The X-Files Recap With Spoilers: Founder's Mutation

Before the episode fully starts, the recap notes that in 2001, they had a son named William and gave him up for adoption. Their child was alluded to in the premiere, but this particular piece of information hadn't been imparted to potential new members of the audience.

The episode proper opens with a Dr. Sanjay entering a high security building using biometric security. He's hearing a high-pitched, painful sound and is miserable — but doesn't want to talk to his coworker about it.

In a corporate meeting, they get news that the company founder wants them to start over. Augustus Goldman is apparently a recluse, who is consumed by his other interests and hasn't been seen in years.

During the meeting, Sanjay keeps hearing the high-pitched sound, which seems to be driving him crazy, as time slows around him and he screams, then runs out of the room.

In a server room later, he hears voices telling him "Do it, now. Data is the key," and watches files transfer on a computer screen while people from the meeting pound on the door outside. When he looks away from the screen, he collapses. Soon enough, security starts drilling into the door. Unable to stop the squealing noises, Sanjay picks up a screwdriver and inserts it into his own ear, killing himself.

Later, Mulder and Scully arrive while a crime scene photographer records the room for posterity. He asks her for her take, and she says witnesses all have consistent accounts of what he did.

Mulder is confused that he chose the most secure room in the building to kill himself. He picks up a hard drive from a desk, and immediately a member of the building's security swoops in to tell him that the drive is classified and property of the Department of Defense. Similarly, he can't put Mulder in touch with the founder to discuss what Sanjay may have been attempting to access. Scully asks for copies of the complex's security videos. While she's talking to security, Mulder uses the body's fingerprint to unlock the victim's cell phone and sneaks out of the room with it.

Over Scully's objections, Mulder scours the phone for information and comes across someone named Gupta, to whom the victim spoke every night. Scully tells Mulder that in the language local to Sanjay's home region in India, "Gupta" means "Secret." On the way out of the building, they nearly bump right into a janitor.

At a bar, Mulder arrives to speak to Gupta, who is waiting alone in a booth. He asks to go somewhere more private to talk, and while Gupta is initially reluctant, Mulder convinces him. The pair head to a bathroom, where Gupta starts undoing Mulder's pants. When Mulder realizes there's been a miscommunication, Gupta gets frustrated and starts to storm out, but Mulder stops him to let him know that Sanjay is dead.

At Sanjay's autopsy, Scully removes the letter opener and begins her examination, but quickly notices that Sanjay had written something on his palm.

At the bar, Gupta tells Mulder that Sanjay was upset about "his kids," who were dying. Mulder notes he was single and had no life to speak of based on his home. Gupta tells him that Sanjay lived two lives at two separate places.

At the morgue, Scully reveals to Mulder that before his death, Sanjay had written "Founder's mutation" on his palm. They look at autopsy x-rays are are somewhat surprised to see that the letter opener went in at one angle, then seemed to veer up to the auditory cortex. Scully mentions that just before he left the meeting he was blurting out something about sounds nobody else could hear. The pair wonder whether Sanjay left more clues behind, but Scully notes that they've already scoured his apartment. Mulder says he had another, and they should find it.

While they're sitting in the car outside Sanjay's second apartment, a young man runs into their parked vehicle, then waves by way of an apology and moves on. They head inside, where they find dozens of photos of children, all of whom seem to have some kind of exotic diseases. The photos seem to have been taken in a clinical setting.

Scully sees lights outside: police are coming. Before she can go meet them, Mulder opens a drawer and starts getting the same strange symptoms, and hearing the same high-pitched squeal, as Sanjay had.

In his office, Skinner tells the pair that their investigation is closed, as the files they took from Sanjay's apartment are classified and not available to them. After a representative for the Department of Defense, who was on hand to take the files, leaves the room, Skinner asks them if they made copies. Mulder says he got a few, and that he thinks the children are failed experiments, intimating that the Department of Defense has been experimenting on humans.

Skinner says that the bureaucracy of the FBI has gotten worse in the last few years, and that it may take days for him to formally finish closing the investigation.

Downstairs, Scully has synched up timestamps on the security footage to around the time of Sanjay's suicide. She asks Mulder what happened to him at the apartment, and he said that he heard a squeal, and the words "find her." He sees birds gathering out on the lawn in the security footage, and suspects that it may have been a sound inaudible to the human ear that drove worms out of the ground and made the grounds so attractive to the birds at that moment. Scully still wonders, even if he's right, what it all means.

Mulder says they need to talk to Goldman, who is the only one who might know how it all fits together.

Scully tells Mulder that she's concerned he could suffer the same fate as Dr. Sanjay. When he says danger hasn't ever stopped them before, Scully says she might have a line on Goldman.

At the hospital, Scully appeals to the nun who was in charge of where she used to work, and asks her to get in touch with Goldman on her behalf. When Sister Mary leaves to call the Founder, a girl named Agnes motions the pair of them into a side room where she begs them to get out of there, as she worries they're going to take away her child. When she sees Mary returning, she panics and says she was just joking around, so Mulder surreptitiously hands her his card. He asks Mary how the women are chosen for the charity ward Goldman pays for, and Mary says they're all homeless, addicts or otherwise people nobody else wants.

Outside, Mulder proposes that taking poor women off the streets and experimenting on their babies for the Department of Defense could be another phase of the project they were working to uncover with O'Malley. Scully asks him if this is what he thinks happened to her 15 years ago, and whether he ever thinks about William. He admits he does but says he's felt he had to put it behind him. Scully says that she hasn't been able to completely, that she sometimes hates herself for not being a part of her child's life. She asks if Mulder believes he was an experiment, and Mulder says he doesn't know. She asks, what if William is out there somewhere like one of the kids on Sanjay's wall. Mulder says all they can do is try to expose the truth and see what happens.

Cut to a scene of Scully walking William to his first day of school; they enter, and then the door closes and he comes back out; he leaves the school campus, and she tells him to be home in time for dinner. Suddenly, a wind blows and she runs to the street, where he's been in a car accident; he's hurt. She hears his voice over her shoulder, and suddenly she's at home, where he's asking for her help. He has large, all-black eyes and asks her what's happening to him. She's taken aback. Suddenly, she's alone at her desk, looking at a baby picture — the only true memory she has of him.

At Goldman Technology the next day, Goldman tells Scully and Mulder that his work is to save children. He walks them around a wing of a hospital where children are suffering from bizarre and terrible ailments. He offers Scully to talk to one of the patients and Scully says OK. She taks a boy with a large tumor completely covering one of his eyes — a form of Cruzon Syndrome. Scully challenges Goldman on why the kids are being isolated, and he says that because they're working with totally unique treatment methods, environmental factors have to be eliminated. When Scully asks whether the Department of Defense is involved because he's looking into alien DNA, he gets frustrated with her — and then excuses himself when they see a teenage girl fighting with an orderly and seemingly spilling a cart of meds with telekinesis.

As they leave, Mulder gets a text: something has happened to Agnes. She was killed by a hit-and-run, and local police found Mulder's card in her pocket. What's more, her baby is gone.

At the morgue, Scully confirms that the baby was surgically removed before she was hit by the car.

Mulder suggested that The Syndicate might still be trying to create alien-human hybrids, and ultimately the conversation turns to Goldman's wife, who has been in a hospital for the criminally insane for years, since she was convicted of murdering her baby — a body which was never found.

At the hospital, Mulder tries communicating with Mrs. Goldman, but she's non-responsive. She isn't catatonic, though; she throws the apple from her lunch tray at a cat when it tries to enter the room. Finally, she says that she won't answer questions about her husband, as he's the one still keeping her in the hospital.

Mulder asks if she misses her daughter, and Mrs. Goldman remembers finding her daughter Molly at the bottom of the pool when she was two. She survived ten minutes under the water, happy and breathing down there. She says she knew her husband had done something to the baby's embryo.At the time, she was nine months pregnant and wasn't going to let her husband have her son. She tells them about stabbing her husband in the arm and making an escape, but that she knew the government wouldn't let her get away. She says she hit a deer and crashed the car in her panic, and then she heard a high-pitched, loud squealing sound. She says her husband was talking to her, and she knew what she had to do. She stabbed herself in the belly with the knife she had used to escape, delivering it at the side of the road. She tells them she passed out from loss of blood and woke up in the hospital, and never saw her son again.

As they leave, Mulder posits that the baby would no longer be a baby, and that it's possible it "told" its mother to release it and then also reached out to Mulder to find her. On the way out the door, he sees a janitor and stops, noticing that the same subcontractors who provide janitorial services to the psychiatric hospital, do so for the Goldman building.

Back at the FBI, Mulder sees that while Sanjay was in the server room, a janitor from A1 was in the room directly above it. The janitor, too, was in pain while Sanjay was. Mulder gets a text that the janitor's name is Kyle Gilligan; he's a high school dropout who also worked at St. Elizabeth's Psychiatric Hospital recently.

On a country road, Mulder and Scully get out of their vehicle near a farmhouse and introduce themselves to a woman who identifies herself was Kyle's mother. She tells them she won't allow them to talk to him. When Mulder asks where she found the child after the accident, the woman starts to scream at them to go away. Suddenly, birds gather nearby and Mulder collapses, hearing the noise. As he rolls around on the ground, Scully heads to a barn to look for Kyle.

They arrest Kyle, over his mother's sobbing objections, and drive away with him. They ask Kyle why he killed Dr. Sanjay, but Kyle says he didn't want Sanjay to die — that Sanjay was helping him. He says he wants to find his sister, Molly. He says he knows Jackie Goldman is his real mother.

They take Kyle to Dr. Goldman for an examination. He asks to take some blood, and Kyle asks him where Molly is. Goldman asks him how he knows that name, and what he would do once he found her. When he says he doesn't know, Goldman tells Kyle he's going to let him meet Molly, and takes him to a girl.

Kyle quickly realizes that the girl isn't his sister, and runs away. He speeds through the hospital, looking for Molly, and finds a girl who looks very similar to the one he just met. The two look at each other through a glass door and communicate with their minds, then they touch hands through the glass and break it and all the glass in the area telekinetically. Holding hands, they use the sonic attack on their father, then Molly throws Scully and Mulder around with her mind when they try to intervene to save him. Eventually the two of them kill Goldman.

Soon, the place is swarming with soldiers. Skinner is there, and tells the pair that they're off the case as it's now designated Top Secret. There's been no trace of Molly or Kyle since Mulder and Scully lost consciousness. Scully, though, had stolen the vial of Kyle's blood before leaving the lab.

Later, Mulder is sitting on the couch with a young William, watching 2001: A Space Odyssey, then flashing forward two setting off rockets together in a field, after which time William says he's going to go to space someday. Mulder turns around to hear William shouting for him, then enters his son's room to see him being abducted like Samantha was; then, the fantasy dissolves back to Mulder staring at that same baby photo alone in his kitchen.