Title: War of the Races.
Main characters: Princess Twilight Sparkle, Nyx, Spike.

Genre: Alternate Universe, Dark, Adventure.

Canonical Placement: After Equestria Girls.
(Past Sins is also cannon to this story)

Premise:
While Twilight is studying the Mirror Portal, Nyx attempts to cast a spell to help her see into other worlds through the mirror, however the portal reacts negatively to her magic and ends up warping her, Twilight and Spike into an alternate dimension…

When the three awaken, they find themselves in a world where the "Fire of Friendship." never shined, and the three Pony Races are at war with one another, each race having built their own kingdoms in place of the other worlds major location:

Pegasopolis:
Ruler: Princess Cadence (She is not an alicorn in this reality)
Founded by Commander Hurricane. It replaces Cloudsdale in this reality, shaped more like a kingdom. While consists almost entirely of clouds, it is built to withstand even the strongest hurricanes. This Kingdom sits close to the peak of a mountain plateau where the "Wonderbolt Academy" was. However in this reality it is a prison for non-pegasus ponies.

Unicornia:
Ruler: Prince Blueblood
Founded by Princess Platinum.This Kingdom replaces Canterlot in this reality, however instead of on the mountainside, it rests at the base on the opposite side, facing away from Ponyville.The gates of Canterlot castle separate the more "high-class" ponies from the "commoners". It's also has a special cave leading to abandoned mines that lead to the Diamond Dogs mines (who let them pass in exchange for crystals), allowing them to launch sneak attacks on their enemy's.

Ponyville:
Ruler: ???
Founded by Chancellor Puddinghead. While in the same place as the original Ponyville, it separated from the outside world by a massive wall. Despite not having magic, they hold several means of combating the other races, such as magic inhibitor collars for Unicorns, and specialized nets for holding Pegasus'.

Twilight's Princesshood is put to the test when the three tribes starts targeting her in hopes of capturing her and Nyx in hopes of using them as means of winning the war! Now she must find a way to unite the three tribes and get back to her own world! But why has the war gone on for so long? Is their hatred really that thick, or is someone else pulling the strings?

I'd maybe do things a bit differently, but still a solid idea.