We consider the evolution of the unstable periodic orbit structure of coupled chaotic systems. This involves the creation of a complicated set outside of the synchronization manifold (the emergent set). We quantitatively identify a critical transition point in its development (the decoherence transition). For asymmetric systems we also describe a migration of unstable periodic orbits that is of central importance in understanding these systems. Our framework provides an experimentally measurable transition, even in situations where previously described bifurcation structures are inapplicable.