Seven years after the wedding on Twilight Sparkle and James Wanderer, life in Ponyville is pretty normal.

Apple Bloom runs the library for Twilight Sparkle. Applejack and her son have a happy family life. Sweetie Belle attends music school in Canterlot, living with her sister in Rarity's new shop. Scootaloo works full-time for Rei, who is finally married to Inkie, while training to join Rainbow Dash as a Wonderbolt. Fluttershy and Sunshine raise two lovely foals of their own. Pinkie and the Cake twins work to make everypony in town happy. Trixie, Stormy and their daughter travel the world performing. Just normal life for everypony.

One day, The Master shows up in Ponyville to torment his old 'friend', The Wandering Physicist. Instead, he ends up harassing everypony TWP cares for as a distraction while he tries to conquer Equestria. Everypony will have to keep their wits about them to survive the threat of the deranged Time Lord and prevent him from destroying the land they love.

Sequel to The Wandering Physicist Adventures - Written in a manner so that all necessary backstory is covered within. No real need to read TWP, but it is appreciated.
Prequel to Starlight Chronicles

Character References: On tumblr - On Deviant Art - Warning: Contains spoilers and peanut products.