Nanometer-sized gaps between plasmonically coupled adjacent metal nanoparticles enclose extremely localized optical fields, which are strongly enhanced. This enables the dynamic investigation of nanoscopic amounts of material in the gap using optical interrogation. Here we use impinging light to directly tune the optical resonances inside the plasmonic nanocavity formed between single gold nanoparticles and a gold surface, filled with only yoctograms of semiconductor. The gold faces are separated by either monolayers of molybdenum disulfide (MoS2) or two-unit-cell thick cadmium selenide (CdSe) nanoplatelets. This extreme confinement produces modes with 100-fold compressed wavelength, which are exquisitely sensitive to morphology. Infrared scattering spectroscopy reveals how such nanoparticle-on-mirror modes directly trace atomic-scale changes in real time. Instabilities observed in the facets are crucial for applications such as heat-assisted magnetic recording that demand long-lifetime nanoscale plasmonic structures, but the spectral sensitivity also allows directly tracking photochemical reactions in these 2-dimensional solids.