Simple explanation would have been The Master using a Tardis (either one provided by The Time Lords to help fight in the war or one he stole) and fleeing to the future.
Once he got there and used the chameleon thingy to make him human and remove his memories, he would have simply forgotten about it.
So when he got his memories and Time Lord DNA back he no doubt would have remembered his Tardis, but he also would have remembered how much he hated The Doctor. He had The Doctor's Tardis, so why risk making a break for his own when he can still his most hated enemy's and leave The Doctor stranded at the end of the universe
So somewhere, at the end of the universe, is another Tardis. Sitting there, locked down, and lost.
For those who may not know, season 2 of The Sarah Jane Adventures started in the UK last week and season 1 is set to start on the 31st October on Nickelodeon. If you haven't seen it it's aimed at kids but if you're a DW fan you should find it pretty enjoyable.