What if, not all but quite a bit of, the missing children who are around four to six years old aren't kidnapped by pedophiles or murderers, but by a government ran school.
They find a child who is all alone and take them to a school where they will learn to be spies. By the time they finish their fifth year, the child already knows basic algebra. When they finish their seventh year, they are allowed to choose what kind of courses they would like to go into (Fighting, repairing, programming, hacking, teacher, etc.) and finished learning the basic things we learn in school. After thirteen years at the school, they graduate and are given a task depending on the subject they studied after their seventh year. Such as if you were an expert in hacking, you could get a task for the military to hack into enemy files.
The two main characters in my head, are both given the task of Assassination. They can get normal jobs and have a normal life, but every now and then, they are given a file that explains the person they have to kill quickly with no one around. They go about it until the other's girlfriend/boyfriend is next on the list to kill. They have no records but distracted the other from getting their kill down on time.
They choose not to do it. They are being tracked down to be killed when they go to the other and get their help. They run off and try to avoid the people trying to kill them.