The Princesses find an alien creature barely clinging to life at the scene of a terrifying crash. Can the Combined Power of the Elements of Harmony save it, or more importantly, should they save it? Will the arrival of this strange creature tear Equestria apart?

TV Tropes
https://tvtropes.org/pmwiki/pmwiki.php/FanFic/Article2

This is the story of the end. This is the story of the death of Equestria. It is the story of the reign of her royal majesty, Princess Twilight Sparkle of the Fading Sun.

The alicorn sisters are dead and Equestria has turned to Twilight Sparkle to guide it. However, just maintaining a dim sun a fraction as bright as her mentor's keeps the new princess near her limits.

Years have passed and Twilight Sparkle is sure of only one thing. Equestria is dying.

NOTE: Written before "It's about Time" in season 2. Everything after "Read it and Weep" was ignored throughout this story.

On the eve of the Gulf War, a US Navy ship sails through an intense storm and into a different world.

Equestria and the other members of the United Lands are attempting to remove the dragons from their encroachment into Zebrica, but diplomacy is failing. While nopony wants a war, it appears that there might be no other option.

Captain John Mittal and the rest of the sailors aboard USS Wisconsin have some tough political and ethical choices to make. This isn't their fight, but can they stand by while the rest of the world prepares for war?

Sequel to Battleships are Magic-

A few years have passed since first contact between ponies and men. The gap between worlds has secretly been bridged and it is possible to travel between the United States and Equestira.

The President hopes that the American public will be receptive, but on the way to the press conference something goes terribly wrong.

Twilight Sparkle is summoned to settle a legal matter involving The Great and Powerful Trixie... What in Equestria did she do now?

What if Twilight Sparkle's letters to Princess Celestia started a religion?

This is the story of Brother White and Brother Scroll. One of them is an upstanding young unicorn eager to do whatever he can to make other ponies happy. The other is a shy little loner who's never had a real friend before. What do these two young stallions have in common? They are both members of the Fraternity of the Joyous Friends of Princess Celestia, an organization dedicated to teaching Equestria and the world about the magic of friendship. When Scroll and White are assigned to Earthquake Island, however, they find themselves in over their heads. Can the teachings of the Book of Friendship help them save an island run by a brutal warlord, wracked by war, poverty, and hatred?

Stoic. Calm. Unflappable. And above all, Professional. These are attributes that the pianist Frederic Horseshoepin likes to pride himself on.

But sometimes it's difficult to stay professional. Frederic finds it difficult to maintain a veneer of stoicism when he has to deal with his own feelings. What can he do when he's in love with a mare that he cannot hope to have?

Hoofston is a normal town, for the most part. It has its shopkeepers, its eccentrics, its shut-ins, and its civil servants. It's quite dull, really. One day, a vagabond with a song in his heart (and not a lot in his head) comes to town, to see if he can't spark a little music into everypony's hearts.

Snowstorm is new in Ponyville, has just met the mare of his dreams, and landed a great job. But how will he react when the object of his affection is not only his partner, but his manager? Lessons of life, love, loss, and laughs, as well as everything in between.

Everyone's favorite musical pairing is back in another fanfic! Octavia and Vinyl are now room-mates, and are like any other couple...but how will they react when they discover there's another about to show up?