In a night, half of the Equestria population disappeared, and the evidence pointed out that they were, indeed, kidnapped.
Twilight soon found an ancient scroll that describes there is a fourth tribe called Thracians, and soon believe that they were the ones who cause this tragedy.
Twilight and the others soon arrange a rebel village to protect anyone from disappearing, but the young six decided to head to Thrace themselves.
Meanwhile, a young mare desperately tries to escape her dungeon and reunite with her friends.
Will they succeed?

I highly recommend you read the IDW publishing comic miniseries: Feats of Friendship first. Mostly about this story is about the miniseries's plot.
Comedy is for the humor.