This work aims to address unresolved questions in physics through a coherent framework built upon a unified understanding of the interdependence of gravity, quantum physics, and classical mechanics, ultimately leading to the emergence of physical reality. The approach builds upon Madelung’s quantum hydrodynamic representation, extending it by incorporating stochastic perturbations from gravitational background noise (GBN). The consequent stochastic quantum hydrodynamics model (SQHM) bridges the quantum and classical domains, unveiling a natural quantum-to-classical coexistence. For the first time, the model provides a theoretical foundation for the Lindemann constant and can be experimentally tested via a photon entanglement experiment. It also accurately reproduces the experimental data for the fluid–superfluid transition in helium. The framework resolves long-standing theoretical conflicts between quantum mechanics and classical mechanics, addresses the EPR paradox, and provides novel insights into the emergence of flowing time in 4-D spacetime and the evolution of the universe, potentially accommodating free will. The proposed framework highlights the inadequacy of both deterministic laws and a purely measure-dependent conception of reality governed by unpredictable probabilistic evolution.