Context. Betelgeuse, a red supergiant star of semi-regular variability, reached a historical minimum brightness in February 2020, known as the Great Dimming. Even though the brightness has returned to the values prior to the Great Dimming now, it continues to exhibit highly unusual behavior. Aims. Understanding the long-term atmospheric motions of Betelgeuse and its variability could be a clue to the nature of the Great Dimming and the mass-loss process in red supergiants. Our goal is to study long-term dynamics of the photosphere, including during the Great Dimming. Methods. We applied the tomographic method, which allows different layers in the stellar atmosphere to be probed in order to reconstruct depth-dependent velocity fields. The method is based on the construction of spectral masks by grouping spectral lines from specific optical depths. These masks are cross-correlated with the observed spectra to recover the velocity field inside each atmospheric layer. Results. We obtained about 2800 spectra over the past 15 yr that were observed with the STELLA robotic telescope in Tenerife. We analyzed the variability of five different layers of Betelgeuse’s photosphere. We found phase shift between the layers, as well as between the variability of velocity and photometry. The time variations of the widths of the cross-correlation function reveal propagation of two shockwaves during the Great Dimming. For about 2 yr after the dimming, the timescale of variability was different between the inner and outer photospheric layers. By 2022, all the layers seemingly started to follow a similar behavior as before the dimming, but pulsating with higher frequency corresponding with the first overtone. Conclusions. The combination of the extensive high-resolution spectroscopic data set with the tomographic method revealed the variable velocity fields in the photosphere of Betelgeuse, for the first time in such detail. We were also able to find new insights related to the Great Dimming event and its aftermath, namely the discovery of another shockwave and the subsequent rearrangement of the photosphere. Our results demonstrate that powerful shocks are the triggering mechanism for episodic mass-loss events, which may be the missing component to explain the mass-loss process in red supergiants.