The Muon $g-2$ Experiment at Fermilab aims to measure the muon magnetic moment anomaly, $a_{\mu} = (g-2)/2$, with a final accuracy of 0.14 parts per million (ppm). A $3.1$-GeV muon beam is injected into a storage ring of $14\,$m diameter, in the presence of a $1.45\,$T magnetic field. The anomaly $a_\mu$ can be extracted by accurately measuring the anomalous muon spin precession frequency $\omega_a$, based on the arrival time distribution of decay positrons observed by $24$ calorimeters, and the magnetic field. In 2023, the experiment published its second result based on the two datasets Run-2 and Run-3, reaching the unprecedented sensitivity of $0.21\,$ppm --- a factor $\sim2.2$ improvement since its first result published in 2021, based on the first dataset (Run-1). In this paper, we will focus on the measurement of the $\omega_a$ frequency, describing the techniques and major sources of systematic uncertainty in the 2023 publication, and outlining the improvements since the 2021 result. We will also cover the status of the ongoing $\omega_a$ analysis for the last three datasets, collected from 2020 to 2023, along with the projected uncertainties on the final Muon $g-2$ measurement at Fermilab.