Initially started in 1958 under the so-called Head Start program, the full-scale Airborne Alert Indoctrination program known as Chrome Dome resulted in at least two overflights Greenland a day with nuclear weapons for almost a decade. Another route headed east across Spain into the Mediterranean, and a third main route crossed the Pacific from Alaska toward Japan. In addition to Chrome Dome flights, an additional nuclear-armed aircraft was "parked" right above Thule Air Base where it circled continuously as part of the Hard Head mission. The objective of Hard Head was to ensure continuous visual surveillance of the Thule Air Base and its important BMEWS-radar, a critical element for the U.S. response to a Soviet surprise-attack on North America. The bomber that crashed on the ice off Thule Air Base on January 21, 1968, was on such a Thule monitor mission, codenamed Butterknife V, when fire broke out onboard bringing the aircraft and its four nuclear bombs down.

The Danish government was not informed about these overflights, but was aware of frequent overflights by B-52 aircraft in general. Moreover, Danish government officials were aware of occasional emergency landings by presumably nuclear-armed B-52 bombers at Thule Air Base during the 1960 (see image). Denmark's non-nuclear policy prohibited the presence of nuclear weapons in all parts of the kingdom (including Greenland) and the Danish government stated repeatedly during the 1960s that the United States was aware of this policy and there was no reason to assume the policy was violated.

U.S. military operations over Greenland were governed by the 1951 joint agreement for the defense of Greenland, and the United States considered that it was free to perform nuclear overflights under the arrangement, although the treaty does not specifically mention nuclear weapons. During the 1960s, nuclear-armed B-52s conducted emergency landings at Thule Air Base on several occasions, something the Danish government was aware of, but given the emergency involved, these cases were not considered violation of the non-nuclear policy.

When the Chrome Dome airborne alert program started in July 1961, the U.S. Air Force told the Joint Chiefs of Staff that "in accordance with current governmental understandings, there do not appear to be any restrictions on overflights of Spain or Greenland with nuclear weapons." Even so the overflights proved politically explosive. The crash happened less than 48 hours before a national election in Denmark, and the U.S. Embassy warned the State Department about the severe repercussions in light of the "special nuclear sensitivities" in Denmark. In doing so the Embassy emphasized that "it is iverative [sic, probably meant to be "imperative"] to stress that [the] crashed plane was 'diverted' to Thule and not on [a] 'routine flight to Thule'." And that lie became the official story and the root to more than 30 years of nuclear rumors in U.S.-Danish relations.

Airborne Alert Aircraft carried a variety of nuclear bombs. The bomber involved in the 1968-crash carried four B28 thermonuclear bombs. In general, alert aircraft on Hard Head and Chrome Dome missions carried either four B28 bombs or two larger bombs such as the B36 (only on early flights) and B53. Due to the frequency of the flights, four to eight nuclear bombs were continuously present in the airspace over Greenland for almost a decade.

Following the accident in 1968 and the nuclear scandal, the carrying of nuclear weapons on Airborne Indoctrination Flights was discontinued. The day after the accident, Strategic Air Command ordered the nuclear weapons removed from airborne alert aircraft. In December 1969, when SAC briefed the Danish military liaison at Thule Air Base about the 1969 Thule Monitor mission, the flight route avoided Greenland airspace even though the aircraft no longer carried nuclear weapons. This was also the case in 1971 for the Giant Lance routes: Greenland airspace was avoided.