Answer
The energy is stored in the capacitor.
Work Step by Step
As the plates are pulled apart, the capacitance decreases. For a parallel-plate capacitor, $C=\frac{\epsilon_oA}{d}$.
The charge Q stays the same, because the capacitor is isolated.
The stored energy increases, because $U=\frac{Q^2}{2C} $ and the capacitance decreases while the charge stays the same. The work done to separate the charged plates is stored in the charged capacitor.
