I'm going to put it right on front street: this episode was not for the faint of heart. In fact, this had some of the most graphic and disturbing imagery I've seen not just in an X-Files episode, but on network TV period.
The episode opens in the building of Nugenics Technology and we meet researcher Dr. Sanjay, who we quickly learn is hearing a high-pitched noise that no one else is. During a meeting, the noise becomes so loud and maddening that he runs to a server room and locks himself in. While security tries to break in, the sound of their drilling mixed with the mysterious noise becomes too much and, in a desperate attempt to stop the sound, Sanjay drives a letter opener into his ear and brain, killing himself.
During their investigation of the death, Mulder and Scully are stonewalled by the people at Nugenics. Because of this, Mulder steals Sanjay's phone, which leads him to Sanjay's gay lover, Gupta, who informs Mulder that Sanjay had a secret apartment on top of the one that had already been investigated by the authorities. At the same time, Scully is performing an autopsy on Sanjay and finds the words "Founder's Mutation" written on his hand. This turns out to be a reference to the reclusive Dr. Augustus Goldman, a man everyone at the company refers to as "The Founder." Mulder and Scully then go to search Sanjay's real apartment where they find several pictures of severely disfigured children. They also trigger a silent alarm and, as the police arrive, Mulder is overcome by the same high-pitched sound that Sanjay heard.
Of final note are the rather touching scenes in which Scully and Mulder have separate fantasies about what life would have been like if they had gotten to raise their son, William. In fact, the episode ends on Mulder's.
While I said the episode got muddy, I think that is more due to my own inattention than the writing. The episode was a fine return to form for the show and contained some really great moments. B+, bordering on A-. I'd have to see it one more time to be sure.