Peter had always hoped that Nikki would be stronger than this, he wasn't taking into account how hard of a situation this was for her though. She was taken away from her husband and son to this messed up place.
"Because he first decided that we are bad and we needed to be rounded up, and then once he found your other twin or whatever she was Barbra, they teemed up and decided that they could sell powers, give them to people. So while I'm still hunted by the newest version of the Company, Nathan is sitting high and mighty."