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For the Doctor’s exile in Hong Kong in the late 1990s, the Time Lords fitted the TARDIS with an inhibitor which prevented it from leaving Earth, though according to the Doctor it could move about in space though not in time.
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 Alistair 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 Alistair decided to travel together. (AUDIO: Sympathy for the Devil)
The collapse of the universe after the Great War made travel in the TARDIS difficult, something Bernice Summerfield picked up on after comparing the sounds it made compared the one she was used to. The Doctor attempted to use the TARDIS to escape through the Gateway to Benny’s universe, attempting to use her as an anchor. This failed and the TARDIS returned to his universe, with Benny aboard. The Doctor noted that the TARDIS probably no longer liked him because he had used her to try to escape the 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 as the Doctor exhausted it finding gifts from the past for the survivors of the Library. (AUDIO: The Library in the Body) The Doctor and Benny continued to travel in the struggling TARDIS (AUDIO: Planet X, The Emporium At The End) until the Doctor was forced to adopt his responsibility as President of the Universe. (AUDIO: The City and the Clock)
During the Doctor’s time as President, the TARDIS appeared to able to move in time again, as the Doctor used it to attend his therapy sessions out of sequence and rewrite his therapist‘s timeline to try to make her happy. (AUDIO: Asking for a Friend) As part of his plan to hand over the presidency to the Master and return Benny to her universe, the Doctor downsized the TARDIS to the size of a cupboard. The TARDIS latched onto the energy released when the Master activated the Apocalypse Clock, preventing the awakening of the Great Old Ones and enabling it to travel to Benny’s universe. (AUDIO: The True Saviour of the Universe)