One dark twist in Smallville season 2 hinted that Clark was actually right about Jor-El being evil. In the show’s early seasons, the Kents were fearful of the plans Clark’s biological father had for him. But as time passed, perceptions of Jor-El began to change.
Jor-El’s determination to get Tom Welling's Clark to accept his destiny and his Kryptonian heritage accounted for one of Clark’s greatest concerns during his high school years in Smallville. Desiring to live his own life, Clark fought back against Jor-El for years, but eventually found himself reluctantly listening to Jor-El’s advice. It was Jor-El’s words that helped Clark stop the second meteor shower in season 4, revive Lana Lang and stop General Zod in season 5. Thanks in part to these experiences, Clark slowly came to realize that he had misunderstood Jor-El’s intentions. In fact, Jor-El was trying to guide Clark into becoming a force for good on Earth.
A Smallville Season 2 Twist Suggested That Jor-El Really Was Evil
Interestingly, what Clark came to believe about Jor-El contradicts a key detail from Smallville season 2’s “Rosetta.” Using the octagonal key, Clark unlocked his spaceship and uncovered a hidden message left by his father. Calling him a “god among men,” Jor-El instructed Clark to “rule them with strength.” It was this revelation that made Clark worry that Jor-El wanted him to use his powers to conquer Earth. Given the wording of the message, Clark’s suspicions seemed well-founded at the time.
Clark turned out to be wrong about Jor-El, but it was completely understandable for him to suspect the worst about Jor-El. The message found in season 2 made the assumption that Jor-El was evil a logical conclusion for Clark to reach. After all, it did sound like Smallvillle's take on Jor-El expected Clark to rule over the humans. His word choice left little room for any other meaning to be found. As Smallville moved on and revealed more about Jor-El’s true plan, it never did circle back to this twist or offer a different interpretation, which reinforces the idea that the show wanted him to be a villain.
How Jor-El Being A Villain Would’ve Changed Smallville’s Story
Jor-El had an antagonistic presence in the second and third seasons, but the show avoided turning him into a full-fledged villain. But had the show followed up on season 2’s twist, it’s likely that things would’ve played out very differently for Clark as his story developed, particularly in Smallville's later seasons. Turning his back on Jor-El for good would have seen Clark forge a path completely independent of the AI’s guidance. That would mean Clark would never build the Fortress of Solitude or begin his Kryptonian training. Just how huge of a shift this would have been from the Superman formula may be the reason why Smallville changed directions with Jor-El.