The season-long subplot involving neural clone of Scorpius appearing in John's head via a special chip Scorpius had implanted, had not been created when he appeared in this episode. The writers had been trying to think of ways to have the villain appear in more episodes, to keep up the tension throughout the season. They hit upon John hallucinating Scorpius in this episode, and then realized it worked so well, they retconned the neural clone into the story.
