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The eye was a body part used for vision.
The Bruce Master used Chang Lee's human eyes to open the Eye of Harmony in the Doctor's TARDIS (TV: Doctor Who)
After failing to rescue Omega from the black hole he was trapped in, he 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)
A Dogon's sixth eye allowed someone to look back clearly on their life and make better choices, especially if swallowed. (TV: Random Shoes)