MacArthur Nils
XCOM:_Gray_Dawn#Supporting_Cast
MacArthur Nils was a decorated Air Force fighter pilot. He served as an airman during the Korean War, and by the time the Vietnam war came, he had become an officer and combat pilot. In early 1970, on a long-range air patrol (a common mission label for aerial spy missions chartered by the CIA), his F-4 Phantom II was lost. His reported flight path would have brought him over Vietnam, which is not unusual, but no wreckage of his plane was ever found.
Disappearance
Some believed he may have defected to the Russians or (more likely) the Chinese, but no one who knew him believed it. Investigations soon ran cold; he was only a major and didn't know any particularly sensitive material, and it wasn't like he was piloting a U-2 or SR-71 Blackbird. He was piloting a regular line aircraft that had seen service for a decade. The official story became that a series of instrument malfunctions coupled with poor flying conditions caused Major Nils to go way off course and splash into the South China Sea. Years later this mythology was dredged up by conspiracy theorists (when such activities became fashionable) and promptly raked over the coals. Over the years, more attention has been paid to his disappearance by people trying to discredit the US government than the US government ever paid trying to find him. The most popular among their theories was that he was killed or abducted by aliens (based on declassified flight reports he made in the early sixties), or he was eventually seen as a liability that didn't know when to keep his mouth shut and was disappeared by the CIA, NSA or the MiB.
Return from the dead, current employment
In reality, MacArthur Nils was recruited by the founders of Project Covenant because of inexplicable things he had seen flying combat missions over the years. His reports fell on deaf ears with his superiors, but agents of the Project knew the key words that came up so often and took his reports a bit more seriously; not only to find out what he knew and get him on board, but also to shut him up before his superiors did start listening to his UFO stories. When they showed him evidence of what he had seen, he was all in, and has served a major role in Project Covenant as a strategic planner and military consultant.
Nils' eventual "promotion" to general was mostly honorary, and served to show the reverence in which the people of the Project held him. The rationale being that if the aliens ever did come and the ranks got filled out, the people within the Project wanted a man like Nils to be their general.
Current whereabouts
Nils' permanent base of operations is Project Covenant Bunker Alpha, covertly located deep underground at Groom Lake (more commonly known as Area 51).