In a parallel universe, a version of the Doctor had decided it was time to flee Gallifrey and he found an antiquated Type 40 TARDIS and saved it from being decommissioned by the Quadriggers. But before the Doctor could leave Gallifrey as he had intended originally, he was caught by Ordinal-General Quences and Badger and made him forget about leaving Gallifrey although he was locked inside the TARDIS.
Quences used Badger to brainwash the Doctor into becoming the Lord President of the Time Lords, and he was imprisoned in the TARDIS for centuries. Instead of following through with the plans Quences tried to force on him, the Doctor became an author and published works such as A Journey to Ice-Ashkar and The Winter Star among others which become popular with generations of Gallifreyan children. In that time the console room became littered with pieces of paper which covered the console.
After centuries of being trapped and brainwashed by Quences and Badger, the Doctor eventually managed to defeat Auld Mortality with his granddaughter Susan's help and regained his memories of wanting to leave Gallifrey. Susan discovered that the Doctor had been living in the TARDIS the whole time by pulling out the paper covering the room, and found the console, and the Doctor suddenly remembered his original intentions to leave Gallifrey. Susan urged the Doctor to leave and that he should have left a long time ago.
The Doctor urged Susan to come with him, but Susan had recently become Lady President of Gallifrey and she had commitments. Desperately wanting company, the Doctor used a Possibility Generator to create a version of Susan to travel with him in the TARDIS. (AUDIO: Auld Mortality)
The TARDIS' chameleon circuit was working at this time. It took the form of a cold mansion on Gallifrey, and later became a sarcophagus and then later a barrel. Also, the TARDIS seemed to travel where the Doctor wanted it to go.
Later the Time Lords began to hunt the Doctor's TARDIS through the universe after he began changing history such as taking Leonardo da Vinci travelling with him and Susan and taking him to the planet of the Ore, and da Vinci learnt about the astrodynamic principles of the harmonies derived from the Spheres. This helped da Vinci learn and master the power of flight, changing human history, (PROSE: The Innocents) rescuing the princes from the Tower, and giving Beethoven a hearing aid. In other parts of the universe, the Doctor's TARDIS took him to places where the Doctor changed the outcome of battles and other events without realising the minor events he believed he was changing would have a wider impact. In this case, wherever the Doctor's TARDIS landed, the Doctor and Susan would find history different from established and predicted lines.
The Doctor and Susan had several run-ins with Agent Zeuro who was pursuing them in his own TARDIS. Eventually, Zeuro caught up with the Doctor and locked their ships together to drag the Doctor back to Gallifrey, but the Doctor reversed his TARDIS' time vector drive and tore a hole in the Time Vortex.
The altercation with Zeuro had drained the TARDIS of energy until there was only a small amount left with no way of moving. The Doctor believed, once he and Susan were caught by the Elizabethan spaceship the Golden Hind, that the hole had deposited them into a parallel universe "sideways in time" and didn't realise he had changed history so drastically that the events he was caught up in had never happened. The Doctor tried, unsuccessfully, to draw energy from the Golden Hind.
Caught by the Elizabethan astronauts, the TARDIS was disguised as a barrel. The Doctor jokingly said his TARDIS was like "an old tub." He also tried to tap into the Golden Hind's solar sails to repower his TARDIS, which had been drained of power when he'd tried to evade Zeuro. The Doctor's plan, as well as the Hind was put in danger the Mayans, using their own spaceship, attacked, and the Golden Hind was defenceless.
Eventually, President Susan arrived personally with a Time Ring to find the Doctor and take him home, but she changed her mind and used her Time Ring to re-power the Doctor's TARDIS. The version of Susan created by the Possibility Generator was sent back to Gallifrey where she could die in peace, leaving the President Susan to take her place in the Type 40. (AUDIO: A Storm of Angels)