The degradation of colors in historical paintings affects our cultural heritage in both museums and archeological sites. Despite intensive experimental studies, the origin of darkening of one of the most ancient pigments known to humankind, vermilion (α-HgS), remains unexplained. Here, by combining many-body theoretical spectroscopy and high-resolution microscopic x-ray diffraction, we clarify the composition of the damaged paint work and demonstrate possible physicochemical processes, induced by illumination and exposure to humidity and air, that cause photoactivation of the original pigment and the degradation of the secondary minerals. The results suggest a new path for the darkening process which was never considered by previous studies and prompt a critical examination of their findings.