In this article, we present the results of a gap-plasmon tip-enhanced Raman scattering study of MoS2 monolayers deposited on a periodic array of Au nanostructures on a silicon substrate forming a two dimensional (2D) crystal/plasmonic heterostructure. We observe a giant Raman enhancement of the phonon modes in the MoS2 monolayer located in the plasmonic gap between the Au tip apex and Au nanoclusters. Tip-enhanced Raman mapping allows us to determine the gap-plasmon field distribution responsible for the formation of hot spots. These hot spots provide an unprecedented giant Raman enhancement of 5.6 × 108 and a spatial resolution as small as 2.3 nm under ambient conditions. Moreover, due to strong hot electron doping in the order of 1.8 × 1013 cm-2, we observe a structural change of MoS2 from the 2H to the 1T phase. Owing to the very good spatial resolution, we are able to spatially resolve those doping sites. To the best of our knowledge, this is the first time reporting of such a phenomenon with nm spatial resolution. Our results will open the perspectives of optical diagnostics with nanometer resolution for many other 2D materials.