Engineer II, Flight Systems

COMPANY DESCRIPTION Flagship Pioneering is a platform innovation company that invents and builds companies that change the world. We bring together the greatest scientific minds with entrepreneurial company builders and assemble the capital to allow them to take courageous leaps. Those big leaps in human health, sustainability and beyond exponentially accelerate scientific progress in areas ranging from disease detection and treatment and nature-positive agriculture to novel applications of AI that are driving the creation of new technologies. What sets Flagship apart is our ability to advance science and technology by uniting innovation, company creation, and capital investment under one roof in a way that is largely without precedent. Our scientific founders, entrepreneurial leaders, and professional capital managers are each aligned around an institutionalized process that enables us to innovate and transform for the benefit of people and planet. Many of the companies Flagship has founded have addressed humanity’s most urgent challenges: vaccinating billions of people against COVID-19, curing intractable diseases, improving human health, preempting illness, and feeding the world by improving the resiliency and sustainability of agriculture. Flagship has been recognized twice on FORTUNE’s “Change the World” list, an annual ranking of companies that have made a positive social and environmental impact through activities that are part of their core business strategies and has been twice named to Fast Company’s annual list of the World’s Most Innovative Companies. THE ROLE We are seeking a UAS Flight Engineer II to join our growing hardware team. This is a hands-on engineering role focused on fixed-wing UAV development, BVLOS operations planning, and systems integration. You will focus on a critical component of our platform — designing, building, operating, and iterating on a purpose-built aerial system where the airframe, autopilot stack, and payload integration are all co-developed from the ground up. This role will work alongside a small, highly technical team at the intersection of advanced science, cutting-edge engineering, and field operations, moving us from early prototype flights toward a hardened, field-proven platform capable of executing precision missions in demanding international environments. KEY RESPONSIBILITIES Configure, tune, and iterate on autopilot firmware for fixed-wing airframes, including PID tuning, failsafe logic, auto modes, and mission scripting; Design, build, and iterate on fixed-wing airframes suited to a variety of payload designs, working across aerodynamics, structures, and propulsion integration; Plan BVLOS operations planning and flight test execution, including waiver compliance, pre-flight risk assessment, and real-time mission monitoring; Develop C2 link architecture, RF link budget, electronics integration, and spectrum compliance for long-range operations; Design software for custom ground station capabilities and user interfaces; Analyze flight logs (MAVExplorer, Flight Review) to diagnose anomalies and drive iterative improvements to vehicle performance and reliability; Collaborate with the science and field teams to integrate and validate onboard sensors, ensuring data quality and mission success; Document designs, test results, and standard operating procedures to build a scalable engineering knowledge base for the drone program. PROFESSIONAL EXPERIENCE & QUALIFICATIONS Bachelor’s or Master’s degree in aerospace engineering, electrical engineering, mechanical engineering, computer science, or a closely related field; equivalent hands-on experience will be considered. BS and up to 4 years or MS and up to 2 years of hands-on experience with Ardupilot-based autopilot systems, preferably in production-ready or real mission contexts; Proficiency in C++ and/or Python with experience reading, modifying, and debugging ArduPilot source code; familiarity with MAVLink protocol and GCS softwa