During the storm, the glass in three of the windows was broken.

The correct choice, "was broken," is appropriate because it utilizes the passive voice in the past tense. In this context, the structure indicates that the windows experienced the action of being broken by an external force during the storm. The passive construction is suitable here because the focus is on the resulting state of the windows rather than on who or what caused the breakage.

Using "was broken" conveys that the action occurred at a specific point in the past and is a complete thought within the sentence. It also aligns with the singular subject "glass," which has been treated as a collective noun in this instance, demonstrating proper subject-verb agreement.

This choice effectively emphasizes the impact of the storm on the windows, making it a clear and grammatically sound selection for this sentence.