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.