This is my vaguely chronological interpretation of Padgett through the episode. Interpretation is a very key word! It picks up with the scene in the church because that's where Padgett and Scully first interact and Padgett has to move out of his head.

The most important facet of the scene at the church was that Padgett was right. Scully went to the church and her expression told him loudly that he was correct, or at least close enough, when he told her the reasons why she was there. Padgett became giddy from this triumph, and this one success pushed him subtly from observer to manipulator. Rather than seeking to learn the 'why' of the real Agent Scully, the author became a Pygmalion sculpting Galatea in the image of his own greatest desires. He no longer needed to observe because he thought he knew everything - he wrote, even, "The stranger had looked her in the eye and knew her more completely than she knew herself."

Padgett was not proven wrong immediately. Scully was drawn to his door, linked either by cause or effect, just as he wrote, "…the compulsion was overwhelming." And she stayed. But it slowly began to go awry. Scully stayed but spoke of her discomfort. She stayed but sat awkwardly on the edge of the bed, coffee cup in hand, as Padgett stared at her profile and puzzled about what step to take next. She did not lie supine and welcome his gentle touch - nor was she wild, feral. But why? Mulder's interruption told the author that he had failed to account for all the characters; perhaps this is where Padgett began to see the ending of his story.

In the prison cell Padgett told Mulder the truth - the one question he could not answer was, "Why?". The characters were there but they were playing the wrong parts because the author didn't understand their motives. When Scully grasped Mulder's bare forearm and whispered his name, and when her hand slid down Mulder's arm as she released him, Padgett saw how what he thought had been a 'why' had really been an incomplete collection of 'why not's'. Scully's loneliness, the yearnings of her self-contained heart had been key to his incomplete seduction. But he had not seen until then that the Scully he thought he knew so well was not the complete Scully. Padgett wrote that Agent Scully falls in love, but after seeing the touch he knew that she could not. She had no reason to. She was already in love with the character that the author had underestimated from the beginning.

Without an ending Padgett's story had no meaning. He knew only that the ending for which he wrote the book is out of reach. And now it is the killer who must ask, "Why?," because his motive must be the justification if the ending cannot be. Padgett told himself - ego told id, creator spoke to killer - that it was to meet Scully, to love her, to feel love. But id won; killer told creator that the only truth lies in destruction. The truth was in the creation of the killer, and he must kill the final lover for the crime of his existence to be perfect.

The author finally found the 'why' within the darkest, most empty part of himself. There was only one possible ending for Padgett's story - but it was the wrong ending because it was the wrong story. The author hadn't known what story he was writing because he didn't know himself as well as his character knew him. Padgett saw his own ending when he realized that his story shouldn't have been written. In the end, the author had to kill the killer - but the creation could not die while the creator lived.

"And in this final act of destruction, a chance to give what he could not receive."