The sequentially plasma activated bonding of silicon wafers has been investigated to facilitate the development of chemical free, room temperature and spontaneous bonding required for nanostructure integration on the wafer scale. The contact angle of the surface and the electrical and nanostructural behavior of the interface have been studied. The contact angle measurements show that the sequentially plasma (reactive ion etching plasma followed by microwave radicals) treated surfaces offer highly reactive and hydrophilic surfaces. These highly reactive surfaces allow spontaneous integration at the nanometer scale without any chemicals, external pressure or heating. Electrical characteristics show that the current transportation across the nanobonded interface is dependent on the plasma parameters. High resolution transmission electron microscopy results confirm nanometer scale bonding which is needed for the integration of nanostructures. The findings can be applied in spontaneous integration of nanostructures such as nanowires/nanotubes/quantum dots on the wafer scale.