This is how Orion and Nightfall become Decepticons goes in Orion Pax and Nightfall Twinkle Part 1.
Optimus Prime: (voice) Previously on Transformers Prime: Friendship is Magic.
Megatron: Orion Pax and Nightfall Twinkle are one of us.
[End of recap]
Ratchet: When Optimus used the Matrix of Leadership and Twilight used her Magic of the Alicorn, they not only lost the wisdom of the Primes and Alicorns. They lost themselves. They have reverted to their old names, Orion Pax and Nightfall Twinkle.
Rainbow Dash: No way!
Pinkie Pie: Seriously?
Applejack: They think they're Cons?
Fluttershy: Oh my.
Starlight Glimmer: [gasps]
Thorax: How can this be?
Discord: They are fool-proof.
Princess Celestia: But not anymore, Discord.
Princess Luna: Twilight may have given her magic up already.
Princess Cadance: We can only hope they are okay.
Shining Armor: We have to save my sister.
Megatron: Attention, crew. Our guests are currently in isolation, to help ease their transitions. But when Orion Pax and Nightfall Twinkle emerge, they are to be shown every courtesy. And the first to adress them as Optimus Prime or Princess Twilight will have their voice box ripped out.
Airachnid: Lord Megatron, is it wise to allow an Autobot and Princess, current or former, take full run of the Nemesis?
Megatron: Oh, Nightfall and Orion will indeed earn their stripes.
[Meanwhile, Knock Out replaces Orion Pax's Autobot insignia and Nightfall Twinkle's six pointed star cutie mark with Decepticon insignias]
Knock Out: Welcome back to the winning team.
[Megatron, Orion Pax, and Nightfall Twinkle walk into the bridge and Vehicons look at them]
Megatron: You two have been captives of the Autobots and have been locked in stasis for quite some time, Orion and Nightfall. Long enough for us to gain exodus on another world.
Orion Pax: Exodus?
Nightfall Twinkle: Why?
Megatron: Because the warlord Ratchet's and deadly friendship Princess Cadance's careless actions lead to this.
[He shows them Cybertron as it is now on the screen]
Orion Pax: [gasp] Cybertron.
Nightfall Twinkle: Equestria. I can't believe Ratchet and Cadance capable of such horrors.
Megatron: Yes. And to think their mad quest for power continues their marauders pursued us to this planet's orbit. We feel its species are not ready to behold us. But we have resolved to protect this world from the same tragedy which was dealt to our own.
Orion Pax: One question, Megatron.
Nightfall Twinkle: Why are we called Decepticons?
Megatron: Another craven Autobot scare tactic. The name was meant to demonize us. Instead, we wear it as a badge of honor, for if speaking the truth is deception, then we are gladly guilty.
Orion Pax: [nods]
Nightfall Twinkle: [nods]
Megatron: There will be time for catching up. You two need to rest.
[He walks away from them but stops when Orion speaks up]
Orion Pax: Megatron! We will do our part to stop Ratchet and Cadance's unspeakable crimes of aggression.
Nightfall Twinkle: This I vow. With all Orion's Spark and my heart.
[Megatron smirks and moves on]
Megatron: Orion and Nightfall how fares Project Iacon?
Orion Pax: There are a lot of entries.
Nightfall Twinkle: We only managed to decode three.
Megatron: And what do these entries comprise?
Orion Pax: They were locked by Autobot archivists during the war after we entered stasis. Our only knowledge of its content so far is that they are coordinates, targeting locations on this very planet. We surmise that they could indicate hiding places for vessels shuttled from Cybertron for safe-keeping.
Nightfall Twinkle: Yeah. What he said.
Megatron: Such as historical documents or cultural artifacts?
Orion Pax: Our greatest fear would be weapons of mass destruction.
Nightfall Twinkle: Hidden away for later use.
Megatron: All the more reason it is essential that we do everything in our power to keep said vessels from Autobot reach. We are fortune to have you on our side Orion Pax and Nightfall Twinkle.
[He walks off but stops as Orion once again speaks up]
Orion Pax: Lord Megatron. We are puzzled by one particular finding. We have discovered several historic references to Starscream as your second-in-command.
[He shows him a picture]
Orion Pax: Yet we have not seen him aboard the ship.
Nightfall Twinkle: Tell us. Where is he now?
[Megatron turns to them]
Megatron: Sadly Commander Starscream is dead.
[Megatron turns and leaves]