To realize large-scale socially embedded multiagent systems, this paper proposes a new system design methodology towards society-centered design. We have already developed the scenario description language Q, which describes interaction protocols that link agents to society. Using the virtual space called FreeWalk, wherein agents behave under given Q scenarios, we explain each step of society-centered design. The process consists of participatory simulation, where agents and human-controlled avatars coexist in virtual space to jointly perform simulations, and augmented experiment, where an experiment is performed in real space by human subjects, scenariocontrolled agents, and human extras. As an application of society-centered design, we are working on mega navigation, where millions of humans and socially embedded agents collaborate for developing services for traffic control, crisis management and large-scale event navigation.