The thunderstorm here acts as a symbol for change and signals bad things to come: now that Genji has been discovered with Oborozukiyo, which is clearly not okay no matter what Suzaku said about it previously, he's angered the most powerful family at court. This also reinforces that now, Genji is on his own to manage his conduct and doesn't have the Emperor around anymore to protect him or to reprimand him for acting foolishly. As such, Genji may finally have to pay the price for his transgressions.