Why isn't Mulder afraid of super soldiers?

Question

By the end of the original X-Files television run, Mulder is

a fugitive, having been convicted of the murder of Knowle Rohrer.

Both the "victim" and at least one member of the tribunal were "super soldiers" — nearly immortal replicants who were amassing greater and greater power, becoming the primary antagonists of the series by its end.

In the film I Want to Believe, Mulder is pardoned by the FBI and is reasonably comfortable coming out of hiding. He doesn't seem to think that it might be a trick by the super soldiers to make him drop his guard. In the new miniseries, he doesn't seem wary at all of super soldiers — they're not even a topic of conversation in the mytharc episode "My Struggle".

By the second and third episodes of the miniseries, he is comfortably situated in the FBI headquarters again — a place that was once infiltrated by several super soldiers.

Why is Mulder no longer afraid of super soldiers? What happened after 2002 to make him think that they are no longer a threat to him?

Answer 1

In terms of the 2016 mini-series of 6 episodes, this was a short revival with no one signed up to do anything beyond it. It wasn't intended as a series 'follow on' to the original story line but rather an attempt to return to the original 'Twilight Zone' type quirkiness of the first couple of series, set now in our contemporary time space of 2016. Each episode is a story within itself, albeit connected by central characters that we recognise and care about. One of the episodes is a 'Monster' flick for example, 'Mulder and Scully Meet The Were Monster', a fun nod in itself to the Wallace and Gromit take on horror possibly.

So, Mulder isn't worried about super soldiers in the latest episodes because each story takes place in its own universe, a universe in which the super soldiers are not the central plot and may not exist at all. There is a good deal of evidence for this conclusion.

Carter, talking to the New York Times, was keen to ensure that the series still stays true to what we, the fans, loved about the original show: “We’re going to tell X-Files the way that we’ve always told them; we will of course set them in the time and place that they exist. We’re telling contemporary stories about contemporary situations, true to Mulder and Scully’s characters and their relationship and the passage of time.”

~ _{^{David Duchovny and Chris Carter talk new X-Files}}

Contemporary references such as Alex Jones and former astronauts Gordon Cooper and Ed Mitchell's alien revelations are included in the first episode.

Answer 2

At the end of S8, it is implied that William's birth is threatening to the Super Soldiers. Krycek said that the birth was influenced by a "higher power" in protection of humanity (Scully was barren and her body previously rejected the eggs Mulder fertilized). In essence, he says that the baby is “more human than human” and the aliens “didn’t even know about it” until just before they attempt to assassinate/protect Scully. The aliens are “afraid of its implications” because it “could somehow be greater than them” so insofar as you trust Krychek, the potential threat William poses to the aliens is all but confirmed. Additional hints include that in S9, we see William display vastly abnormal abilities and in S11, Cigarette Smoking Man tells us that William is immune to ALL viruses human AND alien.

We are told that the Alien colonists have left the planet sometime before 2012. It is reasonable to infer that the Super Soldiers were threatened by William and have vanished or been vastly diminished as a threat.

This raises the question: if William is such a threat, why don't the Super Soldiers kill him immediately at the end of S8? Our only inkling here is that Mulder cryptically says "Maybe he wasn't what they thought he was". We have enough context to know what the aliens are looking to kill or take: hybridized human-aliens. Well, the best we can do is note that William's powers don't manifest immediately, the Super Soldiers don't always act totally rationally (e.g. they spare Mulder, Krychek, and Skinner several times), and perhaps when they saw that William looked like a regular human, they let their guard down. Tracking his development, they are shocked when he develops powers and the more rational aliens decide to leave the planet before other "organics" (what Krychek and the aliens call human-born human-alien hybrids whose powers seem to outstrip the Super Soldiers) like William come into existence.

Also, Mulder's relative fearlessness is one of his character traits. One wouldn't be surprised to see him leave hiding out of boredom.