Even after all these centuries the Doctor still wonders how his childhood friend became the manipulative monster he is.
Like the Doctor, the Master was born and raised on Gallifrey, a highly advanced and civilised world of scholars and scientists. Millennia ago they set aside prejudice and hate, greed and jealousy, and many other negative character traits, yet the Master has all of them in abundance, along with the insanity that rules his existence.
He’s a throwback, an unwelcome reminder of the past, yet despite his evil, the Doctor cannot wish him gone.
It might be simpler if he could.