The Time Lords 'resurrected' him to fight in the Time War. Presumably this meant that he was provided with a new regenerative cycle (like he was offered in "The Five Doctors"). Russell T Davies confirmed that explanation out-of-universe.
After the Dalek Emperor took control of the Cruciform, the Master fled the field of battle. He went to the end of time and used the Chameleon Arch to hide out in the character of Yana.