I have finally picked up RtL and just finished reading the rule book and noticed it didn't explain one set of chits. Its a small oval black token with a blue, what looks to be a flame, in the center, Can someone please enlighten me on what the use of this token is.

You mean the comet tokens? These are used in the Ascension plot, once the Overlord has erected the four temples. Read the plot card entitled "The Harbinger Approaches" for instructions on how to use them.

The rulebook in general doesn't give you any detailed information on the plots in RTL. The info is all in the cards associated with each plot.

Zealot is rioght.

there are a lot of token in RTL that you will use only with specific plot o situations, so many of them never leave the box in a rtl game