What structure of the hair must be altered in order to create permanent haircolor changes?

Temporary and semi-permanent colors affect only the cuticle layer, unless the cuticle is highly damaged, in which case the cortex can be stained. Permanent haircolor works in the cortex by opening the cuticle layer so that color molecules can be built inside the cortex by way of oxidation, while natural pigments eumelanin and pheomelanin are broken down to contribute to a balanced final result. Interestingly enough, not all hair has a medulla, and the term "core" is something created by the advertising world to sell shampoos to an unsuspecting public who don't realize that the correct term for that part of a hair strand is "midstrand".