Hehe, I was thinking along the lines of David Morrell's "The Brotherhood of the Rose" - in the book an old guy, a really important figure in the secret service, was taking in orphaned boys. He trained them and made them secret agents. That's what they thought. In reality, he was using them to do his bidding and further his own causes, they weren't working for the secret service at all, but they didn't know it.

So, what if there was this older guy who took in Neal from an orphanage. He taught him everything he knew, he took him all over the world - without Neal knowing that the guy was working for the government. And then the guy wanted Neal to do something that went against everything he believed in - like, something that could hurt someone - so Neal ran. The guy was keeping an eye on him the whole time, trying to find some leverage and bring Neal back under his control. Something like that.