Modern science is commonly understood to have advanced by methodologically excludingtheology, metaphysics, andsubjectiveelementsinordertosecureobjectivity, universality, and reproducibility. While this exclusion has yielded remarkable empiricalandtechnologicalsuccesses, ithasalsogeneratedpersistentandfundamental difficulties, including the observer problem in quantum theory, the failure to unify quantummechanicsandrelativity,andtheinabilitytoaccountformeaning, subjectivity, and relational coherence within scientific theory itself. The exclusion of subjectivity appeared, in the short term, to safeguard scientific rigor, yet it resulted in leaving the very ontological basis of observation itself theoretically unaddressed. This paper argues that these difficulties do not arise from technical limitations or incomplete theories, but from a deeper structural operation performed during the formation of modern knowledge. Specifically, it contends that what was systematically removed from theoretical frameworks was not God as an object of belief, but God as an absolute subjectivity that had functioned as a foundational point of reference for knowledge. Following this removal, subjectivity was relegated to an unresolved residue within philosophy and entirely excluded from science, while relational structures came to be treated as secondary or eliminable. As a result, modern epistemic frameworks have become almost entirely dependent on binary oppositions—such as subject/object, law/phenomenon, and observer/system—while implicitly containing a structure that cannot be theoretically closed without presupposing a hidden third term. Through a historical and structural analysis spanning theology, philosophy, and physics,thispaperdemonstratesthattheobserverproblemisnotaquantum-mechanical anomaly, but a necessary consequence of this exclusionary structure. It further shows that, although quantum theory implicitly reintroduced relational structures from its inception, it lacked the conceptual language required to define them explicitly. In response to this structural deficiency, the paper introduces the concept of O3, not as a new ontological entity, but as a recovered structural position. O3 designates a relational locus generated when multiple terms enter into relation, and serves as a minimal conceptual device for making explicit the conditions tacitly presupposed by modern knowledge—without reverting to theological claims or abandoning scientific rigor. In conclusion, this paper argues that humanity now stands at a clear point of bifurcation: whether to continue operating within a framework that systematically excludes the conditions of its own intelligibility, or to reconstruct a new structure of knowledge that explicitly incorporates subjectivity and relation. The consequences of this choice extend beyond any single discipline and will shape the future trajectory of human knowledge itself.