To make things simple for the audience, the result of this is: kanji is taken for the meaning value only, as usual, and two parallel sets of rules were developed for the pronunciation: the on'yomi that plots to the Chinese pronunciation(s) of the kanji, and the kun'yomi that plots to the indigenous Japanese pronunciation(s) for the same idea.
— Alternate Character Reading from allthetropes.fandom.com
Here the use of plot relies on one of its secondary definitions, "to locate (a point) by means of coordinates." This construction also relates to one definition of plot as a noun, referring to "a measured piece of land."
There's a spatial metaphor underlying this use of plot. Another way to say this might be "map," or more precisely "map onto" or "map to." Instead of "map," one could also use "point" or "trace" or something similar. Along with plot, these examples all indicate a connection between distinct but related things--in this case, meaning and pronunciation, where two sets of pronunciation rules develop in "parallel," as the author says. To expand on the spatial metaphor, you might say that the pronunciations begin at a single point, the "meaning value" or the "idea", and follow divergent paths, or plots. These paths consist of language use, which changes over time and varies by geographical location. The single "meaning value" or "idea" takes divergent paths to arrive at the different points we see now, i.e. different pronunciations of the same symbols.