Rabbi Yonathan asked: what is the purpose of specifying "You shall not light a fire" when the Torah already prohibits all labor on the Sabbath? If all thirty-nine categories of labor are forbidden, why single out fire?
Rabbi Yonathan traced a chain of reasoning. From "And Moses assembled" (Exodus 35:1), which introduces the Sabbath laws, one might think a person is liable only if he violates all thirty-nine categories of labor simultaneously. Perhaps transgressing just one or two would not trigger the death penalty.
(Exodus 34:21) narrows this: "From plowing and from harvesting shall you rest." This verse mentions only two labors, which might suggest you are not liable until you transgress at least two categories.
Then comes "You shall not light a fire" — a single labor, standing alone. This verse establishes that a person is liable for violating even one category of forbidden labor. Fire is just one of the thirty-nine, and the Torah singles it out to make the point: each labor is independently prohibited. Transgress one, and you are liable.
Rabbi Yonathan's analysis moves from thirty-nine to two to one, progressively narrowing the threshold for liability. The specific mention of fire was the final, decisive step — proving that every individual labor is a separate violation in its own right. You do not need to desecrate the Sabbath comprehensively to be guilty. A single forbidden act is enough.