The APPO was born without a formal structure, and that was the point. Students, teachers, anarchists, Marxists, and churchgoers all received the same invitation. Decisions were made by consensus in a general assembly; a State Council of 260 representatives — roughly ten from each of Oaxaca's seven regions, plus delegates from urban neighborhoods — carried the assembly's decisions outward. Commissions covered everything from human rights to natural resources to gender equity. It was messy, improvisational, and remarkably effective. When Governor Ruiz fled to Mexico City, the APPO filled the vacuum, directing traffic, organizing neighborhood defense, and broadcasting updates over seized radio stations. For weeks, the movement operated as a parallel government in one of Mexico's oldest colonial cities.

On August 1, APPO members began taking over television and radio stations across Oaxaca City. The broadcasts became the movement's nervous system — warnings about police movements, calls for protest, demands for Ruiz's removal. Pro-government groups struck back with late-night armed raids on the stations, damaging equipment and escalating a conflict that had remained mostly nonviolent since June. Armed men attacked the APPO's street barricades in what was called a 'cleanup operation.' Six APPO supporters were killed in these nighttime assaults, the first deaths of the conflict. The individuals responsible were identified as members of pro-PRI organizations and plainclothes local police. On October 27, American journalist Bradley Roland Will was shot and killed while filming a confrontation in the Santa Lucia del Camino neighborhood, along with Professor Emilio Alonso Fabian and Esteban Lopez Zurita. Will's family dismissed the government's claim that a protester fired the fatal shot, calling it 'ridiculous, false, without substance.'

On October 29, approximately 3,500 federal police and 3,000 military police moved into downtown Oaxaca to retake the Zocalo. Five thousand army troops waited outside the city as backup. Helicopters dropped tear gas on protesters who had been pushed from the plaza. Roberto Lopez Hernandez, a Social Security Institute worker, and Jorge Alberto Beltran, a nurse on the APPO safety commission, were among those killed. The APPO retreated to the Benito Juarez Autonomous University of Oaxaca, whose legal autonomy barred police from entering without the rector's invitation. When thousands of supporters surrounded the police cordon, officers were forced to withdraw. A massive march on November 25 devolved into the conflict's worst single night of violence — tear gas, rubber bullets, rocks, homemade PVC rockets, more than 160 arrests, and fires that damaged government buildings and hotels.

At the center of it all stood Ulises Ruiz, a member of the Institutional Revolutionary Party (PRI), which governed Mexico for most of the twentieth century. Opponents accused him of electoral fraud, press suppression, and the destruction of historical monuments in the colonial city center. The APPO made his removal their single non-negotiable demand. The Mexican Senate debated whether constitutional provisions allowed removal of a sitting governor and decided they did not apply. Business groups, the Secretary of the Interior, and international observers all called for Ruiz to step aside. He refused. In December, APPO leader Flavio Sosa was arrested in Mexico City. The movement's remaining leaders went into hiding, alleging a crackdown in which teachers were pulled from classrooms and detainees beaten. Ruiz served out the remainder of his term.

The rebellion left at least seventeen people dead, scores detained, and deep scars across Oaxacan society. But it also produced something unexpected. In June 2006, at the height of the crisis, artists formed the Asamblea de Artistas Revolucionarios de Oaxaca — ASARO — the movement's creative wing. They used woodblock and linoleum printing, stencils, wheat-pasting, screen printing, and large-scale graffiti murals to amplify the APPO's message. Numerous printmaking collectives emerged alongside ASARO, creating what practitioners described as 'brotherhood and sisterhood amongst our spaces.' The prints traveled far beyond Oaxaca, carrying images of resistance into galleries and protest movements around the world. International figures including Noam Chomsky, Naomi Klein, and Arundhati Roy signed an open letter supporting the Oaxacan people's efforts. In a city celebrated for its indigenous art traditions, the rebellion added a new chapter — one created not for tourists but for survival.