When there is significant uncertainty in an innovation project, research literature suggests that strictly sequencing actions and stages may not be an appropriate mode of project management. We use a longitudinal process approach and qualitative system dynamics modelling to study the development of genetically modified (GM) mosquitoes for malaria eradication in an African country. Our data were collected in real time, from early scientific research to deployment of the first prototype mosquitoes in the field. The 'gene drive' technology for modifying the mosquitoes is highly complex and controversial due to risks associated with its characteristics as a living, self-replicating technology. We show that in this case the innovation journey is linear and highly structured, but also embedded within a wider system of adoption that displays emergent behaviour. Although the need to control risks associated with the technology imposes a linearity to the NPD process, there are possibilities for deviation from a more structured sequence of stages. This arises from the effects of feedback loops in the wider system of evidence creation and learning at the population and governance levels, which cumulatively impact on acceptance of the innovation. The NPD and adoption processes are therefore closely intertwined, meaning that the endpoint for R&D and beginning of 'mainstream' adoption and diffusion are unclear. A key challenge for those responsible for NPD and its regulation is to plan for the adoption of the technology while simultaneously conducting its scientific and technical development.