When a scientist suddenly commits suicide, Mulder and Scully investigate what unseen force may have driven him to it. What they uncover is a laboratory where extreme genetic experimentation has been going on for decades, breeding subjects who possess unexpected and dangerous powers - and who harbor deep resentments in the all-new "Founder's Mutation" Source
Dr. Sanjay, a research scientist, attends a meeting during which a sudden sharp ringing noise causes him to flee the room. He locks himself inside a server room and attempts to export files. The ringing, which no other person can hear, grows too loud so he writes a message on his palm and commits suicide by jabbing a letter opener through his ear.
Agents Fox Mulder and Dana Scully are called to the scene because the facility operates with the Department of Defense and the server room is highly classified. After being chased away by a DOD agent, Mulder reveals he stole Dr. Sanjay's phone. He contacts Gupta, a contact named "secret" and discovers he is Dr. Sanjay's secret gay lover. Meanwhile, Scully performs her autopsy and discovers the message written on the victim's hand - "Founder's Mutation." She also pieces together his outburst about the sound he claimed to hear and the fact that he punctured his brain's auditory cortex.
Mulder and Scully investigate Dr. Sanjay's secret apartment and discover images of children with mutations. They collect some patient files but Mulder begins to exhibit effects of the sound that drove Dr. Sanjay to suicide. The police enter the apartment while Mulder cowers in pain on the floor.
Later in Walter Skinner's office, Mulder and Scully are told that the case is closed. Another DOD officer threatens action if they reveal anything they read in the files. He leaves and Skinner tells his agents they have a few days to complete their investigation.
Following records they found in the files they recovered from Dr. Sanjay's apartment, the agents visit Our Lady of Sorrows hospital and discover that Augustus Goldman, the man funding the research performed by Dr. Sanjay, was also responsible for donating money to a pregnancy ward for women expecting birth defects. A pregnant woman, Agnes, has decided to keep her baby and asks Mulder and Scully to help her escape. Mulder slips her his contact information.
Outside of the hospital, Mulder posits that the DOD is continuing the work of the Syndicate and continuing to breed alien-human hybrids using the maternity ward to attract homeless or impoverished women. Mulder and Scully talk about William and both share their worries that they have no way of knowing if he was the result of similar experiments.
At home, Scully dreams of a young William on his first day at school. The dream continues to an accident where William breaks his arm. She wakes abruptly when she dreams that she enters his room and discovers that he appears to be mutating into an alien-like form.
The next day, the agents visit Augustus Goldman at Goldman Technology to inquire about his research into genetic mutations. He shows them children, many of whom were seen in pictures in Dr. Sanjay's apartment, and informs the agents he is working on research to cure them. A patient throws a tantrum in the hallway and Dr. Goldman asks them to leave.
On their way out, Mulder receives a message that Agnes has killed in a car accident. They visit the crime scene and notice that her baby is missing. At the morgue, Scully concludes the baby was surgically removed. Mulder discovers that Goldman's wife Jackie was admitted into a mental institute after she killed her child. At the hospital the agents attempt to ask Jackie some questions. After initially refusing she tells them a story of how she discovered her 2-year old daughter Molly breathing underwater in the bottom of their swimming pool, and had been there for about 10 minutes. She knew her husband had performed tests on her, so she decided to flee in the night with her unborn son. However, a deer jumped in front of her car, flipping the vehicle. Crawling out she gave herself an emergency C-section when a very loud ringing sound told her to. When she woke up the baby was missing and she was in the hospital.
While leaving, Mulder notices the uniform of the janitor, who confirms that the company he works for is sub-contracted to provide cleaning services to many companies. Mulder then pieces together that another company janitor was the same person that worked at Jackie's institute, and was working near Dr. Sanjay when he killed himself. Security video shows the janitor, who was standing in the office above Dr. Sanjay, having some sort of reaction which affects Sanjay, causing his death. Mulder and Scully visit the home of the janitor, Kyle, and ask his mother questions. Mulder realizes that she is not Kyle's biological mother, though she does care for him, and asks where she found him. She grows upset and Mulder once again hears the painful ringing noise, causing him debilitating pain.
Scully searches the property and finds Kyle, who apparently stops the noise. They apprehend him and tell him they know his past including his involvement in the suicide. He unloads, telling them that it was an accident and Dr. Sanjay was trying to help him find his sister, whom he can "hear." Mulder realizes that Kyle can't control his abilities.
They visit Goldman Technology and Dr. Goldman draws blood from Kyle, not knowing he's his son. Kyle asks to see Molly and Dr. Goldman takes him to a teenage girl. Kyle quickly learns that she is not Molly so he races through the facility and finds his true sister. They communicate via telepathy and break the glass window on her locked door and all the nearby windows with their minds. When Dr. Goldman and Agents Scully and Mulder arrive, Kyle angrily attacks Dr. Goldman with the ringing noise, causing lethal bleeding from all the orifices of his head as he screams, while Molly telekinetically throws and knocks out Scully against the wall, and then pushes and pins Mulder to the opposite end of the hall where he can only watch helplessly.
Later, outside the facility, Skinner passes onto Scully and Mulder that the teenagers have escaped, and the DOD has locked down everything to do with the building and removed the case from the FBI's jurisdiction. On being asked about Dr. Goldman's cause of death, Mulder reveals that before he blacked out, he witnessed the man's eyes popping out of his head, a memory he could have done without. They walk away and Mulder shows Scully that he has stolen the vial of Kyle's blood.
Mulder dreams about raising William. They watch 2001: A Space Odyssey together and discus the monolith. They build and shoot rockets together. Mulder approaches his son's door to horrifically discover his son is being abducted in the same manner Samantha Mulder was abducted.
Mulder wakes from the nightmare and the episode ends with him sitting at his kitchen table, looking at William's baby picture.
- This episode was originally Episode 10.05 in the Production Order.
Cast and Characters
- As of this episode, Fox Mulder and Dana Scully have both been reinstated as FBI Special Agents and assigned to the newly reopened X-files unit.
- Fox Mulder is back in the X-files unit officially for the first time since the Season 7 episode "Requiem". His following appearances working the X-files during Season 8 were unofficial and against orders until he was finally fired in the episode "Vienen".
- Dana Scully is back working the X-files unit full-time for the first time since the Season 8 episode "Alone" but she was often called upon to assist and advise Agents John Doggett and Monica Reyes in their investigations during Season 9.
- Ryan Robbins (Murphy) previously played Mailer in the Millennium episode "The Sound of Snow".
- Christine Willes (Sister Mary) previously played Karen Kosseff in The X-Files episodes "Irresistible", "The Căluşari" and "Elegy".
- David Duchovny as Special Agent Fox Mulder
- Gillian Anderson as Special Agent Dana Scully
- Mitch Pileggi as Assistant Director Walter Skinner
- Jonathan Whitesell as Kyle Goldman
- Rebecca Wisocky as Jackie Goldman
- Doug Savant as Augustus Goldman
- Aaron Douglas as Lindquist
- Vik Sahay as Gupta
- Ryan Robbins as Murphy
- Christine Willes as Sister Mary
- Kacey Rohl as Agnes
- Christopher Logan as Dr. Sanjay
- Omari Newton as Rogers
- Nikolai Witschl as Dr. Hill
- Alison Wandzura as Cynthia
- Daniela Dib as Sarah
- Megan Peta Hill as Molly Goldman
- Craig March as Detective Gordon
- Simon Chin as Janitor #2
- Amanda Burke as Rebecca
- Dean Redman as Police Officer
- Hannah Longworth as William (6 Years Old)
- Aiden Longworth as William (10 & 13 Years Old)
- Rowan Longworth as William (15 Years Old)
- Jaiven Natt as Adam
- Anja Savcic as Girl