This dissertation presents a hierarchical, hybrid point of view to the control of large-scale systems. The analysis is based on a new hybrid dynamical system formulation that allows for the modelling of large scale systems in a modular fashion. Three problems are addressed: controller design, closed loop performance verification and the extension of system autonomy. A control scheme based on semi-autonomous agent operation is first proposed. An algorithm, using ideas from game theory, is presented to produce continuous controllers for hierarchical, hybrid designs. A discussion of design issues involving controller autonomy is presented. The emphasis is on hybrid effects. The hierarchical and hybrid issues involved in the design of a fault tolerant control scheme are investigated. The study concludes with a case study on the application of the proposed techniques to the control of an automated highway system (AHS).