Oliver and Barry are running from the police when they are confronted by a dark version of Superman in episode 7x09 "Elseworlds, Part 2".
Dr. Jones tries to kill Rand O'Reilly who is saved by Kara & Hank who have to be saved in turn by the DEO in episode 2x06 "Changing".
Barry and Oliver learn that Deegan has taken on the guise of Superman in this altered reality but they manage to escape him despite not having any powers in episode 4x09 "Elseworlds, Part 3".