Dr. Sanjay is clearly ill when he heads into work at Nugenics Technology. His eyes are bloodshot and he hears loud, high-pitched sounds that cause him pain. He appears to not have slept in a while. In the morning meeting, the noise gets worse, but only he can hear it. The world around him goes slo-mo, he can’t focus, and there is an enormous flock of birds on the lawn outside. The noise gets to be too much for him, and he screams, “Can’t anyone hear that??” Of course, no one can. Sanjay rushes from the office and locks himself into the server room, where voices in his head tell him “data is the key.” His co-workers are pounding on the door, desperate to get to him. The sounds in Sanjay’s head are deafening. He scribbles something on his hand, then stabs a letter opener into his ear.
Mulder and Scully come in to investigate, and are immediately stonewalled by the Department of Defense, who have the facility on lockdown. The FBI is investigating because they do have government clearance, but apparently that is just to be in the building – Mulder gets chastised when he tries to collect a hard drive as evidence. He does manage to pocket Sanjay’s phone before they leave. Outside, he discovers that Sanjay spoke to someone named Gupta every night.
While Scully does Sanjay’s autopsy, Mulder meets Gupta at a bar. He wants to go somewhere more private, promising he is safe and can be trusted. Gupta leads him into a backroom, where he immediately drops to his knees and starts unbuckling Mulder’s pants. “Woah!” he cries, backing up. Signals were definitely crossed, and Gupta is offended and annoyed that he wasted his time. He storms out, but not before Mulder tells him that Sanjay is dead. The men sit down to speak, and Gupta admits that Sanjay has been distant for a while and refused to be physical. He was upset that his kids were dying. Mulder mentions there was no sign of children at Sanjay’s “antiseptic” apartment, but that was his “for show” apartment.
Scully calls Mulder in to show him what she found during the autopsy. The letter opener in the brain was definitely cause of death, but it was at an angle, like Sanjay was digging around for something. More interesting was what she found written on Sanjay’s hand. “Founder’s Mutation.” Dr. Goldman is the founder of Nugenics Technology, and creepily enough, those who worked there often called him “the Founder.”
The agents go check out Sanjay’s “real” home, and find that being gay wasn’t Sanjay’s only secret. The walls are covered with photos of hideously deformed children in a clinical setting. Before they can learn much more, Scully sees the police pull up outside. Quickly, they scramble to find some files before they are “caught,” and Mulder is hit with the same ear-piercing tone that makes him double over in pain. Scully rushes to him until the police show up, then goes to calm them down. Mulder is deaf to the outside world, except for one phrase: “find her.”
Requisite meeting with Skinner, who won’t look at the files they took, with no warrant, from the apartment. Mulder wants to research what is going on with the kids in those photos, but a representative from the DoD is there to collect the files and shut down their investigation. He leaves with the files, but Skinner assumes Mulder made some copies. (Of course he did – plus, he has a “photographic memory.”) Scully wants to investigate more, and while Skinner can’t approve that directly, he does assure them that the FBI is less efficient nowadays, so it will be a few days before he can officially close out the case. “Welcome back you two.”
Scully waits until they are back in their basement office to ask Mulder what happened to him in the apartment. She didn’t hear anything, and wants to know how this is all connected. Mulder wants to talk to Goldman, which will be tough. She shows him some of the Neugenics surveillance footage, which shows Sanjay doubled over in the same pain that gripped Mulder. She is worried. “It could be you, Mulder. This is dangerous.” “When has that ever stopped us?” he asks with his trademark Mulder grin.
Dr. Goldman is elusive and not willing to speak to the authorities. Luckily, he is also a huge donor to the hospital Scully works out of. She meets with Sister Mary, who oversees the ward that Goldman created. She finally agrees to call Goldman and relay a message to him. Mulder tells her to ask him about the “founder’s mutation.” A woman named Agnes motions for them to join her in the “common room” of Goldman’s wing. She is pregnant and wants to leave. This ward that Goldman has created is meant to help pregnant women who have sick, deformed babies. All the women there are homeless, “damaged,” without fathers for their babies. All the babies are deformed, so the mothers are cared for in exchange for giving up their babies. But Agnes has changed her mind; she wants to keep her baby. When she sees Sister Mary heading back in, she changes her mind. Mulder slips her his card before being escorted out. Dr. Goldman has agreed to meet with them.
Mulder finds this whole ward “insidious,” thinking these women are incubators. Scully gets mad. “This is what you suspected all along, but were afraid to articulate,” she charges. “Is this what you believe happened to me 15 years ago, when I got pregnant, when I had my baby? Was I just an incubator?” (Note: she says MY baby. Not OUR baby.) He admits he thinks about William, but had to put it behind him. Scully hates herself for not having the courage to protect him. Mulder assures her she did the right thing, and she asks if he believes William was an experiment. Mulder doesn’t know. “All we can do is pull that thread, see what unravels.”
They meet with Goldman at Goldman Technologies. His research deals with genetic manipulation and promises there are no secrets or experimentations here; they are just trying to save children. The children there suffer from things like Proteus Syndrome (overgrowth of bones, skin, and other tissue) and Ectodermal Dysplasia (abnormal development of hair, skin, teeth, nails) and have all manner of heinous defects. One of them, Adam, with one eye and a huge, swollen bald head, has been here his whole life. He is in a hermetically-sealed room, to “prevent environmental factors” that may affect his treatment. Scully gets down to brass tax and asks him if these children have alien DNA, and if that is why the Department of Defense is funding his research. “I was told you were the rational one,” Goldman says, vaguely offended. He leaves without answering, supposedly to help with a girl named Molly at the end of the hall who has become violent. Mulder gets a text – something happened to Agnes.
Arriving at the scene (called by local cops because Mulder’s card was in her pocket), they find Agnes was the victim of a hit and run accident. She is no longer pregnant. Scully’s autopsy reveals that she died of blunt force trauma, and the baby was surgically removed but could not tell if it was alive or dead when removed – it was unlikely that a baby could survive that amount of trauma. Mulder points out that that is only if it was a human baby, and reminds her of the Syndicate’s plan to create alien-human hybrids. “The project was unsuccessful, but I doubt they stopped trying.” Each generation starts with the Founder’s Mutation, which would be the next step in evolution. Mulder has a new lead: Jackie Goldman, the good doctor’s wife, currently being held in an asylum after being convicted of killing her baby.
Mulder and Scully visit Jackie, who hasn’t said a word in the time they have been there. She finally speaks, only to say she won’t speak about her husband. Mulder tries a different tact and asks about her daughter, Molly. Then you can’t shut Jackie up, and she spills all, much of it told in flashbacks.
When Jackie was pregnant with her son, Molly was about six years old. She knew there was something “weird” about Molly from the moment she was born, but at age six, Molly fell in the pool. She was there for ten minutes, and should have rightly been dead. But when Jackie jumped in to rescue her, Molly was alive, smiling, and even breathing underwater. It was then that Jackie knew her husband did “something” to the embryo. She was nine months pregnant with her son and scared of her husband. She leaves him in a panic, holding a kitchen knife to his throat, and rushes away. She didn’t know what to do or who to trust, so she just drove. She crashed her car and pulled herself out. Then she heard the high-pitched tone and knew her son was talking to her in the only way he knew how. She cut open her belly, but insists she didn’t kill him. In the flashback, we see the baby reach out from her belly, very alive and seemingly sentient. Jackie passed out from the loss of blood and woke in the hospital. She never saw her son again.
As the agents leave, Scully is confused. Her medical training says that Jackie is delusional, but there is something about her that she trusts. Mulder points out the similarities between Scully and Jackie’s connections to their children, and Scully asks Mulder if he thinks he was communicating with him. Mulder doesn’t answer, and instead asks a janitor if he is a contractor. The pieces are coming together for Mulder. Back at the office, Mulder discovers that A1 Janitorial hires out janitors to both St. Elizabeth’s Hospital and Neugenics. According to the surveillance footage, there was a janitor cleaning the floor directly above Sanjay when he killed himself. That janitor is Kyle Gilligan, and he also worked at St. Elizabeth’s last month.
Mulder and Scully arrive at Kyle’s house, and they are greeted by his mother, an angry woman who won’t let them near her son. “He’s simple, and he’s a minor.” Mulder confronts her about having Jackie Goldman’s baby and she screams at them to leave. The birds gather and the mom gets scared, whispering, “bad things happen when the birds gather.” Mulder is struck by the high-pitched sound and falls off the porch in pain. Scully screams for Kyle’s location, and mom just points weakly. She runs through the birds and finds Kyle in a barn. They put him in the backseat of the car (Mulder is fine, by the way) with mom begging them not to take him. Mulder tries to talk to him, knows that Kyle didn’t know what he was doing. “I didn’t want Sanjay to die,” Kyle says. He just wants to find his sister.
They take Kyle to Dr. Goldman, who examines him and takes a blood sample. He asks to be taken to Molly, and Goldman is surprised – how do you know that name? Kyle doesn’t know, but Goldman takes him to meet Molly. Kyle instantly freaks out and knows that this girl is not his sister. He runs and finds another girl (who appears to be younger than he is). Her eyes open wide, though she doesn’t know who he is. Kyle can hear her thoughts; they know each other immediately. Molly is sealed in a room, and they put their hands up against the glass. The glass breaks, as does all the other glass in the area. The siblings clasp hands, which Goldman screams at them for. Molly sends the high-pitched noise into Goldman’s brain and telepathically throws Mulder and Scully against the wall.
A huge government force is outside, cleaning up the situation. The DoD is firmly in control. Mulder was the last to see Molly and Kyle, but he blacked out after Goldman’s eyes popped out of their sockets. But Mulder does reveal to Scully that he pocketed Kyle’s blood sample.
