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Well this is just my opinion, but throughout the series he was always focused on getting Mulder on his side, and Scully was Mulder's weakness so I felt that CSM was curious as to why and perhaps that episode he was trying to see if there was a way he could find her weakness.  |
But isn't her weakness obvious? Mulder? From what I can remember I would say, he envied Mulder because of his weakness. He wanted to get to know Scully personally in order to get behind the secret why Mulder cares so much about her. Maybe he enjoyed this innocense because it's something he lost a long time ago. I would even say he enjoyed being with Scully. And he needs also to show how mighty he is. Knowing the weakness of the enemy just made him stronger and it' s the only reason I can imagine why he didn't kill her. He wants to show Mulder how mighty he is.