Playing with time sometimes has dire consequences. When the universe reshapes itself, some things are lost. The thing about lost things? They could be found again. But losing something can also make space for something new entirely.
Twilight Sparkle is still Princess Celestia's student, scholar, and unicorn. She's once again tasked with researching Elements of Harmony, which eventually leads to uncovering fragments of the dark history of this Equestria and the secrets it hides. Meanwhile, she tries to atone for her past, defend Equestria, save a broken mare, make some friends and prevent the destruction of her little brother. Her world, in the meantime, becomes more and more dark with each secret unearthed.
The chapters with fractional numbers are bonus chapters. They are out of order, more like flashbacks exploring the things only touched on in the regular chapters.
Romance tag added in advance, it starts to influence the story since ~middle of the storyline (chapterwise). I think you can guess it's Twilight x Tempest. I won't go heavy into it, but you've been warned.
I removed the Mystery tag. It occurred to me that the intro kinda spoils almost everything, and then Celestia being chatty later spoils the rest. There are still some secrets, but the big ones are more or less out of the bag, and it hinged only on characters not knowing. A combination of 'adventure' and 'slice of life' is more descriptive.