The paper presents a coherent framework for the architecture of a Universal quantum computer (UQC) under the hypothesis that the Universe represents a complex cybernetic system (CCS). For this purpose, the author poses some questions that such an architecture should answer and construct a persuasive account of UQC’s ontology by defining and postulating main concepts, categories, and their relationships. The proposed account permits the UQC’s functionality to agree with fundamental concepts of computer science, complex systems theory, and all known laws of nature. Moreover, it pretends to answer some science puzzles such as the quantumness of 3D reality, black matter, and black energy.