We present an in-depth analysis of the LISA Pathfinder differential acceleration performance over the entire course of its science operations, spanning approximately 500 days. We find that: 1) the evolution of the Brownian noise that dominates the acceleration amplitude spectral density (ASD), for frequencies $f\gtrsim 1\,\text{mHz}$, is consistent with the decaying pressure due to the outgassing of a single gaseous species. 2) between $f=36\,μ\text{Hz}$ and $1\,\text{mHz}$, the acceleration ASD shows a $1/f$ tail in excess of the Brownian noise of almost constant amplitude, with $\simeq 20\%$ fluctuations over a period of a few days, with no particular time pattern over the course of the mission; 3) at the lowest considered frequency of $f=18\,μ\text{Hz}$, the ASD significantly deviates from the $1/f$ behavior, because of temperature fluctuations that appear to modulate a quasi-static pressure gradient, sustained by the asymmetries of the outgassing pattern. We also present the results of a projection of the observed acceleration noise on the potential sources for which we had either a direct correlation measurement, or a quantitative estimate from dedicated experiments. These sources account for approximately $40\%$ of the noise power in the $1/f$ tail. Finally, we analyze the possible sources of the remaining unexplained fraction, and identify the possible measures that may be taken to keep those under control in LISA.