This is how Orion and Nightfall find out the truth goes in Orion Pax and Nightfall Twinkle Part 2.
Orion Pax: Okay, Optimus Prime and Princess Twilight Sparkle. Optimus Prime and Princess Twilight Sparkle: leader of the Autobot and Equestrian invaders. We reminded Starscream of him and her. And Megatron said Ratchet was the Autobot leader and Princess Cadance was the Princess of Friendship. Someone is not telling the truth.
Nightfall Twinkle: Your guess is as good as mine.
Orion Pax: Why would the Decepticon archives be so heavily encrypted?
Nightfall Twinkle: Not sure. It's highly complicated.
[Nemesis Computer shows image of Optimus Prime and Princess Twilight Sparkle]
Orion Pax: How could I possibly be Optimus Prime?
Nightfall Twinkle: And me Princess Twilight Sparkle?
[Soundwave shows Megatron image of Optimus Prime and Princess Twilight Sparkle]
Megatron: Even our encryptions couldn't keep them from the truth! Orion and Nightfall have much to accomplish and they will stay the course! Even if I must inflict great pain to ensure the completion of Project Iacon!