Operation Proteus was a secret British government project active in 1963, and operational for an unknown number of years prior to that. Its main goal was to use captured aliens to assist the British military in the improvement of their weaponry. A hidden entrance to the facilities was located at King's Cross, London.

The First Doctor and Susan paid a visit to Operation Proteus shortly before the Doctor first encountered Ian Chesterton and Barbara Wright. They discovered it was run by a being named Raldonn. He had crashed to Earth quite some time before, and had been essentially forced into helping the British. Unbeknownst to them, however, he was using the project's facilities to mutate humans into his own species, so that he could gain a co-pilot to help him fly his downed craft back home.

His efforts at mutation, however, were flawed because only one of every million humans could successfully accept the adaptive gene. The rest were simply mutated into protoplasmic monsters. To speed up the process, Raldonn effectively weaponized his adaptive gene into an airborne virus. The Doctor and Susan thus had to neutralise the virus, but not before Raldonn's previous failed mutants turned on him.

The fate of Operation Proteus after Raldonn's death was unknown. (COMIC: Operation Proteus)

Any connection between Operation Proteus and other secret organisations having to do with aliens — like the Torchwood Institute or UNIT — would be speculative.