Will a large complex system be stable? This question, first posed by May in 1972, captures a long standing challenge, fueled by a seeming contradiction between theory and practice. While empirical reality answers with an astounding yes, the mathematical analysis, based on linear stability theory, seems to suggest the contrary - hence, the diversity-stability paradox. Here we settle this dichotomy, by considering the interplay between topology and dynamics. We show that this interplay leads to the emergence of non-random patterns in the system's stability matrix, leading us to relinquish the prevailing random matrix-based paradigm. Instead, we offer a new matrix ensemble, which captures the dynamic stability of real-world systems. This ensemble helps us analytically identify the relevant control parameters that predict a system's stability, exposing three broad dynamic classes: In the asymptotically unstable class, diversity, indeed, leads to instability a la May's paradox. However, we also expose an asymptotically stable class, the class in which most real systems reside, in which diversity not only does not prohibit, but, in fact, enhances dynamic stability. Finally, in the sensitively stable class diversity plays no role, and hence stability is driven by the system's microscopic parameters. Together, our theory uncovers the naturally emerging rules of complex system stability, helping us reconcile the paradox that has eluded us for decades.