Migrating birds fly thousand miles and more, often without visual cues and in treacherous windsyet keep direction. They employ for this purpose, apparently, as a powerful navigational tool the photoreceptor protein cryptochrome to sense the geomagnetic field. The unique biological function of cryptochrome must arise from the photoactivation reaction occurring in the protein: exposure to blue light results in electron transfer to a flavin pigment co-factor, leading to formation of an electron spin-entangled pair of radicals. Theoretical and experimental studies established long ago that such radical pairs, indeed, can act as a magnetic compass. The photo-reaction pathway in cryptochrome is not fully resolved yet. We employ ab initio quantum chemistry and classical all-atom MD simulations for Arabidopsis thaliana cryptochrome to determine how the radical pair is formed, becomes stabilized through proton transfer, and how it decays back to the protein's resting state.