The Master steals the Doctor's TARDIS and escapes, though at the last second the Doctor configures the TARDIS using his sonic screwdriver so that the Master is only able to travel between present-day Earth and the year 100 Trillion.
In "The Sound of Drums"/"Last of the Time Lords", the Master rescues four Toclafane from the end of the universe and beyond, using them to fake a first contact situation in order to draw the world's leaders into one place for easy capture. He then uses a "paradox machine" (in fact the Doctor's captured TARDIS, reconfigured) to allow the future of the human race to slaughter many in the present, in short bringing the six billion humans that were alive in the year 100 trillion to return (in the form of the Toclafane). The paradox machine creates a temporal paradox, allowing them to kill their ancestors without damaging themselves, and thus establish the Master's rule over Earth. After subduing Earth, the Master aims to establish a new Time Lord empire with himself as the leader and the Toclafane as his people and ground troops. This plan is foiled when the paradox machine is destroyed, causing time to rewind and trapping the Toclafane back at the end of the universe.

So it came to pass, that the human race fell... and the Earth was no more. And I looked down upon my new dominion, as Master of all, and I thought it... good