As a scientific and engineering endeavor, the Algenol IBR Biorefinery project has been a success by almost any measure. The vision for the system evolved significantly over the course of the project, always due to recognized opportunities for improved performance, lower energy consumption, and reduced costs. Our commitment to thorough, realistic, techno-economic and life cycle assessments has been an essential element for system innovation, technology guidance, and change management of the overall facility. The biological tools developed during this program for cyanobacteria are second to none, and are the primary reason for the remarkable improvements in organism performance. The breakthrough was the successful transformation of our most robust wild type organism (AB1) early in 2012. That was followed by a series of improvements over the next several years that produced strains wherein over 80% of the fixed carbon was converted into ethanol. At the same time, our expertise in cultivation, physiology, process engineering, CO2 management, and photobioreactor design and manufacturing grew at a comparable pace. We learned enormous amounts from the various upsets, weather variations, contamination events, and new technology related disappointments. We overcame those challenges to produce fuel grade ethanol with a low carbon footprint, and are within striking distance of economic viability even with the challenges of low fossil fuel prices.