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 either leaving Earth or travelling through time as well as removing the knowledge from the Doctor's mind to repair his ship, though the craft was still able to move through space.
When the Doctor reunited with the Master, he learnt that his old friend had lost his own TARDIS. The two Time Lords struck a deal where the Master would repair the TARDIS in exchange for passage off the planet. When the group reached the harbour where the TARDIS was, the Master reneged on the deal and demanded the keys to the TARDIS. Having anticipated this, 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 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 impact of the bomb disabled the inhibitor, restoring the TARDIS' full range of mobility. When the TARDIS landed on another planet, 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)
The TARDIS returned to its normal configuration and was used by the Doctor and Benny to explore her universe. (AUDIO: Pride of the Lampian, Dead and Breakfast, Have I Told You Lately?, The Undying Truth) Whilst in hiding from the Time Lords, the Doctor turned the TARDIS off and refused to let Benny enter it, though did occasionally retrieve items from it himself to her annoyance. (AUDIO: Inertia) After they were captured by the Time Lords, the TARDIS was brought to Gallifrey in a tractor beam. After defeating the Now, the Doctor reclaimed it. (AUDIO: Gallifrey)