In the series, the Doctor meets the Master early on. We get some parts of his background. He claims to no longer hears the drums, and remembers dying in " the end of time" Doctor who episode. His Tardis entered the "ponyverse" where he destroyed the pony versions of Gallifrey(Gallopfrey) because he was afraid of the idea of there being another Master, and another Doctor. He then destroyed the Pony versions of the Daleks, sontarans, shadow proclamation, and others. He then arrived in Equestria and set himself up as an advisor under the princesses using an ability timelords have that is basically hypnosis, but not quite.( this is how the Master and the Doctor make people trust them) He makes a cameo in the MLP gala episode, as does the discorded Doctor(Its difficult to say if he has a relationship with Twilight at this point, though at one part in the blog, he meets her as a filly, and in another part we see the Doctor flirting with Twilight during the events of the " putting your hoof down" fluttershy episode, which didn't feature Twilight, thus explaining what she was doing) The Master says he could conquer equestria easily but, doesn't see the point without a worthy opponent to challenge him( the doctor). He considers the Doctor a " broken toy" since he's discorded. The Discorded Doctor does nothing to stop the Master. In one story arc in the series the Master attacks Twilight, which results in one of the most heartfelt scenes ever( see it here:
www.youtube.com/watch?v=6qH3z5… The master also has two companions: Inky( pinkie's sister briefly seen in the cutie Mark Chronicles) and Pinkie Pie( in her " pinkamena" persona).