Here's how the others find out the truth and tell Sunset about the bad news in Revenge of the Giant Chicken.
Brian: I've recalibrated the code, to make the remaining Jedi to stay away.
Twilight: And it will take the Clones a long time to discover the recalibration.
[then Brian heads for the security recordings]
Stewie: Brian, What are you doing?
Brian: I'm finding out the truth.
Zecora: That, I would not advise. If you look into the recordings, you'll only find pain, that will only lead to cries.
Brian: I must know the truth!
[Soon he comes to the security recordings and shows Chris killing the Jedi and younglings]
Brian: [as Megatron] No. No!
Lois: No, this can't be!
[we then see Ernie on the hologram]
Ernie: A job well done, now fulfill your destiny!
Chris: [rises up]
Peter: Turn it off! Turn it off! I can't watch anymore!
[Brian shuts it off]
Quagmire: So, that psychopathic chicken's behind this chaos!
Vinny: Now it makes perfect sense! The Clones, The War, This. He's the one behind it.
Peter: I'll kill Ernie! Just give me a Lightsaber and I'll kill him in no time! No one makes my son turn to the Dark Side!
Zecora: No, Peter! You're not strong enough to take on a Sith. You'll surly be killed!
Peter: I don't care!
Zecora: The boy who has defeated the First Order, is gone. Consumed... [drops her ears] By Darth Griffon.
Brian: We don't know where Ernie's sent him. I don't know where to look.
Zecora: Use your feelings, Brian. And you'll find him.
Princess Luna: [soon walks way]
Hero: Luna, what's wrong?
Princess Luna: I'm going to duel Ernie.
Lois: You're dueling Ernie?!
Princess Luna: It's for the sake of Chris' life! And I sensed Tia, is in danger. [she flies away]
Brian: [leaves the others]
Sylveon: Brian, where you going?
Brian: To talk to the woman he's in love with.
[He hops in a speeder and takes off]
Thomas: Guys, we have to go to Kamino!
Percy: Why's that Thomas?
Thomas: Because, if the Clone Equines turned on us, Ernie would use the Kaminoans to make an army, and will crate a new empire!
Twilight: That's right! We gotta do something!
Cadance: Then we must go to Kamino, and destroy the Clone life pods!
Clone Equine Trooper: Hey!
[Some Clone Equines arrive]
Clone Equine Trooper 2: Put your hands in the air!
[The others do so]
Clone Equine Trooper 3: We have a special message for you.
[Ernie shows up on a hologram]
Ernie: Hello, pretties! It's been a long time. What do you think of me this time?
Dudley Puppy: It's terrible! You've killed the Jedi!
Ernie: I know. And to make matters worse for you, I have Celestia hostage!
Princess Jasmine: You wouldn't!
Ernie: Oh, I would. Jasmine.
Peter: Ernie.... [holds out his fist] (as Rambo) I'm coming to get, you!
[He then elbows the 2 troopers as Lois kills the third and second troopers, and Peter grabs the first trooper, and slams his head on the hologram projector and breaks it. Then fist punches him and Shining Armor impales him with his lightsaber. Another trooper arrives, Nick tries to shoot him but he hides. This got the attention to some troopers and they go to check it out, and Kitty kills one with her claws and Dudley takes out two with his Thompson. The troopers get closer, and Vinny grabs some grenades]
Vinny: Come on!
[They run to the Equestrian Starfighter, but soon they hear blaster fire. Ariel takes some down with her blaster and they hurry to the shuttle]
Vinny: [throws a grenade and kills some of the troopers] Hurry, get us out of here! [throws another one and hops on the ship as it takes off]
[It screen wipes to Brian and Sunset]
Brian: Where was the last time you saw him?
Sunset Shimmer: Yesterday. Why?
Brian: Do you know where he was going?
Sunset Shimmer: He said he was going to Cloud City to end the war. Why are you asking this of me?
Brian: Sunset, I need your help. He's in danger.
Sunset Shimmer: From the Sith?
Brian: No. From himself. Sunset Shimmer, Chris has turned to the Dark Side.
Sunset Shimmer: [slaps him] You're wrong! How dare you say that!
Brian: It's the truth! I'v seen a security video, of him... [a tears streams down] killing younglings.
Sunset Shimmer: Not Brian, he couldn't!
Brian: He was deceived by a lie, we all were! It shows that the Senate was behind everything, including the war! The fact of the matter is, Ernie is alive! After the death of Nightmare Moon, and King Sombra, Chris became his new apprentice.
Sunset Shimmer: [walks toward the edge of a seat and sits down] I don't believe, you. I can't.
Brian: Sunset Shimmer, we must find him.
Sunset Shimmer: [tuns back] You're gonna kill him, aren't you?
Brian: I don't have a choice. He has become a very great threat.
Sunset Shimmer: You can't.
[As Brian prepares to leave, he looks back at her]
Brian: Chris married you, didn't he?
[Sunset Shimmer doesn't answer]
Brian: I'm sorry.
[He leaves to he'd towards Coruscant
[It cuts to Palpatine's hideout with Chris staring at the carnage he caused, then after a long stare and a tear streams down his face]