This chapter offers a comprehensive analysis of the complex relationship between metaphysics and dialectics during the formative period of modern science, highlighting the significant shift from ancient and medieval philosophical conceptualisations to contemporary empirical inquiry. It analyses how ancient and medieval philosophy, were increasingly challenged by emerging scientific disciplines that prioritised empirical evidence. By critically examining the metaphysical underpinnings inherent in both rationalism and empiricism, the chapter uncovers the conflicts and paradoxes that arose with the rise of modern scientific thought. It also explores the crisis that traditional metaphysical systems experienced in response to rapid scientific advances and the intellectual transformations of the Enlightenment. This crisis marked a crucial shift, as established metaphysical frameworks were progressively undermined, paving the way for new dialectical approaches in both philosophy and science.