In this work the authors develop a decomposition theory for subgroups of $\mathsf{Out}(F_n)$ which generalizes the decomposition theory for individual elements of $\mathsf{Out}(F_n)$ found in the work of Bestvina, Feighn, and Handel, and which is analogous to the decomposition theory for subgroups of mapping class groups found in the work of Ivanov.