This episode of The X-Files was, as most are, dreadfully short of answers to the big questions. If you need to catch up on what happened before, click here.
As all of the "My Struggle" episodes have, this one opens with a monologue, now by William. In it, William explains that he knows who he is. He hasn't met Scully but they are mentally connected. He has visions of his role in the future. He knows about his powers. And has used them and had a troubled childhood because of it.
He wants to ask Scully questions, but says he'll only get answers from the Smoking Man, whom he calls his father yet already knows he hates.
The title card this week says "Salvator Mundi," Latin for Savior of the World (and also a popular Leonardo da Vinci painting).
In a huff to Skinner, Kersh shuts down the X-Files over Mulder going on the Tad O'Malley show and talking about the contagion. He wants their badges. Scully tells Skinner that was actually her. Because she knows from her visions with William.
Monica Reyes calls them about William's whereabouts but sends Mulder on a wild goose chase after the Syndicate's man, a.k.a. Mr. Y, who addressed Mulder in "My Struggle III." Mulder is then ambushed by agents but manages to get away.
"Your son has what everybody wants. What everybody would kill to have." – Mr. Y
Mr. Y's group, which may or may not be the Syndicate leftovers, found William because he won a bunch of lottery money in a row in Tennessee. Mulder gets on the case, and someone gets on his case at a gas station, attaching a tracker.
Scully calls Tad O'Malley and gives him more of the story about "death in the streets" and "a man-made contagion from an alien pathogen."
Scully sees Mulder dying, presumably shot by the Smoking Man, and tries to warn him, but like always, Mulder just does not listen.
The Syndicate leftover man following Mulder spots and picks up William when Mulder thinks William has gone in the opposite direction. When he reaches where he needs to be, William kills the man, gruesomely blowing him up from the inside but missing the tracker.
Mulder goes to one of William's old girlfriends' house. William goes to the other girlfriend.
William thinks that he's "a freak." And thinks people want to put him in a cage, poke him and prod him the rest of his life. By threatening his life, he convinces the girl to meet him at the shitty hotel. But she snitches to Mulder, who then finds William at the hotel.
"My name is Mulder. I'm your father." William, who earlier referred to CSM as his father, does not argue.
William thinks no one can help him and that these people are never going to stop looking for him. But Mulder tries to convince him otherwise, and that none of the things in his vision are his fault, and isn't able.
"Your mother" sees the visions, Mulder says. "Then why don't you see them too?" William asks. Mulder has no answers. This is probably Chris Carter's way of emphasizing the idea that the Smoking Man is actually the father, which I will never believe.
"You die too," William tells Mulder. Just wait until you see how.
William kills the Syndicate leftover people by making them explode, the aftermath of which Tad O'Malley gets his hands on footage of, broadcasting to the world. William also gives Mulder the slip.
"This isn't about the FBI, sir. This is about our son," Scully when Skinner tries to butt in and tell her Kersh wants them out. But of course Skinner manages to butt in and go along because he is also seeking William for the Smoking Man.
Scully seems to know Skinner is working with the Smoking Man, pressing him for answers even though she's already gone with him. And they then follow Mulder to the shipyards.
Instead of shooting William, Skinner shoots Reyes and tries to shoot the Smoking Man. He then dives under a car to avoid being run over by the Smoking Man; it's unclear whether he is actually killed or survives.
William, masquerading as Mulder, asks Scully to leave him alone and says that they can't protect him.
William maintains his Mulder disguise as he flees, and all are following him, but the Smoking Man catches him first and seems to think he is Mulder. To "Mulder," CSM calls himself William's creator.
"You'd shoot your own firstborn son?" William as Mulder asks. (How does he know Mulder is CSM's son?)
"I shot my secondborn son once," CSM responds. Who hasn't he shot, really?
CSM then shoots who he believes is Mulder, but is actually William. He falls off of the dock into the water. The real Mulder then shoots the Smoking Man and pushes him into the water.
"He was our SON, Scully," Mulder weeps. In response, Scully uncharacteristically distances herself, saying that he was actually just an experiment, "born in a laboratory." She has to have known the entire season that William was partly an experiment, but now she seems wholly convinced — perhaps by Skinner during their drive — that William is not hers at all.
"For so long I believed," Mulder cries. "What am I now if not a father?" But alas, he is a father because somehow Scully is pregnant again even though it's "more than impossible." Yes, you guys, that is where this great conspiracy ended. With Scully being pregnant again.
But also, though, William is still alive because no one on The X-Files is ever dead the first time.