After rewatching Existence last night, you all's points on Mulder's feelings about fatherhood (father to William but didn't raise him, he himself raised as Bill's son, and reveal that he is bio son to CSM) are really interesting now that I'm looking at My Struggle IV though that lens. These are of particular note for me:
In Existence, I read Mulder's expressions upon meeting his newborn son as pure joy. In that last scene, as you all may recall, he and Scully go through all processes of elimination on what people (Frances Fisher, Rohrer, Krycek) have told them about the baby (alien? hybrid? super human? miracle? pregnancy via chip??) and why the super soldiers didn't take him away after he was born. They determine for themselves that William is THEIR son. With that determination, Mulder leans in for the kiss. It's a lovely moment. And, although he does go to Lamaze classes with her (for which she thanks him!), I thought he did downplay his role as the father during Scully's entire pregnancy, including describing the baby as "hers" and leaving it up to her to decide whether she was going to tell others who the father is - even with Skinner's direct question to him, and downplaying it throughout.
In the seasons/movies afterward, and not surprisingly, William is an undercurrent for them in their relationship, and therefore it is just so disappointing that MSIV ended the way it did for both Mulder and Scully with regard to William - I share your feelings @eleanorofaquitaine with my dislike of the ultimate reveal, when yet another thing is taken away from him, for not plot purpose I can figure out months later.
On a lighter note:
ME TOO!!! My fear and behavior on planes is unfortunately legend in my family. I would also settle for a smidge of Mulder's chill!!!!