I was trying to think of ways how Prometheus could know about the Legends' existence. Then I realized that Nate basically got on Team Legends by knowing Ollie's secret identity, so what if he's a mole for Prometheus? Sure, he said he discovered it himself, but maybe Prometheus told him. Nate could still be a genuinely good guy, but supplies Prometheus with intel in exchange for him getting him on Team Legends.
What do you think about my theory?