McDonald studied at the University of Omaha, the Massachusetts Institute of Technology, and earned his Ph.D at Iowa State University. He taught at the University of Chicago for a year, then in 1953, went to the University of Arizona as a professor of meteorology; he eventually became the head of the Institute of Atmospheric Physics.

His specialty was cloud formation and physics, but his natural curiosity led him to read widely in many other scientific fields. He was a member of the National Academy of Sciences and the American Meteorological Society.

In 1954, while driving through the Arizona deserts with two meteorologists, McDonald spotted an unidentified flying object none of the men could identify with established science. This sighting would spur McDonald’s interest in UFOs. By the late 1950’s he was investigating UFO reports in Arizona, and he had also joined civilian UFO research group NICAP.

Following a widely-publicized series of mass UFO reports from Michigan in 1966, McDonald was one of several scientists who urged various authorities to undertake a formal study of UFOs. This pressure eventually culminated in the Condon Committee, directed by esteemed physicist Edward Condon.

Though McDonald shared the initial general enthusiasm towards the Committee, he eventually became one of its sharpest critics. While the Condon Committee was in progress, the Office of Naval Research granted McDonald a small budget in order to conduct his own UFO research, ostensibly to study the idea that some UFOs were misidentified clouds. He was able to peruse the files of Project Blue Book at Wright Patterson Air Force Base, and eventually concluded that the Air Force was mishandling UFO evidence. Following the Robertson Panel's recommendations, the Air Force was following a debunking directive, and only discussing UFO cases which were considered solved by a mundane explanation, while unexplained accounts were classified secret.

McDonald was particularly disturbed that his friend, astronomer J. Allen Hynek, had not alerted the scientific community to the fact that Project Blue Book was withholding some of the most anomalous and compelling UFO reports. Hynek argued that if he had exposed this, the Air Force would have dumped him as Blue Book’s consultant; Hynek was the only scientist formally studying UFOs for the government. This was the beginning of a rift between the men that would never be entirely reconciled.

From the mid-1960’s, McDonald devoted much of his time to trying to persuade journalists, politicians and his colleagues that UFOs were the most pressing issue facing American science. He wrote volumes of letters to newspapers, to his peers (especially at scientific journals) and to politicians. He wrote the Air Force Office of Scientific Research, arguing that they needed to radically shift their superficial perspective towards UFOs. In response, the Air Force determined that they needed to "fireproof" themselves against McDonald’s statements.

McDonald knew that promoting the extraterrestrial hypothesis could damage his credibility, but he was so convinced of its viability that he plowed ahead, regardless of consequences. He managed to secure limited support from a few prominent figures, such as United Nations Secretary General U Thant, who arranged for McDonald to speak to the UN’s Outer Space Affairs Group on June 7, 1967. Additionally in 1967, McDonald noted, “There is no sensible alternative to the utterly shocking hypothesis that UFO’s are extraterrestrial probes”.

McDonald formed alliances with those on the Condon Committee who disagreed with Condon’s leadership and who wanted to undertake long-term UFO studies. McDonald inadvertently played a major role in the Condon Committee’s controversy when he was given a copy of the so-called "Trick Memo" which outlined how the Committee could reach a forgone conclusion while simultaneously appearing neutral. Edward Condon tried to get McDonald fired from the University of Arizona following the exposure of this memorandum.

When the Condon Committee issued their final report, its conclusion that there was nothing unusual about UFO reports (and that further research was not worthwhile) was generally accepted. McDonald, however, was one of a few prominent figures offering detailed critiques against the report’s conclusions and methodology.

McDonald engaged in an often savagely adversarial relationship with aviation journalist and UFO debunker Philip J. Klass, who had argued in his first book (UFOs" Identified, 1968) that nearly all UFOs might be explained as a type of previously unknown ball lightning. McDonald offered a detailed rebuttal against Klass's thesis. To many observers--even those skeptical of UFOs--McDonald's critique of Klass's arguments demonstrated that Klass lacked even a basic understanding of the theories he proposed.

In late 1967, McDonald secured a modest grant from the Office of Naval Research in order to study cloud formations in Australia. while in Australia, McDonald conducted some UFO research on his own time. Klass mounted an extended, concerted campaign against McDonald, arguing that he had squandered government funds. The ONR responded by announcing that they knew of McDonald’s UFO interests and had no objections to his personal hobbies. Klass then demonstrated that McDonald was spending at least a small sums of government research funds on UFO research, and the ONR, apparently fearing controversy, decided to no longer fund McDonald’s cloud research. Tom McIver writes that afterward, "Klass accused McDonald of misusing public funds, resulting in a traumatic government investigation and audit (in which he was cleared, though he committed suicide not long afterwards)."

McDonald spoke before the United States Congress for a UFO hearing in 1968. In part, he stated his opinion that “UFO’s are entirely real and we do not know what they are, because we have laughed them out of court. The possibility that these are extraterrestrial devices, that we are dealing with surveillance from some advanced technology, is a possibility I take very seriously.”  McDonald emphasized that he accepted the ETH as a possibility not due to any specific evidence in its favor, but because he judged competing hypotheses as inadequate.

In 1969, McDonald was a speaker at an American Association for the Advancement of Science UFO symposium. There he delivered a lecture, “Science in Default”, which Jerome Clark calls "one of the most powerful scientific defenses of UFO reality ever mounted." McDonald discussed in detail a handful of well documented UFO cases which seemed, he thought, to defy interpretation by conventional science.

McDonald’s tireless UFO efforts were exacting a toll on his personal life and he was becoming professionally isolated. Beyond Klass and Condon, McDonald butted heads with many other prominent figures, including Donald Menzel of Harvard University.

In early 1971, McDonald attempted suicide by shooting himself in the head. He survived, but was left blind. Committed to the psychiatric ward of a Tucson, Arizona hospital, McDonald signed himself out against medical advice to the contrary in early June, 1971. On June 13, 1971, a family walking along a creek near Tucson found a body that was later identified as McDonald’s.

Four of McDonald’s peers from the University of Arizona wrote a reminiscence of their colleague, calling him "a man of great integrity and great courage. He was loved and admired by a great many people ... he made a lasting impact on many facets of atmospheric sciences ... and he will be missed much more than we now realize."

UFO Related Papers (Partial List)
Science in Default - 22 Years of Inadequate UFO Investigations 
The Problem of Unidentified Flying Objects 
Meteorological Factors in Unidentified Radar Returns 
UFOs And The Condon Report - A Scientist's Critique 
Statement on UFOs - Hearings Before The Committee on Science and Astronautics Committee on Science and Astronautics, "Symposium on Unidentified Flying Objects -- Hearings Before The Committee on Science And Astronautics," U.S. House of Representatives, 19th Congress, Second Session, July 29, 1968. 

Career
B.A., Chemistry, University of Omaha, 1942.
M.A., Meteorology, M.I.T., 1945. Ph.D., 
U.S. Navy, Intelligence & Aerology, 1942-45. 
Instructor, Physics, Iowa State University, 1946-49.
Physics, Iowa State University, 1951.
Assistant Professor, Physics, Iowa State University, 1950-53. 
Research Physicist, Cloud Physics, Univ. of Chicago, 1953-54. 
Associate Prof., Physics, Univ. of Arizona, 1954-56. 
Full Professor,, Physics, Univ. of Arizona, 1956-57. 
Senior Physicist, Inst. of Atmospheric Studies, 1958 - 1971. 
Member, Weather Modification Panel, NAS, 1965 - 1971. 
Member, Navy Stormfury Advisory Panel, 1966 - 1971. 
Member, NSF Weather Modification Panel, 1967 - 1971. 
Member, AAAS, American Meteorological Society, 
Sigma Xi, American Geophysical Society, American Society of University Professors.