant past.
The Elements of Harmony could have been moved to Manehattan for the ponies to quest for.
Princess Cadance might rule over an Equestria of music, with Octavia as her prized protege.
Or Spike and Twilight might have their roles reversed, the former a stallion and the Element of Magic.

And each one has been chosen by Discord, an Element removed to a seventh Equestria for purposes as yet unknown. Can they survive? Can they get home? Read and find out!

The Lunaverse was created by RainbowDoubleDash and is used with permission. Opening segment was written by Talon and Thorn.
The Hasbroverse was created by RK_Striker_JK_5 and is used with permission.
The Manehattanverse was created by Little Jackie Papercut and used with permission.
The Cadanceverse was created by GrassAndClouds2 and used with permission.
The Flipverse was created by Bed Head and used with permission.
The Dashverse was created by Trinary and used with permission.

And special thanks to dramatic_spoon for getting this all together.

Twilight Sparkle is on top of the world: she's the newest addition to the Equestrian Principality, and everypony admires her success story.

Everypony? Well, yes, but somebody disagrees...

Stranded on a hostile, alien world, Twilight Sparkle and Rainbow Dash must depend on one another and a fellow alien castaway if they want to return home to Equestria.(originally published on FFN)

Chris and Keon are two zoology majors that get separated from their class after following what Chris believed to be an undiscovered species of bird, during a trip into the Amazon rainforest.

Finding themselves stuck in a pit, they discover an ancient ruin adorned with murals and statues of what they believed to be ponies. They soon realize that the bird in question was the orchestrator of their fate, as they’re brought to what they are certain is their deaths.

Waking up, they are not only separated from each other, but in a new land entirely. Will they take this opportunity to learn about creatures only ever seen in legend, or will they be too busy being studied themselves?

Rated teen for sexual themes, crude humor, mild drug use.
(Edited by DF)

The Elements of Harmony. Six artifacts of legendary power that have provided for the peace of Equestria for over a thousand years. While Queen Chrysalis managed to deny the ponies their ultimate defense, she still lost to a different unexpected surprise in the form of a love-powered shield spell.

However, the Elements won't be so easily denied. Unbeknownst to anyone, they awaken in their vault and cast Chrysalis into another world to teach her a lesson or six about life and harmony.

Stripped of her power, trapped in a form unfamiliar even to a changeling, and at the mercy of the locals, Chrysalis must learn how to get along with others before she is allowed to return to save her hive. And if successful, she may just be allowed to keep her new friend... If he's willing, and if he can survive the drawbacks of being one of the rarest changeling classes ever seen:

A breeding drone.

Join a spoiled rotten queen and a workaholic electrical engineer in the retelling of an adventure that brought them together across the boundaries of space and time. Because sometimes, a little change isn't all that bad.

(Changeling Drone 'Gazer' design artwork courtesy of oFimFiction.net member 'More Dakka')

Severe thunderstorms are a commonality when living in a mountain fire lookout tower; an event that comes and goes with ease. However, when a storm takes a turn for the worse and causes the resident lookout to fall unconscious, the scene that greets him on awakening is about as unsettling and unwelcome as can be.
Or is it?

With his radios and cellular service cut off, Equestria's first human visitor is left to his own devices to figure out why he and his tower are now in the middle of an mysterious and dangerous forest. Well, at least the clouds still move on their own, that's a good thing, right?

Look out Equestria, there's a new human in town!

*Takes place during/after Season 9

After Midna sealed the Twilight realm forever, the newly resurrected Zant traps Link in his wolf form and sends his Twilight beasts to kill him. Link escapes, and his friend Ordona helps him flee to a mysterious new land, away from Zant's evil. But is this pony-populated world the heaven it seems? Or is it the hiding place for something much more sinister?

Featured on 11/25/15!