A novel mechanism of hybrid assembly of molecules on surfaces is proposed stemming from interactions between molecules and on-surface metal atoms which eventually got trapped inside the network pores. Based on state-of-the-art theoretical calculations, we find that the new mechanism relies on formation of molecule-metal atom pairs which, together with molecules themselves, participate in the assembly growth. Most remarkably, the dissociation of pairs is facilitated by a cooperative interaction involving many molecules. This new mechanism is illustrated on a low coverage Melamine hexagonal network on the Au(111) surface where multiple events of gold atoms trapping via a set of so-called ''gate'' transitions are found by kinetic Monte Carlo simulations based on transition rates obtained using ab initio density functional theory calculations and the nudged elastic band method. Simulated STM images of gold atoms trapped in the pores of the Melamine network predict that the atoms should appear as bright spots inside Melamine hexagons. No trapping was found at large Melamine coverages, however. These predictions have been supported by preliminary STM experiments which show bright spots inside Melamine hexagons at low Melamine coverages, while empty pores are mostly observed at large coverages. Therefore, we suggest that bright spots sometimes observed in the pores of molecular assemblies on metal surfaces may be attributed to trapped substrate metal atoms. We believe that this type of mechanism could be used for delivering adatom species of desired functionality (e.g., magnetic) into the pores of hydrogen-bonded networks serving as templates for their capture. Recent STM studies of hydrogen-bonded molecular assemblies on crystal surfaces have resulted in significant progress in our ability to create and modify these selforganized networks [1][2][3][4][5][6][7][8][9][10]. The motivation for much of this research is the premise that control of the porous network structure can be achieved by modifying the component molecules which may result in changes to the size and shapes of the pores [4,11]. The pores can be used as a template to host foreign species of required functionality [12]. However, this template approach has intrinsic limitations due to the strict requirements concerning the relative sizes of the pores and guest species. Violation of these requirements may result in defects, such as more than one functional unit per pore, which might compromise the performance of the network. For this reason it is extremely important to develop alternative kinetic pathways, which ensure defect-free fabrication of functional surface networks.In this Letter we describe such a kinetic pathway based on the co-assembly of a network constructed from an organic molecule and an atomic species. We show that there are two key factors in this process that ensure delivery of no more than one atom per pore. First, atomic-molecular dimers need to be formed to take part in the network formation. Second, there is a requirement of a specific...