The origin of life on prebiotic Earth is one of science’s greatest mysteries. Traditional approaches to the search for answers often rely on isolated universe models that fail to account for the open, far-from-equilibrium conditions of natural systems. Such limitations might be hindering progress in understanding the thermodynamic processes that drive the emergence of life. This theoretical study presents the second installment in a series exploring a thermodynamic theory of heat transformation and its role in the development of prebiotic Earth. Building on the foundational concepts introduced in Part I, this work focuses on the dissipation of heat through chemical systems, examining chemical dissipative structures (CDSs) and their ability to store and release energy through endothermic and exothermic reactions. By modeling CDSs as heat engines, the paper investigates the interplay between entropy, order, and complexity, revealing how energy storage and transformation drive the generation of complexity. The analysis extends to the networking of gravitational dissipative structures (GDSs) covered in Part I and CDSs, demonstrating how these networks facilitate the transfer of stored energy and contribute to the development and growth of prebiotic chemosystems. The findings suggest that the dominance of endothermic synthesis reactions in CDSs plays a critical role in the generation of complexity, resilience, and mutualism, ultimately shaping the conditions for the emergence of life. This work provides a novel perspective on the thermodynamic underpinnings of prebiotic evolution, offering insights into the relationship between energy, information, and the development of complex systems.