Here's how Chris tells Captain Emerald about Ernie's existence in Vengeance & Rage!.
[we sideswipe back to Canterlot as we see Chris walk up to Captain Emerald]
Chris: Captain Emerald, I must speak with you.
Captain Emerald: Chris, we've just recieved word that Dawn terminated TD-1000. We're on our way to make sure that Senate knows about it.
Chris: I don't think it's such a good idea. I just found out something terrible. Alter is here, and he's running the Sentate.
Captain Emerald: Alter, is here?!
Chris: Yes, and he's the one who started this war.
Captain Emerald: How do you know this?
Chris: He revealed himself to me.
Captain Emerald: Are you sure?
Chris: Positive, Master.
Captain Emerald: Then our worst fears have been realized. We must move quickly if we're to prevent the Jedi Order from falling again.
Chris: Master, I must warn you. Alter is very powerful, you'll need my help to arrest him.
Captain Emerald: For your own safety, please stay out of this affair. I sense a great deal of confusion in you, young Chris. there's a lot of fear that clouds your judgment.
Chris: I must go with you.
Captain Emrerald: No!
Chris: Why not?
Captain Emerald: If what you told me is true, you'll have gained my trust. But for now, remain here. Wait in the council chambers until we return. [gets into a shuttle]
Chris: Yes, Master.
[The shuttles takes off and leaves]
[Chris then walks out of the hangar]
[Then it sideswipes to Sunset in her apartment and Chris in the temple.]
Chris: [sighs heavily]
[Sunset then walks to the window and gazes out as Chris does the same]
[Soon Chris hops aboard a speeder and takes off]