The Doctor, now Time Turner, is getting along quite comforatbly in Equestria with his new friends. But when a string of disappearances occurs in Ponyville, it's up to everyone to solve the mystery of the who, where, what, and why.
Bob and Royce were the typical idiots that got shipped off to Equestria after the Black Plague from Europonia was claiming lives at a fast rate. So they settled into Canterbury after going through months of poverty in Equestria.
Twilight thought it would be wise to send Fluttershy to the world of humans. Fluttershy met Jake, but the spell brought her back because it was a test run and it brought Jake. When Twilight tries to send him back, she ends up unleashing something.
When one of Scootaloo's guardians starts getting sick, and when the bills start getting high, she needs to leave. But if nopony offers to adopt Scootaloo as their own, she'll have to go back to the orphanage.
They think they’ve stopped me. They think they’ve won. They think I’m going to tuck my tail between my legs and hide. They think wrong. What they’ve done is cause themselves the biggest problem they’ll ever have.
During the most violent storms, Pinkie runs outside and sits on the tallest hill in Ponyville. Everyone says she's "just being Pinkie". But she knows that by showing love for the storms, she shows love for the pony who makes them.