The NUC consultations were intended to discuss: (1) participants' perceptions of the causes of the armed conflicts; (2) their proposals for how government and rebel forces should end them; (3) the issues they deemed relevant to the peace process; (4) the specific programmes, reforms, and entities that could implement proposals and promote peace; and (5) what their own group could do to promote peace. The NUC identified twelve key issues relevant to peacemaking: electoral reforms; human rights; political parties; dismantling of private armies; administration of justice; protection of the environment; socio-economic reforms; autonomy and cultural integrity; provisions for victims of armed conflicts; economic components of national unification; disposition of forces and armaments; and amnesty. They then asked participants to identify additional topics that should be included in the peace programme.
To ensure that it was a truly national process, the consultations were structured through a series of meetings at three levels: provincial, regional, and national. The NUC issued the 'Manual of Operations for the Conduct of NUC Public Consultations' to guide the process and its Secretariat was given overall responsibility for organising the national and regional consultations. The Secretariat was assisted by an Advisory Group with representatives of the NCCP, Catholic Bishops' Conference of the Philippines (CBCP), the department of local governments and the National Coordinating Council for Local Governance. The NUC Secretariat and the Advisory Group designed the consultations process, appointed two members nominated by the NCCP and the CBCP to each Regional Convenors' Group (RCG) and monitored the conduct of the provincial consultations. The RCGs in turn identified the three core convenors for each of the provinces under their coverage. The Provincial Convenor Groups were required to have a minimum of four members, including the governor and representatives from an NGO and a people's organisation as well as a religious leader. Each province could expand membership depending on the number of relevant sectors and different religious groups.
The NUC consulted with national formations, including large multi-sectoral coalitions such as the National Peace Conference and the People's Congress. These groups were responsible for pre-consultation activities among their networks and submitting proposals and documents to the NUC Secretariat before the consultation. The Regional and Provincial Convenors' Groups organised meetings at their respective levels and received and collated peace proposals. Considerable flexibility was allowed at the provincial level because of the diversity in local conditions. Each PCG designed its own pre-consultation mechanisms, with some conducting municipal-level pre-consultations and others arranging sectoral meetings. These events channelled into a provincial consultation, where participants selected their ten representatives to the regional consultation.
The RCGs convened the regional consultations, which the NUC attended. Provincial representatives delivered their respective reports and an open forum followed each presentation. The body was then divided into workshop groups to fill in a matrix that was later consolidated into the regional report. In all, 71 provincial and 14 regional consultations were held and covered almost every province, including Muslim Mindanao.
The NUC identified 24 sectors whose representatives should be invited to participate, along with representatives from local and central government, the judiciary, police and armed forces. These included: women's organisations, child advocates, civic groups, cooperatives, the differently-abled, teachers and researchers, professional associations, farmers, fishermen, indigenous cultural communities, urban poor, media, labour, business, religious groups, social-development NGOs, cause-oriented and political organisations, issue-specific groups and groups of former rebels. In Mindanao communities with sizable Muslim populations, the representatives were also drawn from Muslim social, political and governing bodies. Furthermore, the RCGs jointly with the police and armed forces were authorised to issue safe-conduct passes to combatants that wanted to attend the regional consultations.
Religious and other civil society personalities and groups had leading roles in the consultative structures created. This meant that both practically and symbolically these consultations were led by civil society, rather than the government, at the local and regional levels.