This is how Nyx meets with Zeta Prime, Zeta Prime dies, and Ghost Ryan's revelation goes in My Little Pony Transformers: Return of the Jedi.
[We then see R5 looking in the window
Nyx Sparkle: Zeta Prime? I am here for my training.
Zeta Prime: Nyx....
Nyx Sparkle: Yeah?
Zeta Prime: There is... another..... Sparkle.....
[Zeta Prime closes his optics and disappears]
Nyx Sparkle: You told me Nightmare Nova betrayed and murdered my mother.
Ryan F-Freeman: Your mother was seduced by the Dark Side of the Force. She ceased to be Twilight Sparkle and became known as Nightmare Nova. When that happened, the filly that was once your mother was no more. So what I told you was true from a certain point of view.
Nyx Sparkle: So Nightmare Nova is my mother.