What happened between the Master's first and second visits to the Nexus Follows on from see
this.
It had taken a while for the Master to give in to his instinct to really
trust the Doctor, but in the end he’d let the Doctor take a look inside his head. And the Doctor had found a scarred area of the Master’s mind which carried faint traces of work by both himself and the Master, which seemed to indicate that somehow, without remembering it, the two of them together had been responsible for getting rid of the drums. How on earth they’d done it, they had no idea, but it certainly helped the Master trust the Doctor further.
( Cut for length )