A detailed experimental and theoretical investigation of the dynamics leading to fragmentation of doubly ionized molecular thiophene is presented. Dissociation of double-ionized molecules was induced by S 2p core photoionization and the ionic fragments were detected in coincidence with Auger electrons from the core-hole decay. Rich molecular dynamics was observed in electron-ion-ion coincidence maps exhibiting ring breaks accompanied by hydrogen losses and/or migration. The probabilities of various dissociation channels were seen to be very sensitive to the internal energy of the molecule. Theoretical simulations were performed by using the semiempirical self-consistent charge-density-functional tight-binding method. By running thousands of these simulations, the initial conditions encountered in the experiment were properly taken into account, including the systematic dependencies on the internal (thermal) energy. This systematic approach, not affordable with first-principle methods, provides a good overall description of the complex molecular dynamics observed in the experiment and shows good promise for applicability to larger molecules or clusters, thus opening the door to systematic investigations of complex dynamical processes occurring in radiation damage.