Abstract: A method of generating a microbial deactivation fluid to circulate through an apparatus that has a decontamination chamber for holding medical instruments and devices, comprising the steps of: (a) providing a first compartment and a second compartment in the circulation system; (b) providing a chemical reagent in the first compartment and a builder composition in the second compartment; (c) causing a fluid to flow through the second compartment to mix with the builder composition to create an alkaline fluid; (d) when the alkaline fluid has reached a predetermined pH level, causing the alkaline fluid to flow through the first compartment to mix with the chemical reagent to dissolve the chemical reagent to generate a microbial deactivation fluid; and (e) continuing steps (c) and (d) to continue the generation of the microbial deactivation fluid.