Hierarchical clause structure is an important feature of most theories of grammar. While it has been an indispensable part of formal syntactic theories, functional theories have more recently discovered for themselves a ‘layered structure of the clause’. A major focus of the current discussion on semanto-syntactic clause structure is the hierarchical ordering of grammatical categories such as tense, aspect and modality. However, there are very few empirical studies yet to provide systematic evidence for presumably universal hierarchical structures. This book presents a systematic corpus-based study of the semantic and morphosyntactic interaction of modality with tense, aspect, negation, and modal markers embedded in subordinate clauses. The results are critically compared with extant theories of hierarchies of grammatical categories, including those in Functional Grammar, Role and Reference Grammar, and the Cartography of Syntactic Structures. Also provided is an extensive description of the expression of modality and related categories in Modern Japanese.