This chapter explains the use of modular or motif-based theory to interpret the dynamics of whole food webs. According to Robert Holt, modules are “as motifs with muscles.” Holt's modular theory focuses on the implications of the strength of the interactions on the dynamics and persistence of these units. In this book, the term “module” means all motifs that include interaction strength, whereas the term “motif” represents all possible subsystem connections, including the trivial one-node/species case to the n-node/species cases. Part 2 considers the dynamics of important ecological modules or motifs such as populations, consumer–resource interactions, food chains, and omnivory, while Part 3 uses the logic attained from this modular or motif-based theory in order to elucidate the dynamics of whole food webs. The book argues that ecologists must make a concerted effort to understand how coupling different modules ultimately modifies flux within each individual module.