Timelines

Canon Timeline
This is the original timeline as seen in the TV show My Little Pony: Friendship is Magic.

It came to an untimely end when Discord suddenly and without reason went berserk, destroying most of Equestria and killing many of the ponies who lived there, including Princess Celestia, Princess Luna, Rainbow Dash, and Applejack, and inflicting fatal wounds on many others, including Twilight Sparkle.

After all efforts to stop the draconequus failed, a dying Twilight used a time travel spell to send Wander back in time so that he could stop Discord from destroying everything.

Wander Timeline
This timeline was created when Twilight Sparkle sent Wander back in time to prevent the disaster that befell the original canon timeline.

After convincing Twilight that he was genuinely from the future, and that Discord was going to destroy Equestria, Twilight and her friends decided it was best to seal the draconequus until the events Wander spoke of had passed. With help from Fluttershy they managed to convince Discord to go along with the idea, and he was sealed by the Elements of Harmony just as he had been twice before.

However, while Discord was sealed, the force behind his Canon self's actions was left unchecked. The ancient seals binding Malevolence deep beneath Canterlot, in the underground Crystal Caves, finally gave out, and since she was now free the oryxequus began her plans for revenge.

Due to the overwhelming power of Malevolence and her band of villains, Twilight and her friends were unable to stop her initial attack, and many ponies were killed as a result - including Princess Celestia, though Princess Luna manged to escape. With the rulers of Equestria either dead or in hiding, Malevolence claimed the throne as her own.

After that Twilight and her friends, along with Wander, formed a group of resistance fighters. They utilized guerilla-style warfare - which worked fairly well - but ultimately stood little chance of winning the war. Seeing their slim chances of victory, Wander decided to use the time travel spell that the Canon Timeline's Twilight had taught him, but since he didn't have access to Twilight's castle he was forced to use the regular time travel spell instead of the scroll-based version. As such, he couldn't travel back in time himself, and was forced to send someone else.

In the end he picked Twilight, and sent her back in time with the hope that she could stop Malevolence instead of wrongfully blaming the manipulated Discord.

Merging Timeline
This timeline was created when Wander sent Twilight Sparkle back in time in order to prevent Malevolence from being freed.

Upon arriving in the past, Twilight immediately teleported to the Cystal Caves beneath Canterlot and strengthened the seals binding Malevolence. Mere days later, the Wander Timeline's Twilight was forcefully combined with the Merging Timeline's Twilight, creating a new Twilight with the memories of her future self but the personality of her old self.

Because of the Wander Timeline Twilight's actions, the seals on Malevolence lasted for about another decade - though Twilight thought she had permanently sealed the oryxequus, and as such had not returned to check on the seals. In this time many things happened, including Twilight inadvertently summoning Crimson Nightmare back to the world of Animalia.

With help from the many allies they had been lacking in the past timelines, the Equestrian royalty managed to defeat Malevolence and her group of villains when she started a war over her desire for revenge.

Other Timelines
There are a variety of other timelines that are separate from the main timelines and their events. They are listed below.

The Go Figure Timeline
The timeline in which the Go Figure! series takes place.

The Gender-bender Timeline
The timeline in which all ponies are the opposite gender.