Intrinsic ripples in freestanding graphene have been exceedingly difficult to study. Individual ripple geometry was recently imaged using scanning tunnelling microscopy, but these measurements are limited to static configurations. Thermally-activated flexural phonon modes should generate dynamic changes in curvature. Here we show how to track the vertical movement of a one-square-angstrom region of freestanding graphene using scanning tunnelling microscopy, thereby allowing measurement of the out-of-plane time trajectory and fluctuations over long time periods. We also present a model from elasticity theory to explain the very-low-frequency oscillations. Unexpectedly, we sometimes detect a sudden colossal jump, which we interpret as due to mirror buckling. This innovative technique provides a much needed atomic-scale probe for the time-dependent behaviours of intrinsic ripples. The discovery of this novel progenitor represents a fundamental advance in the use of scanning tunnelling microscopy, which together with the application of a thermal load provides a low-frequency nano-resonator.