This episodes starts with a new character, Dr. Sanjay. One of his eyes is bloodshot and he has a loud ringing in his ear. He enters a meeting at his work where it’s told that their tested and proven stem cell research, overseen by founder Augustus Goldman, needs to be done all over. The coworkers begin to bicker about the validity of the tests when the ringing gets louder for Dr. Sanjay. He sees a murder of crows gather outside the window. Dr. Sanjay screams, “Can’t anyone hear that?” and runs out of the room. He locks himself inside a research lab, writes something on his hand, and drives a letter opener through his ear, instantly killing him.

Our favorite suit-wearing, flashlight toting duo walks in the lab to examine the scene. Mulder asks Scully her professional diagnosis to which she replies that Sanjay had a psychotic breakdown, rather sarcastically noting the letter opener through the ear. Mulder disregards the body and moves to take the doctor’s hard drive as evidence. A man from the Department of Defense walks in and says that it’s not his business and Mulder makes his case that he needs to see why Dr. Sanjay was driven crazy. After being shut down again, Mulder insists on speaking to the company’s founder, Dr. Goldman. While the Defense agent isn’t looking, Mulder quickly steals Sanjay’s phone and acquires his fingerprint to unlock it.

Walking out of the lab, Scully scolds Mulder for taking the phone while he looks through the contacts. He finds someone who has been called many times named Gupta. Scully reveals that in another language, Gupta means “secret”. Impressed, Mulder asks where she knows this information. “I’m old school, Mulder. Pre-Google.”

Mulder meets Gupta at a restaurant. Seeking privacy for their conversation, the two move to a back room where Gupta drops to his knees and begins to unbutton Mulder’s pants. Mulder realizes what he’s gotten himself into and stops the deed. This, of course, offends Gupta and he goes on a rant before Mulder interrupts him with the news that Sanjay is dead.

Scully begins her autopsy on Dr. Sanjay. She sees the message written on his hand.

Meanwhile, Gupta talks to Mulder about his relationship with Sanjay. Sanjay was always telling him about how he was worried about his kids dying. Although Gupta didn’t know about any kids, he says, “I just tried to make him feel better.” Gupta reveals that he lived two very separate lives.

Scully summons Mulder to the autopsy room. After breaking his fingers to reveal his palm, they are able to read Sanjay’s last message: Founder’s Mutation. Examining the x-rays, Mulder notes that the letter opener was not shoved straight into the brain, but at an angle… like Sanjay was hunting for something.

Mulder and Scully drive to Dupont Circle, DC, where Dr. Sanjay lived. Scully expresses her sadness for how Sanjay had to hide being gay. Mulder replies, “Being gay wasn’t his only secret.” They find a large wall full of snapshots of children, all under ten years of age. Each child had some kind of physical deformity and the pair realize that these are the children Sanjay was afraid were dying.

Hearing noises outside, Scully realizes that she and Mulder must’ve set off an alarm and tries to leave. Mulder falls to the ground holding his head, ringing searing through his senses. His world turns into slow motion. He sweats and most noise stops except two words: “Find her.”

Mulder and Scully sit in Assistant Director Skinner’s office, receiving a lecture from a man from the Department of Defense. Skinner plays along, acting to scold the two. The man threatens what could happen to the duo if they are caught doing illegal things again, to which Mulder replies, “I’m familiar with Edward Snowden.” The man leaves and Skinner takes off his mask. He encourages Mulder and Scully do what needs to be done, giving them a warm “welcome back, you two.”

Scully asks Mulder what happened in Sanjay’s house. He tells her about the ringing, the slow motion he experienced, and the two words that were clear in his mind. Scully expresses the concern that Mulder may also be driven to kill himself.

At Our Lady of Sorrows Hospital, Scully talks to her coworker Mary since she knows how to find Goldman. Goldman is a large financial donor to the hospital and. Mary is curious to know why they need to contact Goldman in the first place and Scully tells her he’s under investigation. “Obamacare,” Mulder adds. Mary agrees to make the call and Mulder adds that she needs to ask him about the Founder’s Mutation.

As Mary walks away, a young woman calls the attention of the agents. Her name is Agnes and she desperately wants out of the hospital. She is visibly pregnant and claims that she doesn’t belong there. She says, “I’m not giving him up. I don’t care if he’s sick.” She says everyone there has the same story and begins to explain when Mary returns. She stops talking and asks the agents that they not tell. Mulder gives her his card in case she wants to talk.

Mary claims the people in Agnes’s ward are either homeless, damaged, unmarried, on drugs, or addicted to alcohol. Outside, Mulder theorizes that this is just another phase of the project. Scully asks him, “Was I just an incubator?” referring to the child they had together- the child who potentially has alien DNA. “You’re never just anything to me,” Mulder comforts her. Scully asks Mulder if he thinks that William, their son, is just an experiment. Mulder replies, “All we can do is pull the thread and see what unravels.”

Scully has a vision or a dream about her son. She is walking him to school on her first day. She asks him what’s most important. After his few guesses, she corrects him: the most important thing is to remember that she loves him. Her dream flashes forward to him having a broken arm. He is on a stretcher outside of an ambulance. She tells him he will be ok. Another flash forward has her at home when she hears William calling for her, “Mom! Mom, please?” She walks in his room as he turns around to reveal entirely black eyes and he asks, “What’s happening to me?”

In the real world, she stares at his baby picture.

Goldman meets with Mulder and Scully. He claims that “Founder’s Mutation” is meaningless and that his only goal is to save children. He takes the two on a tour of his facility where they see children with a variety of life-altering maladies. They see a boy from the pictures on Sanjay’s wall and speak to him. His name is Adam. Scully asks him how long he’s been there. “Forever.” She then asks where his parents are. “I don’t have any.” Goldman leads the two away from the children. She asks why, if the children had genetic disorders and weren’t contagious, were they in sealed glass rooms. She brings up the concept of alien DNA to Goldman and suggest that this is the reason his research is government funded. A girl down the hall begins to throw a tantrum and Goldman rushes to aid her. Scully states, “He didn’t answer my question.”

Mulder receives a text. Something has happened to Agnes.

Arriving at the scene of a car accident, Agnes’ body is on the ground. She has been killed in a hit and run. Scully realizes that her baby is gone.

After an autopsy, Scully deducts that Agnes was killed by the accident, but that the baby was surgically removed after. She is unable to determine if the fetus was alive or dead when removed. She and Mulder discuss the reason why she was killed and conclude that it was a setup. Agnes was ready to talk to the FBI about her baby and the experiments, and her baby was the only evidence of her involvement in Goldman’s experiments. Mulder brings up that in 1973, people tried to change the population by creating alien/human hybrids. Scully talks about how that would genetically change the entire world, which is the first step of evolution.

Mulder reveals that Dr. Goldman’s wife was committed for criminal insanity seventeen years ago. She murdered her own baby, who was never found.

The pair visit St. Elizabeth Hospital where Mrs. Goldman resides. Mulder asks her about the husband, to which Mrs. Goldman replies by throwing an apple at a cat. She reveals that Dr. Goldman is the person keeping her locked up. When asked about her first child Molly, she says she always knew something was wrong with her and it was confirmed when she was two. Molly had fallen into a pool and had been underwater for ten minutes when Mrs. Goldman dove in to retrieve her. Assuming she was dead, Mrs. Goldman was surprised to see her daughter not only alive, but breathing underwater. She realized that Dr. Goldman had done experiments on their own child.

Pregnant with their second child, a son, Mrs. Goldman took a large knife, demanded her daughter (who Dr. Goldman took away from her), and left the house. “I had to get away from that monster,” she said, referring to her husband. Alone, she drove away with her unborn son. She accidentally rolled her car. She heard a ringing in her ears and realized it was her baby talking to her. She drove the knife into her own stomach, but not to kill him. “I let him out.”

On the way out of the hospital, Scully says that although Mrs. Goldman sounds insane, there’s “something about her I trust.” Mulder sees a janitor and asks him if he’s employed by the hospital. The janitor replies that he’s from A1 Janitorial, an independent company the hospital hires to come in. Mulder reviews security footage from Sanjay’s death and sees an A1 Janitor who works both there and at St. Elizabeth. His name is Kyle Gilligan.

Mulder and Scully go to Kyle Gilligan’s house and are unwelcomed by his mother. They begin questioning her when she gets defensive. She is unwilling to answer questions and demands they leave the property. Mulder interrupts, “You didn’t give birth to Kyle.” His mother yells and crows flock the field. She quietly says, “Bad things happen when the birds gather.”

Mulder collapses to the ground with the ringing in his ears. Scully screams, demanding to know where Kyle is. With silence from the woman, Scully runs off, gun drawn, to find Kyle. The mom yells after her, “He was trying to protect me!” Scully finds him: “Whatever you’re doing, stop right there!”

Kyle sits in the back of Scully and Mulder’s car. (Mulder is better.) Kyle talks about Dr. Sanjay, “I didn’t want him to die. He was helping me…I just want to find my sister.” Mulder is irked with him, saying he doesn’t know how to find her. Scully quickly responds, “I know who knows.”

At the hospital, Kyle asks Dr. Goldman where Molly is. Taking his blood, Dr. Goldman asks what he would do once Kyle found her. He allows a meeting. A girl in a small room greets Kyle smiling. He soon realizes that this is not his sister and runs to find the real Molly. He sees her in a small glass cubicle room. She telepathically reaches out to him, saying, “I didn’t know I had a brother.” He places his hands against the glass door and says, “You ready?”

The glass shatters, and not just the door. All the windows and glass through both halls in the intersection of the hospital crash to the floor. Dr. Goldman runs toward the noise. Kyle sees him and uses his mind to make Dr. Goldman’s eyes, nose, mouth, and ears bleed. Molly telepathically force-pushes away Mulder and Scully.

Skinner arrives on the scene. Mulder and Scully ask where the children went. “You were the last to see them.” Since the two had passed out, their whereabouts are unknown. Mulder reveals that he passed out after Dr. Goldman’s eyes popped out of his head. “You can’t unsee that.”

At his home, Mulder has a vision or dream about William. The two watch TV and Mulder tells him about evolution, aliens, and scientific theory. A flash forward shows them making small rockets to launch from the backyard. Mulder helps William fix his rocket fins and teaches him a lesson about a hard life being rewarding. William wears a NASA baseball hat and wants to be an astronaut one day. Another flash forward shows Mulder running to William’s room in time to see a beam from an alien ship taking William away.

In real life, Mulder stares at William’s baby picture.

So what did you think of this episode? Let us know in the comments!