Hazel consults her "rules" files when she needs to perform some type of calculation. These calculations might include the cost of shipping an order, any discounts to be applied, applicable sales tax, and any surcharges on top of the merchandise.
See Hazel's overview of line-item rules for details on elements common to those rules which modify the "bottom line" of an order.
Beyond direct modification of an order total, you can use rules files to modify other aspects of Hazel as she serves your customers. A powerful example is the tweak rules file, which allows dynamic modification of actual product values.