This paper presents the second phase of the EMS (Excitation-Mass Structure) theory, systematizing the microscopic structure of matter, quantum mechanical behavior, and nuclear forces (strong and weak interactions) based on a singular geometric origin. In con- trast to the ”fluidic spacetime” established in Phase 1, this paper introduces scale-dependent ”Viscoelasticity” and ”Elasto-plasticity” to the Background Field (FEF) based on the principle of ”Hierarchical Similarity.” We define elementary particles as topological defects (dislocations and disclinations) in the lattice, unifying the derivation of proton mass and confinement potential (elastic regime) and weak boson masses (plastic yield regime). Fur- thermore, we propose a realist reconstruction of quantum mechanics using a dual-structure model of particle (core) and associated wave (guide), eliminating the reliance on probabilistic interpretations.