It is the general premise of this paper that multi-scale modeling with multi-physics balance and constitutive representations of the thermal, electrochemical, mechanical, and chemical phenomena that make a fuel cell work is an essential foundation for design and manufacturing. It is further claimed that such modeling enables a systems-to-science engineering approach that will accelerate technology greatly, reduce cost, improve durability, and bring fuel cell systems to life in our society. It is the objective of this paper to identify and provide a few foundation stones of understanding for such an engineering foundation for fuel cell technology, especially that part of the foundation that relates to multi-scale modeling of materials.