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In Hunted, Dean finally reveals to Sam that John had told him that he must save Sam and if he can't, Dean must kill him. This revelation has left Dean shaken ever since, but Dean admits that John never expanded upon what he actually met.

No, Dean had a relationship with Ben's mom long ago, but Ben is not Dean's son. But Dean did take care of Ben like his own son after Sam went into the cage with Lucifer. And Dean was even prepared to let go of Sam (his own brother) for Ben and Lisa. Dean Winchester is the most amazing person you will ever get to meet.