The design of optical resonant systems for controlling light at the nanoscale is an exciting field of research in nanophotonics. While describing the dynamics of few resonances is a relatively well understood problem, controlling the behavior of systems with many overlapping states is considerably more difficult. In this work, we use the theory of generalized operators to formulate an exact form of spatio-temporal coupled mode theory, which retains the simplicity of traditional coupled mode theory developed for optical waveguides. We developed a fast computational method that extracts all the characteristics of optical resonators, including the full density of states, the modes quality factors, and the mode resonances and linewidths, by employing a single first principle simulation. This approach can facilitate the analytical and numerical study of complex dynamics arising from the interactions of many overlapping resonances, defined in ensembles of resonators of any geometrical shape and in materials with arbitrary responses.