Props Valroa

Came up with an alternate universe.
 

In this alternate universe, Twilight is never enrolled in Celestia's magic school and instead attends some other school in Canterlot. She quickly absorbs herself in her studies, and throughout the years only grows to become only more cynical and hard nosed in her values. Never opening herself up to others, she is able to focus her efforts in for good. The Mane 6 never get together due to no Sonic Rainboom, and the elements of harmony are never found by them

Twilight does not only excel in terms of academia, but also that of magic. She is not trained by Celestia, but rather by a group of elite unicorn wizards who have direct lineage back to the line of Starswirl. It is discovered that she has a line of linage that goes back to that of King Sombra, and upon discovering this she is eventually cast out.

Without opening up to anyone, she turns inward and becomes quite bitter and only becomes more obsessed with magic and understanding it - without understanding the consequences. Twilight eventually goes up against a corrupt education establishment and in doing so pits herself against Celestia, who is the one who established this educational system. The two are at odds, and Twilight is actually able to prove her points in the court of the law but is shot down by Celestia. In rage, Celestia banishes Twilight from Canterlot.

Nightmare Moon in this universe was never a thing, and Luna ruled at Celestia's side up until the present. King Sombra returns, and Twilight finds an interest in the Dark King. Twilight had learned all she could about what was allowed, but her curiosity hungered for much more. She ends up traveling to the Crystal Empire, and upon her dueling with King Sombra to prove her value to him, King Sombra takes her as his prized student. After learning his mistakes the first time around, King Sombra rolls back some of his tyranny and allows for some freedoms in the Empire, this way many Crystal Ponies are more keen to follow him and he does not have to enslave them.

King Sombra as the leader of the Crystal Empire does not instantly attack, rather he bides his time and by further corrupting Twilight's mind he is able to learn hundreds of years worth of knowledge from Twilight, upon Twilight stealing many spell books from Canterlot and allowing him to read. They study, practice, plan and end up having a really good dynamic. After a few years of this, and after constantly dealing with outside threats the Crystal Empire invades Equestria.

Using Twilight's knowledge the Crystal Ponies under King Sombra are able to deal heavy blows to Equestria much sooner on, and defeat the royal guard after gruelling horrific battles. Upon the final battle in Canterlot, when King Sombra was furthering his conquest elsewhere, Twilight is able to destroy the old school she was brought up in and cursed those who sided against her in the court trial, as well as those unicorns who once taught her. They are enslaved by Twilight and forced to bear witness the dual of King Sombra and Twilight, against Celestia and Luna.

Celestia and Luna are defeated and are banished into the Sun, and the Moon respectively. King Sombra and Twilight make some sort of agreement in which the Crystal Empire annexes Equestria and their rule is established. King Sombra transforms Twilight into some sort of Shadow alicorn (shadowcorn).

 They rule for several centuries and there is eventually some sort of disagreement between them and Twilight eventually would overthrow King Sombra, and banish him into the frozen North. However, the conflict between them caused a massive war that ended most civilization and Twilight and those who survived reside within Canterlot.

King Sombra himself is able to curse the land into an eternal winter upon his dying breathe, leading the world to be trapped in ice. Various towns manage to survive by walling themselves off from the rest of the world using advanced technologies that were developed upon centuries in the making. 

These towns and cities reside walled off, disconnected from one another and gradually the planet itself would start to die from eternal winter. Despite this, the ponies manage to survive in their sealed off domes and in underground cities. Twilight, who rules in canterlot became a ruler who hid all knowledge of the outside world and re-wrote history itself.

Throughout the land eventually, after more centuries the sealed off towns of Equestria would develop some sort of sled transport across the vast ice and snow planes across Equestria but contact would remain rare, and seldom. In Twilight's sealed off city of Canterlot there are two ponies named Collapse and Amber Heart.

Collapse and Amber heart eventually somehow escape from Twilight's sealed city, and are the first to do manage an escape. Once they escape, they are confronted by the real world that surrounded the sealed city and manage to hijack one of the sled machines and end up going on an epic adventure where they discover the truth of the real world, and what really happened while exploring their own identity.