I know the answer is that writers had abandoned him, but... I kinda like to think that Jon-El was left to rot because he is not human. Jon-El suffers the fate of Tal, who got imprisoned and experimented on when he was a kid. And both don't speak the language of locals. But the most fun part is the fact that probably through time Jon-El becomes powerless (or significantly weaker), since this world doesn't have red sun. He becomes a regular young person with list of crimes but everyone will see only a monster in him and he won't ever see a glimpse even of a yellow sun.
He won't be experimented on because a criminal or not, turning non-humans into lab rats is a direct insult to a Superman's face and let's better avoid turning Earth's superpowerful protector into an enemy, yeah?
And there is too little years left before Jon-El legally becomes an adult. I doubt anyone would care about him after that.
Maybe his only hope is Jon who after some years will ask "btw what about my evil emo twin" and now he, a mature adult, couldn't just close his eyes on a situation after getting an update, especially since the issue hits kinda personal, on the whole "anti human" topic you know. Jon doesn't know what to do but his self of justice and urge to take actions won't let him just sit tight, he needs to do. something. Cause bad guy or not, that's whole mess is wrong.
Or maybe Jordan-El jumps into this world cause come on they are twins maybe he badly needs to figure out if he should hit his bro with fists personally after all those years, or get some kind of clarification and hug that easily guidable bastard.
Maybe have our Jon and Jordan-El team up on this and our Jordan not liking this at all, protective bro + personal grudge against Els and Jon-El in particular cause screw the end of the world, the biggest problem is that damn Jon-El tried to "kill" Jon, or take away forever and that's not smth Jordan can easily be chill with, and now damn twin of Jon-El is also here and they know nothing about him - and he wants to release his bro? Erm, no!
If both Jordans start at drama fight when meeting Jon-El - both for their own different reasons - and later a drama against each other - Jon will joke "idk If I should have brought band aids or popcorn" and Jon-El supports "Popcorn. I would always prefer to bleed out but with an actual good food in my mouth. Prison food sucks".
Jon is crazy enough to easily bond with his former killer and Jordan is very, very aware of this and in time it's obvious that Jordan has less problems with Jon-El and Jon bonding and more with Jon's tendency to be like this. Dude, have some self-respect? You gave me enough headache- blah blah blah because probably this is noooooot the first time smth like this happens. El twins get some time to actually talk eye to eye because Jordan forgot about supervision, too busy to complain and scold his unhinged twin.
(optionally El twins escape while our twins talk for the sake of stupidity and comedy)
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