The FBI decided to test the reliability of Lothrop's key informant by assigning him to collect information on nonexistent events and individuals. The informant was given background information about a nonexistent upcoming anti-Jewish rally that he was to attend, including a list of specific individuals who would be present. Though the rally did not occur, the informant provided a full report on it. He also filed detailed reports on a nonexistent commemorative celebration of the bombing of Pearl Harbor held in a distant town, and on a fictitious German spy who supposedly had jumped ship in Peru.

Lothrop was instructed not to tell the informant that his duplicity had been detected; instead, he was to say he was out of funds to pay for informants. Lothrop refused to believe his informant was lying and sent a letter of resignation to J. Edgar Hoover. His resignation was accepted and he returned to the United States to resume his academic duties at Harvard's Peabody Museum and the Carnegie Institute.

What is now known about Lothrop's long career of espionage suggests that the censure of Boas by the AAA in 1919 sent a clear message to him and others that espionage under cover of science in the service of the state is acceptable. In each of the wars and military actions that followed the First World War anthropologists confronted, or more often repressed, the very issues raised by Boas in his 1919 letter to The Nation.

While almost every prominent living US anthropologist (including Ruth Benedict, Gregory Bateson, Clyde Kluckhohn and Margaret Mead) contributed to the World War II war effort, they seldom did so under the false pretext of fieldwork, as Lothrop did. Without endorsing the wide variety of activities to which anthropological skills were applied in the service of the military, a fundamental ethical distinction can be made between those who (as Boas put it) "prostituted science by using it as a cover for their activities as spies" and those who did not. World War II did, however, stimulate frank, though muted, discussions of the propriety of anthropologists' using their knowledge of those they studied in times of war, creating conditions in which, as anthropologist Laura Thompson put it, they became "technicians for hire to the highest bidder." Although the racist tenets of Nazism were an affront to the anthropological view of the inherent equality of humankind, Boas (who died in 1942) would probably have condemned anthropologists who used science as a cover for espionage during World War II. Approximately half of America's anthropologists contributed to the war effort, with dozens of prominent members of the profession working for the Office of Strategic Services (OSS), Army and Navy intelligence and the Office of War Information.

In the following decades there were numerous private and public interactions between anthropologists and the intelligence community. Some anthropologists applied their skills at the CIA after its inception in 1947 and may still be doing so today. For some of them this was a logical transition from their wartime espionage work with the OSS and other organizations; others regarded the CIA as an agency concerned with gathering information to assist policy-makers rather than a secret branch of government that subverted foreign governments and waged clandestine war on the Soviet Union and its allies. Still other anthropologists unwittingly received research funding from CIA fronts like the Human Ecology Fund.

The American Anthropological Association also secretly collaborated with the CIA. In the early 1950s the AAA's executive board negotiated a secret agreement with the CIA under which agency personnel and computers were used to produce a cross-listed directory of AAA members, showing their geographical and linguistic areas of expertise along with summaries of research interests. Under this agreement the CIA kept copies of the database for its own purposes with no questions asked. And none were, if for no other reason than that the executive board had agreed to keep the arrangement a secret. What use the CIA made of this database is not known, but the relationship with the AAA was part of an established agency policy of making use of America's academic brain trust. Anthropologists' knowledge of the languages and cultures of the people inhabiting the regions of the Third World where the agency was waging its declared and undeclared wars would have been invaluable to the CIA. The extent to which this occurred is the focus of ongoing archival and FOIA research. When the CIA overthrew Jacobo Arbenz in Guatemala in 1954, an anthropologist reported, under a pseudonym, to the State Department's intelligence and research division on the political affiliations of the prisoners taken by the military in the coup.

During the Korean War linguists and ethnographers assisted America's involvement with little vocal conflict of conscience. Norwegian sociologist Johan Galtung's revelations in 1965 of Project Camelot, in which anthropologists were reported to be working on unclassified counterinsurgency programs in Latin America, ignited controversy in the AAA. During America's wars in Southeast Asia the AAA was thrown into a state of upheaval after documents purloined from the private office of UCLA anthropologist Michael Moerman revealed that several anthropologists had secretly used their ethnographic knowledge to assist the war effort.

As a result of inquiries made into these revelations, the 1971 annual meeting of the AAA became the scene of a tumultuous showdown after a fact-finding committee chaired by Margaret Mead maneuvered to create a report finding no wrongdoing on the part of the accused anthropologists. An acrimonious debate resulted in the rejection of the Mead report by the voting members of the association. As historian Eric Wakin noted in his book Anthropology Goes to War, this "represented an organized body of younger anthropologists rejecting the values of its elders." But the unresolved ethical issue of anthropologists spying during the First and Second World Wars provided a backdrop to the 1971 showdown. Almost two decades later, during the Gulf War, proposals by conservatives in the AAA that its members assist allied efforts against Iraq provoked only minor opposition.

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