We apply numerical simulations at an all-atom level to investigate the switching mechanism of a [2]catenane, a prototype of a molecular machine. This system is able to switch reversibly between two different stable states, upon external stimuli, with a time scale ranging from microseconds up to milliseconds, well over the typical domain of molecular dynamics (MD) computer simulations. However, combining a strategy recently developed for investigating rare events with ordinary MD, we are able to unravel the microscopic mechanism of the conformational rearrangements involved in the switching process, including dynamical effects. Along the path that connects the product and reactant state, we find several intermediate states characterized by pi-pi stacking interactions and hydrogen bonds. Moreover, counterions interact strongly with the system in a correlated way, in agreement with recent static calculations performed on [2]rotaxanes.