After earning his diploma in anthropology in 1928, he set off on an eight-month journey, working with and recording the Indigenous people of Cape York.

On his return, he was falsely accused of dishonesty, because of the loss of some funds, which was later traced to fraudulent activity by a staff member of the Australian Research Council.

The c.1922 residence and surrounding farm site is considered historically significant and is listed on the Victorian Heritage Databases because of its association with Thomson.

[3][further explanation needed] He formed a strong bond with the Yolngu people, studying their traditional use of the land in the Arafura Swamp and elsewhere.

In 1943, as the war moved northward from the Australian coast, the unit was disbanded, and Thomson returned to the Air Force.

He was badly injured in action in Dutch New Guinea, and spent the rest of the war in hospital before being discharged from the Armed Forces.

[5] His ashes were flown to the Northern Territory and, accompanied in the plane by two of the sons of Wonggu, scattered over the waters of Caledon Bay.

[citation needed] The Thomson Collection, which is currently held by Museums Victoria, includes approximately 4000 black and white glass plate photographs.