McRae was a vocal critic of the British nuclear lobby. Early in the 1980s he was a key figure in a campaign against the United Kingdom Atomic Energy Authority plans to dispose of nuclear waste in the Mullwharchar area of the Galloway Hills. Representing the SNP in a public inquiry, McRae asked difficult questions of the UKAEA and famously declared at one meeting that "nuclear waste should be stored where Guy Fawkes put his gunpowder." The authority's plans were rejected, and McRae was credited with "single-handedly" preventing the area from becoming a nuclear waste dump.