Australia is challenged in its aim to introduce a truly inclusive National Disability Insurance Scheme. Despite policy intent Australia's First Peoples have been consistently underrepresented in access to the NDIS trial sites. Research undertaken by the authors highlights the likelihood that Aboriginal people with complex neurocognitive disabilities may not benefit from the NDIS. This situation will be exacerbated for marginalised groups and those living in rural and remote Australia. Research undertaken by the authors establishes a range of inter-connected and multi-causal issues that need to be understood and engaged with at policy and service delivery levels if Aboriginal Peoples with complex ill-health and disablement are to be included in the NDIS. Evidence is needed across a range of domains to address this challenge. A robust research agenda is required that is underpinned by culturally safe and appropriate methodologies. This paper will present a template methodology for Aboriginal and Torres Strait Islander Peoples' research. The Template has been informed by a range of stakeholders and research undertaken with marginalised Aboriginal Australians in Far North Queensland. The Template is not a prescriptive tool, rather it sets out areas that need to be considered when developing a comprehensive research agenda to promote the inclusion of people with complex ill-health and disablement in the NDIS and other national and state policy and service reforms. It is consistent with templates developed, validated and applied nationally and internationally to inform policy and service development and reform in health, mental health and intellectual disability.