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The eye was a body part used for vision.
Pigmentation dispersal could cause the eye to change colour. Leela's eye colour changed from brown to blue after the explosion of a Rutan mothership prompted pigmentation dispersal and left her temporarily blind. (TV: Horror of Fang Rock)
After failing to rescue Omega from the black hole he was trapped in, Savar was forced to leave his damaged TARDIS in an escape pod. The I intercepted the pod, taking all relevant technology. However as Time Lord technology utilised retinal verification, they also extracted his eyes. (PROSE: The Infinity Doctors, PROSE: The Infinity Doctors, Seeing I)
An Ood's eye colour changed with the level of telepathic activity, normally glowing bright-red but turning to white when not connected to a hive mind. Humans, who only knew the Ood in their telepathy-disabled form, misinterpreted the presence of red eyes as a disease, known as "red-eye". (TV: Planet of the Ood) Under the control of House, one Ood's eyes glowed green. (TV: The Doctor's Wife)
During the Thousand Year War on Skaro, it was thought that Davros had lost his own eyes. (TV: Genesis of the Daleks, AUDIO: I, Davros) Whilst attempting to trick the Twelfth Doctor into giving up his regeneration energy to save the Daleks, Davros managed to cry and even chose to open his real eyes instead of using his Dalek eye, to the surprise of the Doctor. (TV: The Witch's Familiar)
Miss Andrea Quill once required surgery that would penetrate the eyeball. The surgery was required so Quill could have her arn removed to regain her free will. Ballon was responsible for administrating the surgery. He also used his shapeshifting abilities, drawn from the blood of his god, to rebuild the eye to approximately its previous state, leaving behind a long scar down her face. (TV: The Metaphysical Engine, or What Quill Did)