I would make one of the employees in the Shinra building a main character. Tell it from their POV, how awful it is to watch their bosses destroy the world. How torn they are between feeding their family and their morality. A family member of theirs is killed when they destroy sector 7 so they decide to settle their past. But then, they also find they they were experimented on by Hojo and are controlled by Sephiroth/Jenova in the same way as Cloud.