Transit has a crucial role in the economics and the society of urban conurbations. To drive its evolution toward environmental sustainability and better user-centric performance, we envision optimally integrating new (Auto- mated) Mobility on Demand and classic Fixed Route Transit. This calls for a deep re-disign of transit. The goal of MuTAS (Latin form of "to mutate") is to provide a general and efficient methodology to guide such a re-design. Our interdisciplinary approach combines Transportation Science, Computer Science and Artificial Intelligence. We jointly design the routes and the frequencies of Fixed-Route Transit and decide in which regions and time of the days Mobility on Demand will operate, as well as its fleet size.