The general formalism of an extended quantum theory of atoms in molecules (QTAIM) dealing with the multi-component quantum systems, composed of various types of quantum particles, is disclosed in this contribution. This novel methodology, termed as the multi-component QTAIM (MC-QTAIM), is able to deal with non-adiabatic ab initio wavefunctions extracting atoms in molecules quantifying their properties. It can also be applied to elucidate the AIM structure of exotic species and bound quantum systems consisting of fundamental elementary particles like positrons and muons. The formalism is based on the previously disclosed density combination idea that is extended to derive the multi-component subsystem hypervirial theorem as well as the extended subsystem energy functional. Through the extended subsystem variational procedure, inspired from Schrodinger’s original variational principle, the surface terms containing the flux of the current property densities are derived. Accordingly, the extended Gamma field is introduced during this variational procedure that is used as the basic scalar field in the topological analysis yielding atoms in molecules and their real space boundaries. The Gamma field is central to the MC-QTAIM, replacing the usual one-electron density employed in the orthodox QTAIM and corresponding topological analysis. Through the multi-component hypervirial theorem, various regional theorems are derived which are then used to quantify the mechanical properties of atoms in molecules; these include the force, virial, torque, power, continuity and current theorems. In order to demonstrate the capability of the formalism, isotopically asymmetric hydrogen molecules, HD, HT and DT as well as YX systems (Y = 6Li, 7Li; X = H, D, T) composed of electrons and two different nuclei, all treated equally as quantum waves instead of clamped particles, are analyzed within context of the MC-QTAIM. The resulting computational analysis demonstrates that the MC-QTAIM is able to yield reasonable topological structures similar to those observed previously for diatomic species within context of the orthodox QTAIM. The asymmetrical nature of these species, inherent in their non-Born–Oppenhiemer wavefunctions, manifests itself clearly in the MC-QTAIM analysis yielding two distinguishable atomic basins with different properties. These differences are rationalized generally by the observed electron transfer from one basin to the other. Finally, some possible future theoretical extensions are considered briefly.