The Serenity crew a running a job in which they acquire Alliance stamped merchandise.  In order to look more legitimate, they put down and load some legal passengers (Shepherd Book, Simon and Dobson).  Dobson, it turns out, is a federal agent but instead of arresting Mal he is after Simon.  After Dobson shoots Kaylee, Mal opens the box that Simon brought on board, only to discvoer a naked young girl.