When Benry was manipulating Locke, telling him Jack doesn't consult him on decisions etc. He told Locke "I came here for you" which John has probably figured out was a lie. So he is 'full of anger' (or whatever Mikhail said.) I think he is with Kate and Sayid because he wants to confront Ben, I also think there is something major about his being paralyzed that ties in here. He grabbed the C4 just in case, never know when you might need to blow something up He found out about the sub after. Where did that cable that Sayid followed to Danielle's go? It went out under the water? Is that something to do with the sub? And..did Benry ever mention a list to John in their little chats?