[2] The school was named by founders as Deganawidah-Quetzalcoatl University, after two Native American leaders of the period before European contact, one from New York and one from Mexico.

The late 1960s and early 1970s saw Native American groups 'occupying' federal lands, including the occupation of Alcatraz Island, as a form of protest, and the US Army high frequency transmit and control site near Davis was no exception.

Conveniently for all parties, the US Army radio transmitter & control site mostly deactivated and operating in a caretaker status, as part of a military-wide reorganization of high frequency radio facilities (similar high-power Army HF radio stations in Kansas and the Washington DC area also had shut down), so while the occupation may have provided a slight nuisance, the Army chose not to attempt to forcibly repel the occupiers, like they certainly would have been obligated to if the site was still performing an important mission and with expensive, classified materials stored on-site.

[5][original research] A group of Native American academics, including David Risling, Jack D. Forbes, Carl Gorman, Kenneth Martin, and Sarah Hutchison, all of whom were involved in the Native American Studies Department at UC Davis,[6] created a board of trustees to apply for use of the site after the federal government decommissioned the site for military use.

They struggled to attract funding and faculty to set up and operate the college, at a time when mainstream universities were also recruiting Native Americans to new programs of studies.

With competition from the growth of Native American programs at other universities, as well as numerous tribal colleges, in the early 21st century D-Q suffered declining enrollment, a high rate of board of trustees turnover, and problems with funding.

In 2003–2004, it lost funding from the Bureau of Indian Affairs because of insufficient Native American enrollment as well as money from the Department of Education.

The university re-opened for some activities later that year, but the board dismissed the president in June 2006 due to continued lack of students and funds.

[16] The Board has arranged for seminars and other activities to retain the university's non-profit status, while working to improve its infrastructure and build a network of support in 2015 to re-open.

He stopped the project when Morrison & Foerster, a law firm closely linked to D-Q U's legal battles, withdrew after some of the film's subjects became involved in mutual lawsuits.