This paper develops a systematic theory of higher-order variations, duality, descent hierarchies, and their discrete algebraic realizations for difference equations. Unlike previous approaches that treat difference operators as discretized derivatives, we build the theory from first principles within the algebra of shift operators. We define higher-order variation operators in the shift operator algebra, prove the discrete Great Descent Theorem using only algebraic manipulations of shifts, and establish the discrete Great Ascent Theorem via a discrete multi-Vainberg construction based on discrete integration. We introduce the concept of shift spectral varieties as the natural discrete analogues of spectral curves, and construct descent towers using symmetric power ideals in difference algebras. Ascent towers are given by dual modules constructed from shift-invariant difference modules. We prove a Discrete Period Number Theorem relating periods of shift-invariant differentials to the rank of the shift operator algebra. A Discrete Unified Rank Correspondence is established, linking geometric, algebraic, moduli, arithmetic, and analytic ranks within the discrete framework. We formulate a Discrete Birch--Swinnerton-Dyer Conjecture for difference equations and prove it in the function field case using class field theory for difference fields. The theory is applied to classify integrable difference equations including discrete KdV, discrete KP, and the discrete Painlev\'e equations by their descent length. All theorems are provided with complete, rigorous proofs using only discrete algebraic methods.