"Never Again" was written by writing partners Glen Morgan and James Wong, making it their final episode of "The X-Files" until they returned to the show during its tenth season; following this episode, the two took over as executive producers of the Fox program "Millennium" (developed, like "The X-Files", by Chris Carter). The initial story the two developed was a "sort of Abraham Lincoln's ghost in the White House type of thing", which would have involved Mulder and Scully investigating the haunting. Morgan explained that he had "done a lot of research and had always wanted to write a feature about Lincoln's ghost". However, due to the massive amounts of rewrites the two were forced to do for "Musings of a Cigarette Smoking Man", both Morgan and Wong lost interest in their original story. Morgan explained, "I felt they didn't want my heart and soul anymore, so I wouldn't give [the ghost story to them". The two later crafted "Never Again" in its place. Years later, Frank Spotnitz said that he "always wondered about" their original story and what the finished product would have been like.