Weakly excited states of dye aggregates and supramolecular complexes can be characterized by single or two exciton states. Stronger excitation results in the presence of multiple excited molecules, and complex processes of internal energy transfer dynamics take place. The direct consideration of all excited states is limited to systems with a few molecules only. Therefore, an approach is used based on transition operators among the molecular states of interest and resulting in a dynamic theory for excitation energy transfer in strongly excited molecular systems. As a first application of this theory a detailed description of exciton–exciton annihilation is given. The obtained novel nonlinear theory is related to the standard description. Possible further approximation schemes in the offered theoretical framework are discussed.