It's from the skull scene in MoS.
I thought he was in blue in that scene. But still he does look like Prime.
I've seen him in the Man of Steel ... and Berrybrick is correct.
I think it's a homage to his black costume from the comics with the shape-shifting "S". Comics were really weird around that time. Supergirl had this weird "angel fire" power. (While I agree that she is an angel, I mean that figuratively)
What do you think?