Okay, so once upon a time a paranoid scientist discovered a baby with a gem in his stomach. He stole the baby from the child's father and fled from Beach City that night.
He made his way to a secluded lab outside Empire City and began his experiments. Over the next 12 years, the boy was raised under the title R-053 and saw the scientist as his father. The scientist convinced the boy that all the tests he'd been doing were important; that the boy was sick, and these experiments were necessary.
The boy wanted to explore, but the scientist would only allow him in the "backyard". A fenced off patch of yard with high walls and a bulletproof glass ceiling. The boy didn't mind, because he didn't know this wasn't how it worked.
The boy would draw pictures for the scientist and hang them up on the walls. The scientist did not care so long as it didn't interfere with his work.