"Wake up, Applejack. Equestria awaits!"

Sixty years have passed, but that fateful day where the six friends faced down the time travelling Ulysses, something went wrong.
Now Applejack has awoken, her friends are missing, her only source of help is the returned Discord, and worse, if she can't figure out what went wrong and stop Ulysses, even the stalemate will have been for nothing.

But what are the pillars of Harmony? What does she have to do with them, and how exactly can she bring an end to Ulysses alone, when the last she saw him, he had malformed and became twisted by the time magic he was using?