Esoterically, the base is (or was) more infamous for its supposed role in the development and deployment of US 'Black Projects' - secret military aircraft deploying futuristic technology. Of such projects now famous aircraft such as the SR71 Blackbird and B1 'Stealth' bomber were born, but many similarly advanced aircraft are rumoured to have been trialled without ever being publicly acknowledged. Those who study black projects are generally drawn to the still officially denied facilities at Groom Lake, Nevada (the so-called 'Area 51') but Macrihanish was long thought to host test flights of experimental aircraft outside the USA.
Part of the reason for this is probably a combination of the site's remoteness and the length of its runway: at a shade over 10,000 feet it is a long runway (although less notable than legend would make out: several commercial airports now have longer runways). There is also the fact that a detachment of the elite US Navy Seals was deployed here in the 1980s - a body of men wreathed in the mythology of military secrecy like their British counterparts the SAS.
The Aurora Spyplane
The primary rumour that has arisen around the base - particularly in the late 1980s and early 1990s was that it was used for test flights of the alleged spy plane known to believers as 'Aurora.' The exact nature of this plane - should it exist - remains unknown, but it is alleged to be a testbed for exotic propulsion techniques or advanced stealth capabilities. Some rumours even proclaim that the aircraft is built on 'reverse engineered' technology from a UFO crash at Roswell, New Mexico in the 1950s.
The exotic nature of its alleged propulsion system has been blamed for some for the 1994 Chinook crash nearby on the Mull of Kintyre (more information here).
In 1990, Archie Hamilton - junior Minister at the Ministry of Defence at the time - described the role of Macrihanish in an answer to a parliamentary question stating:
"RAF Macrihanish is established to support United States navy maritime patrol operations in war. No aircraft are based there permanently in peacetime, although United States navy United Kingdom, and the occasional Royal Netherlands navy aircraft exercise there from time to time."
A briefing note on the subject from the civil service to Tom King (then Defence Secretary) in 1992 directly addressed the notion of Aurora:
"There is no knowledge in the MoD of a 'black' programme of this nature, although it would not surprise the relevant desk officers in the Air Staff and [Defence Intelligence Staff] if it did exist."
Often the Aurora is blamed or credited for the rash of 'black triangle' UFO reports that were prevalent across Europe for much of the 1990s. It is of course conceivable that there is a kernel of truth in this - the USAF has, for obvious reasons, kept many of its experimental aircraft under wraps to maintain their technological supremacy. However, whether an experimental flying design would be flown for many thousands of miles across open water to land at a relatively unsophisticated facility may seem doubtful.
Whether or not Macrihanish ever did play host to secret technology, transmissions from aircraft approaching the base were scanned by amateur researchers until the early years of the 21st century in the hope of confirming their reality and today there are still those who claim to have worked at or around the base and witnessed unusual sights.