i think its the first theory.... i dont really think jor-el is the bad guy.... they make him look like a bad guy but really he is the good guy... like the episode 1961 or whatever... it shows him as a good guy.
I still think that the entity in the caves isn't jor-el.
So one of 2 possibilities:
1. The craft malfunctioned when clark landed
2. [SPOILER - highlight to read]: The entity pretending to be jor-el is actually brainiac. . It wouldn't be too corny to have him on the show. After all, they have had mr.myxypyxalix and krypto the wonder dog on it.
I think he is really a good guy but they have him borderline right now and they have never really said he was evil yes he killed tara and tried to kill johnathan but he was doing what it took to get his son back.
__________________ almost wrote a song about you today but i tore it all up and i threw it away
I could'nt really see it being Brainiac (why u put a spoiler i dont know, but i'll respect that). I never did like how Jor-el was 'bad' in Smallville but maybe it is just to test Clark. Then again maybe the power went to his head. Because we dont see much of Jor-el in the comics and we only see him when he's a young tennage youth in smallville.