On December 26, 1977, the day he was supposed to receive his award as one of the Ten Outstanding Young Men for Public Administration, he shocked the nation—including Marcos himself—by announcing his resignation from the government to join the underground revolutionary movement. For five years he became an active underground organizer and was rumored to have headed the National Democratic Front. In 1982, he was arrested by the military, tortured and detained for four years.
President Corazon Aquino ordered his release, together with other political prisoners, after the People Power of February 1986. He then joined the Philippine Rural Reconstruction Movement (PRRM) as its president and started to initiate programs and organize coalitions that supported the ideals of popular democracy, a new politics that eventually separated him from his former national democratic comrades.
Under the Estrada administration, Morales served as agrarian reform secretary and was said to have been part of the controversial president’s inner power circle. It had also been alleged that he was involved in the mobilization of Estrada loyalists during the May 1, 2001 siege of Malacañang. Morales is currently the secretary general of Pwersa ng Masang Pilipino (Force of the Filipino Masses) and the president of La Liga Citizens Movement and La Liga Policy Institute, organizations that implement programs to address poverty and conduct research and advocacies on good governance and sustainable development.