No, I don't think he's haunting the place. It's the building he owned, and in which he died. I still wonder what his power was, what his role in Gen 1.0 was, and what Gen 1.0's plans were. He was clearly central to the Gen 1.0 conspiracy -- not only did he and Angela meet there in Peter's flashback dream, the rooftop is where Kaito Nakamura gave baby Claire to Noah Bennet.

And I wonder why Simone didn't seem to have any powers, since the other mutants seemed to give power as a dominant trait to their kids. (Which also makes Nathan's legitimate kids a question mark who should come up again.)