After "Body of Water" episode, I finally get the whole Jim/Sam thing. The whole message was that you had to have faith, faith in free will. You can only decide for yourself and for the ones we care about, you can only have faith in their choices.
I think the whole Jim/Sam thing strengthened Melinda and Sam's relationship to the 1000power. This episode was heart wrenching and really moving. It hurt watching it progress, but the fact that Jim/Sam still chose Melinda despite everything working against him was worth it.