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I'm in the middle of Snallville season 7, & we find out that Lionel Luthor locked Clark in a cage. He said it was for his own safety & wasn't built for him. But is this the truth? Did he do it for Clark's safety, or is he still evil? If I find out the answers later in the series, please don't spoil it.

There is no real big answer to spoil for you. Basically Lionel had it because he knows Kryptonians other then Clark have shown up, and they are usually evil.