Question: What exactly have The Company been doing with Adam during his thirty year incarceration? Experimentation of some sort?
Question: What was Bob Bishop hoping to gain by keeping Peter in containment? Was it to simply stop him from causing any further harm to himself and other people? Also, he must have known it would be a risk putting him in a cell next to Adam Monroe? Furthermore, was Angela Petrelli aware of Peter's incarceration? What would she have made of it?
Chosen answer: Angela Petrelli was not the company leader, Bob was. So its safe to asume the Angela didn't know about Peter's incarceration. As for the plan, well i think it's pretty much the same as Adam Monroe, keep him locked up forever without powers. And no, I don't think they figured it was risky to put him next to Adam, as the cells are supposed to be sealed tightly.
Chosen answer: I don't think they experimented on him. He was too dangerous to have constant visit from anyone. So they just kept him locked up.
lionhead