U.N.C.L.E.'s primary adversary was THRUSH (WASP in the pilot movie). The original series never divulged who or what THRUSH represented, nor was it ever used as an acronym. In the U.N.C.L.E. novels written by David McDaniel it is the Technological Hierarchy for the Removal of Undesirables and the Subjugation of Humanity, ("The Dagger Affair") described as having been founded by Col. Sebastian Moran after the death of Professor Moriarty at the Reichenbach Falls in the Sherlock Holmes story, "The Final Problem". But in a 2nd season episode, guest star Jesse Royce Landis plays a character who claims she founded THRUSH.

THRUSH's aim was to conquer the world. Napoleon Solo said, in "The Green Opal Affair", "THRUSH believes in the two-party system – the masters and the slaves", and in the pilot episode ("The Vulcan Affair"), THRUSH "kills people the way people kill flies – a reflex action – a flick of the wrist." THRUSH was considered so dangerous an organization that even governments who were ideologically opposed to each other – such as the United States and the Soviet Union – had cooperated in forming and operating the U.N.C.L.E. organization. Similarly, when Solo and Kuryakin held opposing political views, the friction between them in the story was held to a minimum. Although executive producer Norman Felton and Ian Fleming conceived Napoleon Solo, it was producer Sam Rolfe who created the global U.N.C.L.E. hierarchy and included the Soviet agent, Illya Kuryakin. Unlike the CIA or Secret Intelligence Service (MI6), U.N.C.L.E. was a global organization of agents from many countries and cultures.