I took a completely different message from Serenity. Shepherd new what Mal believed in and was encouraging him to stand for it. Up until that point in the film,

I took a completely different message from Serenity. Shepherd new what Mal believed in and was encouraging him to stand for it. Up until that point in the film, he had behaved as if he were just a leaf on the wind. I'm not sure that Shepherd's advice would have been the same had Mal believed differently.