According to Deep Throat, the Blue Berets were formed during the Cold War to retrieve US aircraft lost over the Soviet Union. However, in the post Cold War-era, they're widely used to retrieve and cover up UFOs. (TXF: "Fallen Angel")
The Blue Berets are first seen in the episode Fallen Angel. When a UFO crashlands outside Townsend, Wisconsin, the Blue Berets are dispatched under Colonel Henderson under Operation Falcon. They place the town under martial law and evacuate the civilian population, claiming the town was the site of a toxic spill. Meanwhile, the soldiers recover the crashed spacecraft, but are unable to locate the pilot, who escapes into the woods. Over the course of the episode, several members of the team are killed by the alien, who at episode's end is apparently rescued by another UFO (along with Max Fenig).
In September of 1994, the Blue Beret UFO Retrieval Team was sent to the Arecibo Ionospheric Observatory, Puerto Rico to retrieve wreckage. They were permitted to use deadly force to achieve their mission and were ordered to prevent knowledge of their activities becoming publicly known. The team was dispatched, in this instance, by the CIA or possibly even the Syndicate.
FBI Agents Mulder and Scully were investigating reports that a project (similar in many ways to SETI) which was shut-down by the US government was in fact still online at that facility and was secretly recording transmissions from an extraterrestrial source.
The Blue Berets pursued a fleeing Mulder and Scully, firing upon them several times. Due to a head-start and their possession of a smaller, more agile vehicle, Mulder and Scully escaped the scene. Had the Blue Berets caught them, the intrepid investigators would surely have been killed. (TXF: "Little Green Men")
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