Over the last few decades, conical intersections (CoIns) have grown from theoretical curiosities into common mechanistic features of photochemical reactions, whose function is to funnel electronically excited molecules back to their ground state in regions where the potential energy surfaces (PESs) of two electronic states become degenerate. Analogous to transition states in thermal chemistry, CoIns appear as transient structures providing a kinetic bottleneck along a reaction coordinate. However, such a bottleneck is not associated with the probability of crossing an energy barrier but rather with an excited state decay probability along a full “line” of transient structures connected by non-reactive modes, the intersection space (IS). This article will review our understanding of the factors controlling CoIn mediated ultrafast photochemical reactions, taking a physical organic chemist approach by discussing a number of case studies for small organic molecules and photoactive proteins. Such discussion will be carried out by first introducing the “standard” one-mode model based on Landau–Zener (LZ) theory to describe a reactive excited state decay event intercepting, locally, a single CoIn along a single direction, and then by providing a modern perspective based on the effects of the phase matching of multiple modes on the same local event, thus redefining and expanding the description of the excited state reaction coordinate. The direct proportionality between the slope (or velocity) along one mode and decay probability at a single CoIn is a widely applied fundamental principle that follows from the LZ model, yet it fails to provide a complete understanding of photochemical reactions whose local reaction coordinate changes along the IS. We show that in these situations, in particular by focussing on rhodopsin double bond photoisomerization, it is mandatory to consider additional molecular modes and their phase relationship approaching the IS, hence providing a key mechanistic principle of ultrafast photochemistry based on the phase matching of those modes. We anticipate that this qualitative mechanistic principle should be considered in the rational design of any ultrafast excited state process, impacting various fields of research ranging from photobiology to light-driven molecular devices.