To establish a profound connection between science and the Quran, it is crucial to acknowledge that both encompass distinct narratives about the world, each with foundational and derived layers. The central hypothesis of this study posits that the “dominant scientific narrative,” characterized by naturalism, and the “primary Quranic narrative” present not merely divergent but fundamentally opposing visions, particularly at ontological levels. The Quranic narrative posits that God is the Creator and axis of existence, with divine providence governing all affairs. The universe, particularly life and humanity, is depicted as created, ordained, and teleologically designed. Conversely, the dominant scientific narrative presents a world governed exclusively by physical causality, devoid of plan or purpose—illustrated by Darwinian evolution’s emphasis on contingency and blind processes. This opposition is most pronounced in the field of anthropology. The Quran portrays humanity with teleological creation, spiritual dimensions (nafs/rūḥ), the capacity for divine vicegerency (khilāfat Allāh), and the apprehension of divine attributes. The prevailing scientific narrative, however, adopts physicalism, denying ontological distinction between humans and nature and reducing mental and spiritual realms to material mechanisms. This significant disparity renders attempts to bridge science and the Quran either superficial or appropriative. Two strategies emerge: questioning the orthodox Quranic narrative through interpretive flexibility (beyond the scope of this article) or challenging the naturalistic narrative’s certainty—the approach advocated here. This article argues that natural theology can serve as a pivotal bridge, offering an alternative to naturalism through two functions: (1) Critique—demonstrating that cosmological and biological data do not necessarily support naturalism; and (2) Alternative Explanation—showing that evidence such as fine-tuning and biological complexity aligns more closely with a theistic, purposeful worldview. Natural theology thus eliminates atheistic interpretations from science and brings scientific discourse closer to Quranic premises (teleology, consciousness), establishing the necessary conditions for genuine synthesis between science and the Quran.