Abstract: We extend the work developed in paper I of this series, by discussing the dynamics in the collec-tive phase space in terms of a generalized Fokker-Planck equation. We are thus able to discuss fluctuations in the collective motion which were neglected in the mean field theory of paper I. In contrast with the standard derivations of Fokker-Planck equations, we do not assume quasi-equi-librium for the internal system, but rather, describe its evolution in time as it is coupled to the collec-tive system. The transport ccefTcients appearing in the Fokker-Planck equation are expressed as functionals ofthe internal density matrix. We use a coarse-grained description to study the devel-opment of the internal system as the reaction progres...