This takes place after the events of Season 3. All events until the precise moment of Twilight becoming a princess and being crowned happen exactly as in canon. Afterwards, who can say? Retcons and merging selves abound. This shows why nopony should mess with the flow of time. (I recommend you read alexwarlorn's Pony POV series in order to better understand what's going on. You don't have to, and I'll try to explain things as I write, but you'll be missing out on one of the most epic My Little Pony fanfictions ever.