WARNING THERE MAY BE SPOILERS FROM DOCTOR WHO SEASONS 5 AND 6.
The Doctor, Amy, Rory and Melody(or River Song) have fallen into the MLP universe. They are now stuck there and there is no way out. The Doctor reunites with his old pony companion Ditzy Do. Over this long series where doctor whooves and doctor who season 5 and 6 come together.
You might need to have seen S5EP01: 'The Eleventh Hour' and S06EP7: 'A Good Man Goes to War' to understand the beginning, but other than that; the story is quite understandable. If you come across something you don't understand: it is probably on purpose, but everything should be clear in the end.
Amy, Rory, The Doctor, The TARDIS and doctor who logo are all from google images.