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]