One way to go about it is that the good boss knows something the PCs don't know. He's trying to save the world, but if the macguffin is released, then everybody is doomed. But because he's trying to save the world, sometimes his actions might not seem good.
And of course, because the PCs eventually defeat the good boss, it then sets up the next campaign where the doom has been released into the world and the PCs need to stop it.
And of course, because the PCs eventually defeat the good boss, it then sets up the next campaign where the doom has been released into the world and the PCs need to stop it.