The Joint Exploratory Missions for an Extreme Universe Observatory comprises a collection of complementary missions dedicated to pioneering technologies and techniques for a future space-based multi-messenger observatory which will have sufficient sensitivity and exposure to measure properties of extremely rare ultra-high energy (E>50 EeV) cosmic rays and very high energy (E>100 PeV) neutrinos. Here we describe a general-purpose software framework designed to facilitate detailed simulation and reconstruction of events observed by the various missions using both detection of fluorescence and Cherenkov light produced when cosmic ray or neutrino induced extensive air showers traverse Earth’s atmosphere. The software builds on a framework developed
by the Pierre Auger Collaboration. We describe the techniques used to organize contributions from numerous collaborators, manage an abundance of configuration information, and provide simple access to time-dependent detector and atmospheric information. We also explain how we seamlessly support a multitude of computing platforms, provide fast installation and maintain the broad testing coverage required for stability of the large and heterogeneous code base. We provide
a few examples of simulated and reconstructed data gathered by some of the JEM-EUSO missions, including the EUSO-SPB2 instrument.