Flight with the Clocksmith
As part of the Doom Coalition's plan, the Clocksmith travelled to the Solvers' homeworld and made trinkets to amuse them so that he could disassemble Lady Risolva and enslave the Solvers to do his bidding. The Clocksmith used his TARDIS to transport them to Earth.
The Eighth Doctor identified it as a Type 70 by the sound alone it created as it materialised whilst he was a prisoner of Thomas Cromwell in 1538. The Clocksmith learnt from a previous visit, which took place a little further ahead, that the Doctor was killed trying to escape from Cromwell and came back through time to make sure it happened, so the Doctor could not interfere. But he didn't know that Cromwell, after seeing the Doctor's TARDIS leave, made Brother Octavian falsify the records making it appear the Doctor was executed trying to escape and giving him the means to ensure the Doctor did not interfere with his plans as he slipped back in time to ensure the events took place. Octavian, who was in fact the Eight, watched the Clocksmith arrive in that point of time and stowed away inside his TARDIS.
The Clocksmith used his TARDIS to pick up metal that had once come from Syra, the first world destroyed by the Sonomancer, and the first major casualty caused by the Doom Coalition. He fashioned the metal into the Doomsday Chronometer, but it was broken up by Risolva, who had returned to save her people from the Clocksmith, and he was forced to travel throughout Earth's history trying to find the pieces. His TARDIS assumed the shape of a wall.
The Clocksmith took what turned out to be his last trip in his TARDIS to 2016 Rome, to complete the chronometer. His death in Rome was an opportunity for the Eighth Doctor, as after the newly regenerated Nine had taken his own TARDIS, the Doctor and River Song used the Clocksmith's instead. (AUDIO: The Doomsday Chronometer)
Brief use by the Doctor
The Eighth Doctor used the TARDIS to track down the Crucible of Souls, where he eventually left it, after being ejected into the future, along with Liv Chenka and Helen Sinclair, in an escape shuttle. (AUDIO: The Crucible of Souls)
Stolen by the Nine
The Nine, trying to escape from the Chancellery Guard following the events on the Crucible, stole the TARDIS. After discovering River Song in the Time Vortex, he had the idea of collecting a "complete set" of the Doctor's companions. He extracted the information regarding the time and location of the Doctor's companions from River, and kept her in a "torture machine".
Using his newly acquired TARDIS, the Nine kidnapped Jamie McCrimmon from Scotland in the 18th century. He also kidnapped Jo Grant, Margaret, Leela, President Romana, Adric, and Charlotte Pollard and kept them in cells in his prison. The Nine used the TARDIS's chameleon circuit to give it a police box exterior similar to that of the Doctor's TARDIS. This trick worked on Liv and Helen, at least, when he extracted them from Deeptime Frontier.
In his penultimate trip in the TARDIS, the Nine kidnapped Bliss from Derilobia University, and in his final trip, he was tricked by River into meeting her past self, who had collected the First Doctor's companion, Katarina. The Nine managed to escape with Katarina, but the delay was long enough for some of his captives to escape. Katarina, being wired to the telepathic circuits in order to revive her, led a psychic attack on the Nine's mind, giving his captives time to overwhelm him.
A TARDIS for River Song
After defeating the Nine, River took the TARDIS for herself, and used it to return all of the Doctor's companions to their proper times and places. Being unable to find her vortex manipulator - it had been taken by the Nine - she decided to keep it. (AUDIO: Companion Piece)