Although there is no clear explanation for these lights, it seems to be a way of making one believe they are UFOs or some experimental craft connected to Area 69, the secret military base in Bone County. Some of the radio stations even discuss the existence of these mysterious goings-on in that area. And of course there is The Li'l Probe Inn just up the road from Area 69, with its flying saucer shaped sign outside, which helps to strengthen the myth.
Once the mission Black Project is undertaken, it doesn't seem such a mystery.
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