Smoky quartz owes its color to a defect, not an impurity in the ordinary sense. Trace aluminum atoms substitute for silicon here and there in the quartz lattice, and on their own they do nothing visible. Expose the crystal to natural background radiation over geological time, or to a deliberate dose of gamma rays or an electron beam in a laboratory, and those aluminum sites trap a freed electron and become color centers, absorbing light in a way that reads to the eye as smoky brown through grey to nearly black. It is close cousin to the mechanism behind amethyst's purple, which uses iron rather than aluminum as the trapped defect, and the two effects can be reversed or combined by heat: heating smoky quartz can drive the color back out, and the two colors sometimes occur zoned in the same crystal.
That mechanism has one large practical consequence for anyone buying the stone today. Because the color comes from irradiation rather than from a rare element locked permanently into the mineral, it is straightforward to reproduce artificially, and the gem trade does so routinely: much of the "smoky quartz" sold in jewelry and mineral shops is ordinary clear quartz, or occasionally amethyst, that has been deliberately irradiated to darken it, a treatment that is stable, widely accepted in the trade, and not always disclosed. Natural, untreated smoky quartz still occurs and is mined in quantity, historically and still today around Scotland's Cairngorm Mountains, but distinguishing a naturally darkened stone from a treated one usually requires laboratory testing rather than inspection by eye, since both are, at the atomic level, the same defect doing the same job.