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The Master tried to steal the TARDIS after he'd been stranded on Earth for 20 years already while he'd been waiting for the Doctor after losing his own TARDIS, but the Doctor had anticipated the Master's move after learning about what the other Time Lord had been doing. The Doctor tricked him by handing the Master the keys to Alistair Gordon Lethbridge-Stewart's pub, the Little England.
The Master fell for the deception, and even complimented the Doctor on the "good camouflage."
The Doctor unlocked the real TARDIS before the Master realised the deception, and he had the last parasite placed inside. By the time the Master reached them, the Doctor and the Brigadier had already gone to Mongolia, where the Chinese were using a nuclear bomb test as cover for the destruction of the remaining parasites. The Doctor stayed a while to absorb the nuclear energy, and used it to disable the inhibitor, restoring his freedom. The TARDIS arrived on another planet, and the Doctor and the Brigadier decided to travel together. (AUDIO: Sympathy for the Devil)
The collapse of the universe made travel in the TARDIS difficult, something Bernice Summerfield noted. The Doctor noted that the TARDIS probably no longer liked him because he had used her to try to escape the universe that was dying for a new universe. He put further pressure on the TARDIS when he used the ship as a shield to protect the Library from the Kareem attack. Later the TARDIS lost the ability to travel through time. (AUDIO: The Library in the Body)