Understanding how crystals nucleate is a key goal in materials, biomineralization, and chemistry. Many inorganic materials are known to crystallize "nonclassically" by particle attachment. However, a molecular-level understanding of small molecule crystallization is hampered by the complexity and time scales of nucleation events, which are often too large to simulate and too small to observe. Here, by combining unbiased molecular dynamics simulations and in situ experiments, we uncover this nucleation "blind spot" to elucidate the nonclassical crystallization mechanism of the nucleobase, guanine. The multi-step nucleation process begins with stacked guanine clusters, whose H-bonding and π-stacking arrangement progressively orders as they attach into nanoscopic fibers (observed by simulation and electron microscopy), partially ordered bundles, and finally, 3D periodic crystals. This work provides a foundation for understanding how organisms exquisitely control the formation of guanine and other molecular crystals, which are used ubiquitously in biology as optical and nitrogen-storage materials.