When the HMS Equestria sets out on her maiden voyage, they're doing nothing more than charting nebulae is search for different forms of life. Officially, that's all they're doing. But, behind sealed doors in a dark room, select crew members are part of a clandestine investigation of a growing faction within the Federation.

An unfortunate turn of events finds Spike changed into an Earth pony. Rarity unintentionally crushed his heart and now she has to fight hard to win back his trust, his friendship, and maybe something more.

The story continues with Curse of the Werepony 2

Don't know what the heck is going on? Then start to story right by going all the way back to the beginning with And Tootsie Flute Makes Three

After discovering that Cadence is not who she appears to be, Twilight is sent to another world entirely by the disguised Changeling Queen to avoid her plan being disrupted.
When Twilight lands, she discovers that not only have Spike, Owlowiscious and Peewee followed her, but that they've arrived in a world where the main sentient species is human.
There's still a place where they teach magic, though.
Crossover with Harry Potter. Twilight will be effectively taking the role of Hermione.

I've marked this story as cancelled to reflect the unlikelihood of it continuing. If I do come back to it I'll revert that.

This Story is CANCELLED

When Princess Celestia tasks the Mane Six with reforming the Spirit of Chaos, they aren't exactly thrilled about it. However, they are still determined to try... even if most think it isn't worth the time or effort.

But when they free him, Discord has other plans. He transports them to another universe, another world, locking away many of their memories and leaving them in a strange and different world in forms they aren't familiar with and their elements drained.

But luckily, Friendship really is magic, and there are those in this world who are ready and willing to help the Mane Six restore their memories, and the Elements of Harmony, so that they can return home.

And if their absence in one world and presence in another causes some chaos? Well, then a certain Chaos spirit is perfectly happy with that!

=======================================
Takes place near the end of Book 1 of the Harry Potter series
=======================================
This story is a revision of my original idea. The original idea never made it here, but I tweaked it to something I'm happier with.

Spike had grown used to being a servant to Twilight in the old library; slaving away most of the day to Twilight, Rarity and Pinkie Pie. Wearing the Apron is just part of the deal.

He is always that odd one on the second row, with no real chance at anything he wanted. Even if they consider him a Hero at the Empire.

His desires are squarely aimed at that beautiful mare at the Carousel. It may be a high goal, but it is what he set out to get from his first day in Ponyville. This dream never faded, the way crushes commonly does.

One day, he found a new and odd Apron down in the basement of the castle. Trying it on more out of curiosity than anything, it leads him on the discovery of his life and Heart.

A choice comes with consequences, and a tiny miscalculation is exacting the price. Once the scene play out, there is no changing your mind.

Why Chrysalis had chosen this white mare at the specific time, but when a certain Dragon sets his eyes on her, it is too late to change your mind.

Feeling the love emanating from the Dragon known as Spike sets off a chain of events, not calculated; but with consequences, just the same. Crysalis tries to ride the Bull, the best she can, answering his call.

Pinkie Pie, the Pony on the mind of the entire village of Ponyville. Throwing the parties and in general keeping the mood and morale at an all-time high.

Seemingly all-knowing and wise, she is the center of any and every party. She is fast and powerful.

What she isn’t is the Pony you cross or lie to.

What she doesn’t know, may not be worth knowing. On the other hoof, she had the tendency to let you know. Then she demonstrated just how wrong we all were.

The one thing she does forget, is her Birthday.

A new Princess had just been crowned, and Pinkie Pie had promised free Muffins to all. Some Ponies were jubilant, as they figured they could save a bundle on food. Not all are as rich as Pinkie Pie and her friends.

The problem is that feeding just one village still require tons of Pastries. If it isn’t a problem to gather the ingredients, but how to bake the Pastries in time, on a Daily basis that is.

Since she is Pink, she comes up with a solution, as extreme as it may sound. The problem is that no Pony else can bake her Muffins, and she only has the one Dragon available. Thankfully, she knows where to go and how to deal, but does it solve the problems?

As the out of control party animal, Pinkie Pie is bound to through another party. Just for the joy of another laugh and smile.

There is nothing stopping her, when she had set her mind on the next party she had to throw. Just so many places to go and so many to please. The laughter has to be heard and the smiles seen.

A scene is set, and the trap is sprung. Who could have resisted?

This story is a sequel to A Spiked Hologram

I was moving out on my eighteenth birthday, since I am now considered of age.

Pinkie Pie came along, bearing gifts in the form of three holographic characters; Rarity, Spike and Sweetie Belle, only she had spent a week, preparing them for me.

She had intended for Rarity to help me fulfil a dream, Spike was to be her assistant, while she simply couldn’t send Rarity off without Sweetie Belle, it just so happened to turn into a complete family, somewhere along the way.