Modern physics has achieved remarkable success by describing reality in terms of particles, states, and information bits. Yet recent developments in quantum matter, unconventional superconductivity, and topological computation increasingly suggest that a purely particle-centric framework may not be the most natural organizing description, but rather a convenient approximation. This work proposes an ontological reframing—from It from Bit to It from Wave—in which physical reality is understood as persistent, collective wave processes characterized by phase continuity, nonlocal coherence, and history-bearing relations. Within this framework, quasiparticles—including magnons, phonons, plasmons, and anyons—are reinterpreted not as entities, but as stable collective excitation modes: enduring patterns of interacting waves sustained by a medium. Building on this shift, localization is reinterpreted as the breakdown of wave connectivity, while delocalization corresponds to the restoration of global phase coherence. Superconductivity is reformulated not as a special property of paired particles, but as a phase-continuous, delocalized regime in which dissipation is not eliminated but reorganized into collective phase dynamics—naturally suggesting disorder-tolerant and non-BCS-like superconducting behavior. Extending the same ontology to computation, we argue that quantum computation is fundamentally history-based rather than state-based. Information is encoded not primarily in localized bits or qubits, but in the topological and phase-coherent histories of wave evolution, where robustness arises from nonlocal distribution rather than active error suppression. Crucially, this framework motivates previously under-emphasized physical observables—such as phase continuity length, history coherence time, degree of nonlocality, and dissipation-reorganized coherence—as primary descriptors of relational persistence. Rather than introducing new equations, this work reorganizes interpretation across domains and specifies concrete experimental and theoretical directions by asking which wave relations persist, under what constraints, and for how long. This paper constitutes the ontological foundation of the “It from Wave” research program. A complementary interpretive study examines the historical and conceptual shift from particle transport to phase propagation in electrical conduction, while a minimal physical model demonstrates how information and conduction can arise from phase-coupled dynamics without particle motion. Together, these works articulate a unified framework in which phase relations, history, and nonlocal coherence are treated as physically primary. This paper forms part of a conceptual trilogy exploring the transition from a Machine OS to a Life OS through an It from Wave perspective. The trilogy consists of:(i) a foundational conceptual work reframing information, existence, and generation beyond the It from Bit paradigm;(ii) a minimal theoretical study addressing nonlinear generative time, resonance, and feedback dynamics; and(iii) an applied interpretation engaging recent cosmological observations, including extreme intracluster heating in the early universe. While each paper is self-contained, together they articulate a unified framework in which reality is understood as a resonant, generative process rather than a sequential, machine-like assembly.