An individual's free will referred to their capacity to think for themselves and make their own decisions.
The Tenth Doctor noted that Mercy Hartigan, even after being converted into the CyberKing, did not have a "Cyber speech pattern", indicating that she still had free will. (TV: The Next Doctor)
The Borg, an analogous species to the Cybermen from the Federation universe, assimilated sentient lifeforms into their Collective. The Eleventh Doctor contemptuously noted to Amy Pond that doing so stripped away their drones' free will. (COMIC: Assimilation²)
The Twelfth Doctor once had Bill Potts write a three thousand word essay on free will. Due to the Monk invasion, she never completed it. (TV: The Lie of the Land)