Scanning tunneling microscopy (STM) is today the most powerful and versatile tool available for imaging and manipulating single molecules on surfaces. Here, we explore its ultimate limit by demonstrating the possibility of controlling sequential di-dehydrogenation of single Co-Salen molecules sublimated on Cu. In particular, we are able to explore the final products of the H-2 dissociation as well as the intermediate state, in which only one H atom is separated from the molecule. This is achieved by low-temperature STM with the dissociation induced by either point spectroscopy or in the standard constant-current mode. Crucial for the interpretation of the data is our ability to perform state-of-the-art density-functional theory simulations of both topographic and spectroscopical STM images. This work demonstrates that STM combined with theory can give access to the atomic details of a chemical reaction even when the reaction products are completely unknown.