Answer
Most of the energy from the citric acid cycle is stored in NADH and in FAD$H_{2}$ which carry it temporarily until the hydrogens in those molecules can be added to the protein gradient in mitochondria where is used, ultimately, to produce ATP.
Work Step by Step
The key here is to see that these two molecules are temporary carriers which are ultimately used to make ATP and to see that almost all ATP production (a little comes from substrate-level phosphorylation) is run by a proton gradient in the mitochondria.
