Well, you see, as part of normal decommissioning procedures, Time Lord technicians uncreated the old Type 40's interior structure, stripping it down to the barest central components before removing and archiving the space-time element, rendering the capsule inert.
The Doctor, however, had managed to acquire a space-time element - it was given to him by a rather stern Time Lady who insisted on remaining anonymous. "I was never here," she said, peering at him through yellow glasses with intense eyes the same brown as his own. "You found it in the trash."
The Doctor, naturally, was unaware, as he approached the old capsule that the component he was given was in fact the space-time element taken from this very TARDIS, procured from the archives far in the future by that mysterious anonymous Time Lady, through a series of adventures that it shall be another writer's privilege to tell.
He had no way of knowing that it was that same TARDIS with that same space-time element that that Time Lady and her various successor incarnations had used in a series of missions while pressed into service for a covert, intergalactic, multispecies cabal known as "Division".
In their flight from Gallifrey, the Doctor and Susan would have to work hard to build out that TARDIS' interior structure, replacing various rooms and equipment deleted by the technicians: living quarters, laboratories, the space-time visualizer, the food machine, the electric kettle.
Somewhere along the way, the Chameleon Circuit tapped into the last recorded appearance of the capsule, and gently reworked the metamorphic shell into the semblance of a very particular type of blue box specific to a tiny portion of place and period on a distant, unremarkable little world.
