"Amor Fati" is a Latin phrase referring to the "love of fate," which is an important phrase and concept in the work of the German philosopher Friedrich Nietzsche.
As writers, David Duchovny was responsible for the Mulder alternative life scenes, while Chris Carter concentrated on the mythology plot developments.
At the start of this seventh season, David Duchovny filed a lawsuit against Fox over their syndication of the show, Duchovny contending that Fox had sold the rights to their own FX network when it could have been shopped to other networks for more money. Duchovny's suit claimed that Chris Carter was fully aware of the move. This lawsuit hung over the production for the entire year, only being resolved by the time the season finale was aired (Duchovny reputedly was paid $20 million in compensation). Reportedly during that time, Duchovny and Carter weren't on speaking terms. Ironically in later years, Carter filed a similar lawsuit - using the same lawyers that Duchovny had.
One of the inspirations for David Duchovny in putting together this story was Nikos Kazantzakis' novel "The Last Temptation of Christ".
Mulder continues to have headaches and exhibit telepathic abilities because the alien artifact reactivated the alien black oil virus he had been infected with even though both he and Scully had been infected with the alien black oil virus at different points in time and they were both given the vaccine. This continues until the Cigarette Smoking Man (believing that Mulder had become an alien hybrid) has the alien genetic material surgically removed from Mulder's brain to be implanted into his own brain so that he would survive the alien apocalypse. Subsequently, in the Season 7 finale Requiem (2000), it is Mulder and not Scully who is abducted. This may have added to Scully's doubt that she had alien DNA and so in the Season 10 premiere My Struggle (2015), her alien DNA is treated as a new discovery even though she discovered that she has DNA from the unclassified chimera cells found in the ice core sample in Redux (1997) and even though she stated that everyone has a genetic remnant or junk DNA that matches the DNA of the alien claw and the alien virus at the end of the Season 6 premiere The Beginning (1998).