Ok, probably not really solved, but it makes sense to me:
At the end of the Cylon war, the final five (who were born on Earth to Cylon parents from the previous cycle) arrive and make a deal with the toasters. They work the technology and create the seven skin jobs we have come to know and love. The #1 model has a glitch in his programming and hates being a replicated human model, so he devises a plan.
The #7 model, Daniel, discovers the plan and John destroys his model before he can leak word back to the Final Five. However, one awake #7 escapes and hides in human society, where he gets married and has a child (Kara Thrace). Before he escaped, he implants a tonal code into the minds of the FF, knowing that one day they would need to be awoken again. He then teaches his daughter this tonal code. He later has to leave his daughter in order to put the code at certain road maps along the way.
John continues with his plan, which is to destroy humanity and punish his creators. He wipes the memory of the FF (or at least hides their active memories at the time), subjugates the toasters (who were the ones who wanted him created in the first place) and removes the memories of the FF from the memories of the remaining six models. He then sets up this faux Cylon democracy and manipulates the remaining models into agreeing to destroy humanity.
In the end, the only real way of everything coming to light and to save the remainder of humanity is to find the Daniel model, who seems to be the only one who knows all and can stop John (at least according to my theory).