Here’s how I’d do it. For the coming sequel, you set it up where Jason, starting to come of age, is beginning to come into conflict with himself and his fathers ideals. He’s not evil, but we can see elements in him which are all too human, and unlike his father he doesn’t quite possess the same benevolence that he does. Because of this, we begin to see that the power is somewhat of a corrupting force, and that without Supes there to guide him he might have begun to go off track.
In the movie, the new villain (I would guess Brainiac) recognizes that it’s impossible to actually physically destroy Superman without Kryptonite (which hopefully will not appear in the film) and instead decides the most efficient course is to simply remove him from the equation by transporting him to a place where he will be unable to interfere with his plans.
By accident (or maybe not) Jason winds up being the one who is hit with this teleportation beam and/or thrown into this portal he creates and Supes subsequently defeats the enemy in a rage for the loss of his son. Unable to bring Jason back, the final act shows Supes and Lois mourning for the knowledge that they may never see their son again, but holding out hope that one day they might just find him.
Then...
Cut To:
Close up on Jason as his eyes open. We pan backwards to reveal him lying on a black marble like floor with his arms chained to the base. He slowly rises to his feet and surveys his surroundings. The room is dark muted, but in the outside windows we see a sky tinted red. Jason looks down at his chains and attempts to struggle with them, but finds that even with his newly found strength he is unable to pull himself free.
SPEAKER (OFF CAMERA)
I see you have awoken young one.
The voice is dark and low pitched with almost palpable malevolence. Hearing the voice, Jason turns towards the speaker, his chains rattling.
JASON
Where...where am I. Where’s my--
SPEAKER (OFF CAMERA)
Silence.
Jason stops speaking, and fearfully gazes at the unseen speaker.
SPEAKER (OFF CAMERA)
Listen to me very carefully boy. You now live and breathe solely at my discretion. You exist for one purpose alone...to carry out my will. Your training will be long, arduous, and now that your powers have begun to emerge, you will...perhaps...be capable of surviving.
Eventually, when you are ready, you will champion my army against your old world...to further my glory.
JASON
...Who are you?
SPEAKER (OFF CAMERA)
I? I am your new lord and master.
We turn towards the direction Jason has been gazing to discover an imposing humanoid grey hulk covered in reflective tinted armor sitting in a tall massive stone throne. His face is a stern gaze of evil, almost rocklike in appearance, with twin glowing red orbs for eyes that gaze directly through us.
SPEAKER
For future reference, I am called DARKSEID.
FADE TO BLACK
Thus setting up Darkseid for the next film, as well as the inevitable confrontation between Jason and Superman. It may actually be possible to make a genuine character out of that kid yet.
