To make a long, multi part story short, Twilight Sparkle tries to raise a Changeling. After a while weird things begin to occur in the small town of Ponyville: ponies begin disappear, continuity begins to contradict itself, and AJ and Pinkie Pie become cops. If you're looking to read something that just likes to take a big crap on any established canon, then come read Pony Shop of Horrors!

And if you find this description too vague, then all the more reason for you to come and read!