The temporal dependence of the astrophysical stochastic gravitational-wave (GW) background (SGWB) in the hecto-hertz band brings a unique avenue to identify multi-messenger signals to these sources by using coincident detection in both GW and multi-band EM signals. We developed a new analysis pipeline, \textit{Multi-messenger Cross-Correlation} (MC2) that can search for EM counterparts to the SGWB signal originating from both modeled and unmodeled sources by harnessing the nearly full-sky gamma-ray sky map. We provide an observation strategy that can be followed by current and future missions to discover EM counterparts to the weak GW signal hidden in the SGWB. We demonstrate the ability of this technique to drastically reduce the false alarm rates when involving EM multi-band analysis. This formalism aims towards advancing the multi-messenger observation frontier and improving our understanding of the population of bright SGWB sources present in the high-redshift universe and can also be applied to other messengers such as neutrinos in the future.