What about this angle ofr the story to go in

[qprno1fan]

The voice and prescence in the fortress of solllitude we have heard since the end of seaosn twoturns out to be a ruse its not really Jor Ell it is really Zod, that would explain why he has been the less then loving father, and why he caused JKs death to inflict pain on Kal ell. Zod was really in the fortress controlling and manipulating everything and it was a a trick. This could lead to a fantastic episode with Ternace Stamp returning as Zod, and Kal Ell defeats him leading to Jor Ell being freed from the phantom zone and finally being able to communoicate with his son.

What about this idea. Well no one would see it coming.

[Die Clana! Die]

I don't mean to insult you, but that would be stupid.

[Timester]

That was one of theories about the Jor-El AI (the Erradicator was the other) before season 4, but everything that happened since season 4 pretty much established the AI as a represention of Jor-El. Especially when Lex was possessed by Zod.