In 1938, the Naval governor of Guam requested that Thompson serve as his consultant on Native Affairs to suggest improvements to the educational and welfare systems for CHamorus. She thus became the first anthropologist to conduct formal studies on Guam. She conducted a "six-month field study of the native Chamorro population, their daily life, land use customs, changing economy, schooling, cultural values, and local government under American military rule since 1899." While stationed in Hagåtña, she soon set up a field headquarters in Merizo. Her primary female field assistant, Rosa Aguigui Reyes, was the first woman elected to the Guam Congress. The resulting work, "Guam and Its People", was described after her death by Guam's Delegate Robert Underwood as "the seminal work on the essence of the Chamorro culture" in his tribute on the floor of the United States House of Representatives. In 1943, the U.S. Navy hired Thompson to tell them how the CHamorus of Guam were fairing under Japanese occupation and whether they would welcome the U.S. retaking of the island, which occurred in 1944. Thompson enjoyed producing several reports for the Navy as she felt that this was in line with her belief that anthropology should be a predictive social science.