The direction of a note's stem is based on the number of voices in its context. If there is one voice, notes written above the middle staff line (B in G-Clef) are down-stem, whereas notes written below the middle staff line are up-stem. If there are two voices, the upper voice takes up-stem notes, and the lower voice takes down-stem notes. It is therefore important to determine how many voices there are.
Consider a phrase with two voices, spreading over multiple bars. In one of the bars, the upper voice is silent, so in fact, the bar consists only of the lower voice. Do we consider this bar to contain only one voice, since the upper voice is silent, and then the notes should be noted based on the one voice rules, or we consider it to contain two voices, and the notes should be down-stem (with a full bar rest for the upper voice)? In other words, is the number of voices determined relative to the bar or to the phrase?
To illustrate, option #1: