In the fall of 1965, when the failed Indonesian Communist Party coup called the September 30 Movement changed the trajectory of Indonesian politics and initiated a violent retaliation from the Indonesian military, she was a researcher at the Cornell University Modern Indonesia Project. Along with fellow Cornell scholar Benedict Anderson, and with research assistance from Fred Bunnell, she wrote one of the first major English-language analyses of the events, a 162-page report entitled "A Preliminary Analysis of the October 1, 1965, Coup in Indonesia" (more commonly known as the Cornell Paper). They wrote the paper at Cornell by studying newspaper reports coming out of Indonesia, radio broadcasts, and communications with friends who were still in the country. They finished the report in January 1966; although it was marked "confidential" and only meant to be circulated among colleagues, it was soon being widely reproduced and read by diplomats and even Indonesian army officers. The paper caused a diplomatic stir; McVey was accused by anti-communists of being sympathetic to the Indonesian Communist Party and Anderson was banned from entering Indonesia.