I think it's something to do with Afghanistan. Wash is being set up for something. Nut has gone and the only one going near bombs is Wash.
I think something happened in Afghanistan (I think she said she'd made an error) and she's being reeled in so that revenge can be taken. Billy is being used to that end. John is a dupe.
Or - the group are bent and the only straight ones - Nut and Wash - need to be offed for a reason that will be one clear later. Nut has gone and Wash is next.