This document provides guidance for the second phase proposal of the ESA Flagship program. It outlines that each of the four regions will have one flagship project focused on one of four production systems: pastoral, agro-pastoral, mixed crop-livestock, or crop-based. Activities will be clustered within each flagship's focus production system, with 5 to 7 activities per flagship. The document also lists the production systems and action sites that different centers will focus on and provides an example work plan for the pastoral production system with activities progressing from exploration to scaling.