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The navigation system was a component of a TARDIS that enabled control on the accuracy of the flight path of the ship. The Doctor's TARDIS possessed a faulty navigation system. (TV: The Name of the Doctor, Twice Upon a Time)
By the end of their second incarnation, the Doctor was unable to steer their ship properly due to the malfunctioning navigational systems. (TV: The War Games) Centuries of travel in the TARDIS eventually allowed the Twelfth Doctor to learn to navigate the ship perfectly in spite of the broken navigational systems. (TV: Twice Upon a Time)