In the 1950s and 1960s McDonald worked in the scientific community to raise the UFO issue as a serious question deserving the highest national attention. He was the first prominent American scientist to recognize clearly the possibility that UFOs were from an extraterrestrial source. With unswerving persistence he urged the scientific and governmental establishments to study the evidence with complete objectivity and adequate funding. His courage, honesty, and stamina through years of official opposition and resistance are legendary.

McDonald's untimely death can be traced, in large part, to his interaction with the widespread official blindness that even to this day prevents powerful people from seeing undeniable evidential data that points strongly to the possibility that Earth is being visited by other-world intelligences.

McDonald recognized that the UFO issue possibly was one of the most important questions that ever faced the human race, and that to ignore it could easily be a mistake of incalculable enormity. He dedicated the last six years of his life to gathering the best available data relevant to the UFO question.

Eltjo Hasselhoff, Dutch experimental physicist, perhaps expressed McDonald's dilemna when he said, "To look at the evidence and go away unconvinced is one thing. To not look at the evidence and be convinced against it is another. That is not science."