Substance magic is the second most common type among the Chosen, with a little under one-fifth of the population being either solely or primarily of this type.

While both Element and Substance magic deal with the control of matter, the fundamental difference between them is that while elementalists control its movements in the aggregate, alchemists instead control its building blocks: to be more precise, their powers extend to the manipulation of first-generation fermions: up and down quarks, electrons, and electron neutrinos. (They could probably also, in theory, manipulate the equivalent antiparticles, but since in a matter-rich environment those wouldn't last very long, the point's probably moot for the foreseeable future.)

Since electron neutrinos interact little with ordinary matter, and since they may indeed change into other types of neutrinos, alchemists can “feel” them but not do anything useful with them. Some have likened it to the factor of air in working with one's hands; while the hand moves through the air, holding something or wielding a tool, this does not appreciably affect the motion of either hand or air. (Air elementalists, it must be said, often find this analogy hugely amusing.)

As for up and down quarks, alchemists cannot control them individually - the effort required to separate them is too great - but can control the particles they make up: protons and neutrons. Together with electrons, these make up atoms, and alchemists therefore have wide leeway in their ability to manipulate atoms: to combine them, separate them from each other, and to alter them. It should be understood that alchemists are not consciously aware of the different particles, especially not on the individual level; they alter substances by what they describe as “feel” or “taste”.

The least strenuous tasks for an alchemist involve the movement of electrons, which are shared and moved relatively easily between atoms. In practical terms, this covers the realm of classical chemistry: the forming and breaking of chemical bonds, the building and restructuring of molecules, and the magical catalysis of reactions. (It also, in an overlap with energists' Spark magic, allows the formation of electrical charges and currents, though alchemists cannot do this on nearly the same scale.)

While a certain amount of the alchemist's mana must always be used to cause a chemical reaction, how much depends on the type of reaction, since the mana effectively substitutes for the reaction's energy requirements. Naturally endothermic reactions, which normally draw heat from their surroundings, require more mana, while exothermic reactions, which generate heat, can require a bare minimum (the alchemist is not, however, able to draw the generated heat back in to reuse as mana; only an energist can do that).

The manipulation of protons and neutrons can be somewhat more taxing, in that more effort is involved in overcoming the strong nuclear force to separate protons and neutrons from the nucleus, and also more dangerous, since protons and neutrons freed from a nucleus - singly or in groups - are the source of several kinds of radiation. But it's also more valuable, because it's through this process that an alchemist is capable of transmutation: the changing of one element or isotope into another.

Alchemists cannot move or shape matter except on very small scales, but can initiate changes over a somewhat wider area. An alchemist can, for example, change water to ice through a restructuring of its molecules, and in the same way can turn rock into sand or back again. (A change that is not stable in the environment in which it happens will eventually be reversed, however; an alchemist could in theory freeze a whole pond, but the amount of effort needed to keep it frozen would soon become unbearable).

Unlike elementalists, alchemists have no inherent magical restriction on which kinds of materials they can affect; the difference between one who simply crumbles stone into sand and one who turns lead into gold is simply a matter of practice and sensitivity. For this reason - and because applying Substance magic of any sort to large quantities of material is effort-intensive - alchemists in the Citadel usually at least begin their careers in workshops with other alchemists, where they have opportunities to learn from their elders and hone their own skills. Those deciding to specialize in some low-quantity, high-value transformation may strike out on their own, but rising to a management-like position within the workshop is also possible. Alchemists often work closely with elementalists; the latter can bring the former base ingredients and raw mass to work with, and others can shape what the alchemists produce. The Citadel cannot be said to be a post-scarcity society, but it's because of the alchemists that many things are much less scarce than they should be.

Another way in which alchemists differ from elementalists is that their powers can be used on organic materials as well as on inorganic ones. A pure alchemist attempting to cause chemical changes in an actual living being is likely to cause something harmful, if not actively fatal; any organism is such a complicated collection of chemical reactions that it's too easy to disrupt one. But they will often have better luck with organic byproducts; in the Citadel, alchemists are sought after to improve the composition of soils and the durability of fabrics, and alchemist-made dyes are among the most sought-after.

Those individuals who have two magic types often find that Substance magic, with its extreme versatility, meshes well with their other powers. Elementalist-alchemists can either produce large amounts of the element they control, or gather large amounts of it to produce something else from it. Shifter-alchemists have an uncanny sense of their own body chemistry, and can modify themselves in ways that pure shifters can't. And lifegiver-alchemists have the potential to sculpt living beings to an unparalleled degree.