Season two finally throws us a bone concerning Ben's death during a flashback to 2006, when the kids are teenagers, for his funeral. Sir Hargreeves is maliciously chastising his children for letting Number Six fall during battle, saying "Despite years of training and weeks of preparation, you allowed Number Six to die on this mission." Hargreeves tells the children to carry around the guilt and pain of Ben's demise with them forever, giving good reason for the adults to still harbour unresolved emotions and grief. While this isn't exactly a theory, it could be all we need to know: Ben died in action, nothing more, nothing less.