An important goal of mechanistic studies of chemical reactions is to understand how atoms in reacting molecules behave at the molecular level. Toward this goal, full quantum mechanical molecular dynamics (MD) simulations, which employed the recently developed fragment molecular orbital (FMO)-MD method, were carded out for the hydrolysis of the methyl diazonium ion in water. The simulations illustrated for the first time how the solvent water molecules participate in the reaction and how the C-N bond cleavage and O-C bond formation take place during the reaction. It was revealed that this typical S(N)2 reaction does not always proceed through the energetically favorable synchronous pathway, but that it shows mechanistic diversity.