From the very first moment he saw Olivia Dunham, standing all feisty and determined in the Iraq hotel, he knew something bad was going to happen. The feeling only intensified as he spent more time with her. He tried to ignore the feelings of impending doom as he began to realize just how much she fit into his life. Without her a part of him was missing. That realization scared the living hell out of him. For weeks he debated running away like he always did, because at this point it could only end in inevitable pain. The longer he stayed, the more painful it would be for the both of him. But he couldn't go through with it, because she needed him just as much as he needed her.
They weren't even together in the societal definition of the term, but their relationship ran deeper than any expectations or regulations society imposed on them. He would die for her and she would die for him. It was as simple as that. And it scared him, and he knew it scared her as well. The moment he leaned in to touch his lips to hers, she became so scared she fled the room. That should have been the big bright warning sign that stopped him in his tracks, but at that point he was too far gone. She made every part of him feel less stable, and more alive than he had in years.
He could physically feel the tension build between them. Every touch, was like a match thrown close to a can of gasoline. The match was never thrown close enough to ignite them, but soon so very soon they would combust.
And then he had run. She had hurt him and betrayed him, and he resigned himself to the fact that she did not care about him like he cared about her. But she had come for him, when he needed her the most. He had stood there numb with hurt and neglect, and there she was asking him to come back with her because he belonged with her. Amidst all the confusion in the universe she made sense. They were like two atoms drawn to each other by a strong inevitable attraction. And when she kissed him, the reaction was complete. For the first time since this whole mess had started, he felt hopeful. Maybe, his place was besides her side. When they returned to the other side it was bliss. She was amazing, and he was the luckiest man in the world. He should have realized that everything was too good to be true. But to be honest, he was doing every thing he could to not question his life. He was happy and she was happy and that was all that mattered.
It wasn't until one of his sources tipped him off that he discovered the real Olivia Dunham remained a prisoner on the other side. What he feared would happen had happened. He should have been more aware. He should have stopped it before it started. He had a freaking IQ of 190. It was child's play to him. He could recite the laws backwards and forwards in his sleep.
This specific law was the 2nd Law of Thermodynamics. In the most simplest terms it stated that every reaction increased the disorder and chaos of the universe. Over the years Peter had fondly reinterpreted the law to mean that the minute something good happened, that some positive reaction had occurred in his life, that something bad was about to follow. Basically once things got good, shit happened. It was scientifically proven, it was a law for heavens sake. All things considered he should have known. But maybe just maybe it wasn't science that governed how he felt about her, perhaps it was something else entirely.