When the eleventh Doctor regenerates in his TARDIS, he is excited to see the new body he has manifested into.
And when he meets an some ponies who truly appeal to him, making him remember all of his fun times with his old companions.
But he isn't the only Time Lord to have regenerated into Equestrian form. The Master, archenemy of the Doctor, appears as well, younger then when he died but yet hating him as much as ever. After he discovers the Doctor's presence in Equestria, the Master will do anything to destroy him. Even if it means pairing up with Discord.
And Daleks, there are Daleks too.

***This is an alternative to the whole "Trenzalore" gig. This takes place after the Day of the Doctor and replaces the Time of the Doctor***