The war produced political prisoners inside the military itself. The Fort Hood Three — Privates James Johnson, Dennis Mora, and David Samas — publicly refused deployment to Vietnam in 1966, calling the war "immoral, illegal and unjust," and were court-martialed and sentenced to three to five years' hard labor in Leavenworth. Captain Howard Levy, an Army dermatologist, refused to train Green Beret medics and drew three years; his case put the Nuremberg defense before American military courts. Stockades filled with resisters, and the coffeehouse movement and underground GI press that supported them became prosecution targets in their own right.

The emblematic case came at the San Francisco Presidio in October 1968, when twenty-seven stockade prisoners sat down and sang "We Shall Overcome" to protest the shotgun killing of a fellow prisoner and the stockade's conditions. The Army charged them with mutiny — a capital offense — and initial sentences ran as high as sixteen years. Public outrage forced drastic reductions on review, and the Presidio 27, most of them working-class draftees who had gone AWOL rather than fight, became the emblem of a military justice system punishing dissent as insurrection.