“The X-Files” have been reopened and agents Fox Mulder (David Duchovny) and Dana Scully (Gillian Anderson) are back looking into cases of unexplained phenomenon in the six-episode miniseries event on Fox. In episode 2, titled “Founder’s Mutation,” Mulder and Scully get reminded of their past while investigating the suicide of a scientist whose labs has been experimenting with genetic mutations.
The episode begins with scientist Dr. Sonny Sanjay (Christopher Logan), who keeps hearing a loud ringing in his head while at a meeting for work at the Department of Defense. In addition to the noise in his head, Sanjay starts to also hear voices. He runs out of the meeting, goes onto a secure computer and stabs himself through the ear with a letter opener.
Scully believes the case is clear and that Sanjay had a mental breakdown and committed suicide. However, Mulder thinks the computer in the secured room could be involved and he wants to know what Sanjay was looking up when he died. He tries to take the hard drive as evidence, but security stops him. Mulder then asks to speak to “The Founder,” Augustus Goldman (Doug Savant), who’s the boss.
When Mulder and Scully get denied, Mulder steals Sanjay’s cell phone and leaves the crime scene. The two find a contact in Sanjay’s phone, an old lover named Gupta (Vik Sahay). Mulder arranges a meeting with Gupta and informs him that Sanjay is dead.
While Scully is doing the autopsy she discovers that Sanjay wrote “Founder’s Mutation” on his hand before he died, noting that "Founder" is referring to Goldman. Mulder and Scully head to Sanjay’s place where they find pictures of kids on the wall with mutations. As they search the apartment for files on the kids, the police show up and Mulder starts to hear the same ringing Sanjay heard in his ears.
The Department of Defense won’t allow Scully and Mulder to access Sanjay’s files, but Skinner covers for Mulder and Scully to give them a little more time to look into the case. Mulder believes the kids in the pictures were failed experiments, meaning the Department of Defense could be experimenting with genetic modification on humans.
Scully uses one of her contacts at the hospital, Sister Mary (Christine Willes), to get a meeting with Goldman. Mulder believes the hospital is serving as an incubator taking women’s children for Goldman’s experiments, which strikes a nerve with Scully as she’s reminded of their son William that they put up for adoption. She daydreams what it would've been like to raise William, but the scene comes to a strange end when she goes into William's room and he starts turning into an alien.
Goldman invites Scully and Mulder to the hospital where he says he’s working on treating genetic mutations. He shows them a number of child patients, who all have some kind of deformity. Scully believes Goldman could be working with alien DNA, but before he can answer her a patient gets loose and sends items flying off a tray without touching them. Scully and Mulder are then escorted out.
Mulder believes Goldman’s work could be part of an experiment to create an alien-human hybrid species, just like what the Syndicate had been trying to do. The two also discover that Goldman’s wife, Jackie Goldman (Rebecca Wisocky), was declared criminally insane for killing their baby, but the body was never found.
When they go see Jackie in the hospital they learn that Goldman used their daughter Molly as an experiment. Jackie found this out when Molly fell into a pool when she was little and she was able to breathe under the water. She tried to leave her husband fearing he’d try to experiment on the baby boy she was pregnant with. However, while leaving town she got into a car crash. The baby inside her communicated to her through a high pitched sound and she cut it out of her and set it free.
Mulder figures out the baby went on to grow up into a boy named Kyle (Jonathan Whitesell), who is a janitor in the building where Sanjay worked. Scully and Mulder go to Kyle’s home, and he tries to fight them off by using his mind to make the high pitched sound on Mulder.
Scully finds Kyle in a barn and takes him into custody. While driving in the car, Mulder tells Kyle he knows he can’t control his ability, but all Kyle cares about is finding his sister, Molly (Megan Peta Hill). They take him to see Goldman, who promises to take him to his sister after he takes a blood sample.
Goldman takes him to a girl he says is Molly, but Kyle realizes he’s being lied to. He runs out of the room and finds Molly, who can speak to him using her mind. Kyle breaks her out, as Mulder, Scully and Goldman come running down the hallway to stop him.
Kyle uses his ability to make Goldman hear the loud pitch and he makes the doctor start to bleed from his eyes and ears. The two siblings with powers are able to escape the facility, while also getting past Scully and Mulder. Skinner arrives on scene and lets them know there’s no trace of Kyle and Molly, but Mulder was able to sneak away the blood sample Goldman took.
The episode comes to an end with a daydream sequence of Mulder imagining what it would have been like to raise William and see him grow. Like Scully's sequence, his also comes to an end badly as William is shown being abducted by aliens. Is there some kind of connection between alien DNA and their child?