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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, he was caught by Ordinal-General Quences and Badger and made him forget about leaving Gallifrey.
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, 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. She 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.
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), and rescuing the princes from the Tower, and giving Beethoven a hearing aid.
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 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.
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, but unfortunately, the Mayan's who were 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)