On December 21, 1997, Agt. Scully and her mother Margaret Scully traveled to the home of Agt. Scully’s brother Bill Scully Jr., and his wife, Tara Scully at the U.S. Naval Station in San Diego, California. Tara Scully was pregnant and close to delivery. On arrival, Agt. Scully and her mother noted that the layout of Bill Scully’s naval housing was identical to the naval housing in which the Scully family had lived when Agt. Scully, Bill Scully, and their deceased sister Melissa Scully were children.

When the rest of her family were upstairs, Agt. Scully answered the phone and heard a voice she later identified to Bill Scully as that of the deceased Melissa Scully. The caller used Agt. Scully's first name and urged her to help an unidentified female. Agt. Scully immediately called the San Diego Bureau office and requested that the call be traced. Bill Scully then drove her to the address produced by the trace, a one-family residence, where she encountered police in the process of investigation. Agt. Scully entered the house and approached the upstairs bathroom, where she encountered a detective identified as Kresge, as well as other officers. Agt. Scully identified herself as a Bureau agent and informed Det. Kresge that she had received a phone call from the residence twenty minutes earlier. Det. Kresge informed Agt. Scully that the police had been in the residence for at least thirty minutes and that the phone had been off the hook when they had arrived. In the bathtub, which was filled with water and blood, lay the body of a woman identified as Roberta Sim, 40 years old, resident with her husband and daughter of the home, an apparent suicide victim who had slashed her own wrists. According to Det. Kresge, Mrs. Sim had been dead for three hours.

Downstairs, Agt. Scully observed a man identified as Marshall Sim, husband of the deceased, and his daughter, identified as Emily Sim. Det. Kresge, having checked with the phone company, informed Agt. Scully that a call had indeed come to Bill Scully’s home from the Sim address but that no records showed a call having been made from the Sim address. He suggested that a software or other error would explain the discrepancy in the records.

Later that evening, at Bill Scully’s home, Agt. Scully called Agt. Mulder’s home phone number. When Agt. Mulder answered the phone, Agt. Scully hung up the phone without speaking. Over dinner, Tara Scully described her happiness at the prospect of giving birth. After dinner, in the kitchen, Agt. Scully privately revealed to Mrs. Scully the fact that as a result of her abduction in 1994 she was unable to conceive a child.

That night, asleep in a guest bedroom in Bill Scully’s home, Agt. Scully dreamed of her childhood. In the dream, Bill Scully and Agt. Scully argued as children, Bill Scully threatening to kill Agt. Scully’s rabbit. Then, the young Agt. Scully proceeded to the basement of the family home and discovered the rabbit’s corpse in a lunch box. Also in the dream, Emily Sim observed Agt. Scully from the basement stairs. When Agt. Scully awoke from the dream, she heard her cell phone ringing. When she answered the phone, she again heard the voice of the deceased Melissa Scully, again urgently insisting that Agt. Scully help an unidentified female. Having traced the call to the Sim residence, Agt. Scully immediately proceeded there, arriving at 2:54 a.m. At the front door, while she interviewed Mr. Sim, she observed two unidentified dark-suited men inside the house. Mr. Sim demanded that Agt. Scully cease her visits to his home. From an upstairs window of the Sim home, Emily Sim observed Agt. Scully drive away.

Agt. Scully proceeded to Det. Kresge’s precinct office, where she requested access to Det. Kresge’s files on the Roberta Sim case. Reviewing the files with Det. Kresge, Agt. Scully learned that precinct officers had recently visited the Sim home in response to a domestic disturbance complaint. She also learned that the toxicology report performed on Mrs. Sim’s body revealed the presence of a powerful drug identified as doritriptan, which Det. Kresge stated was prescribed for migraines, and which had possibly been ingested by Mrs. Sim in order to anaesthetize herself before her suicide. Agt. Scully removed a photograph of Emily Sim, from the file and took it with her.

At Bill Scully ’s home, Agt. Scully compared the photograph of Emily Sim to a photograph of Melissa Scully at three years of age. The two faces appeared identical. Using her laptop computer and modem to check the birth record for Emily Sim, Agt. Scully learned that Emily Sim had been adopted at birth. She called Bureau Headquarters and asked to have complete copies of Melissa Scully’s Bureau case files sent to the Bureau office in San Diego. Falling asleep, Agt. Scully dreamed that she was a child walking down a chapel aisle toward a coffin, holding the hand of an unidentified male. In the dream, the coffin was overflowing blood and water; in the coffin was Mrs. Sim, who opened her eyes as the young Dana Scully looked into the coffin. At that point in the dream, the man holding the young Dana Scully’s hand was revealed to be Mr. Sim . Agt. Scully was awakened from her dream by Bill Scully.

Later that morning, in Det. Kresge’s office, Agt. Scully expressed her desire to perform an autopsy on Mrs. Sim, and her belief that Mr. Sim had murdered Mrs. Sim. Det. Kresge reminded her that Mr. Sim and Emily Sim had been witnessed at a doctor’s office at the time of Mrs. Sim’s death. Agt. Scully countered by noting that Mrs. Sim’s arms had shown none of the hesitation cuts typical of suicides; she also suggested that Mr. Sim had left his phone off the hook after calling police with news of Mrs. Sim’s death. At Agt. Scully’s insistence, Det. Kresge ordered an autopsy on Mrs. Sim. The autopsy, conducted by Agt. Scully in collaboration with a San Diego county pathologist, revealed that while doritriptan had been found in Mrs. Sim’s blood, she had ingested no doritriptan pills before her death. Observing an injection mark on the heel of Mrs. Sim's right foot, Agt. Scully concluded that the drug had been injected into Mrs. Sim to anesthetize her, and the suicide staged.

Det. Kresge, Agt. Scully, and uniformed officers then searched the Sim residence. An officer discovered a syringe in the trash outside the house, which Mr. Sim explained as being necessary to Emily Sim’s treatment for severe anemia. Agt. Scully ordered a blood test on the syringe. Shortly thereafter, Agt. Scully observed through a window the two unidentified, dark-suited men whom she had also observed at the Sim residence the night before. The men drove away.

Late that night, at Bill Scully’s residence, Mrs. Scully discovered Agt. Scully checking the Bureau case files on Melissa Scully. Agt. Scully explained to Mrs. Scully that Emily Sim’s DNA matched Melissa Scully’s to a 60 per cent degree of accuracy, and expressed her belief that Emily Sim was Melissa Scully’s daughter. She announced her intention to have a more comprehensive test, an RFLP, done on the DNA, which would take two more days. Agt. Scully also showed Mrs. Scully the identical photographs of Emily Sim and Melissa Scully. Mrs. Scully expressed skepticism regarding the hypothesis. Agt. Scully reminded Mrs. Scully that in 1994, the year of Emily Sim’s birth, Melissa Scully had been traveling away from home and no one in her family had seen her. Mrs. Scully suggested that Agt. Scully was fantasizing in order to escape a sense of loss.

That night, asleep in the guest bedroom in Bill Scully’s home, Agt. Scully again dreamed of her childhood. In the dream, Agt. Scully relived a Christmas Eve when Mrs. Scully had given Agt. Scully and Melissa Scully identical gold crucifixes on necklaces. As she looked back at her mother, Agt. Scully saw her own face. Tara Scully then awakened Agt. Scully to tell her that Det. Kresge was downstairs, and wished to see her. Agt. Scully met with Det. Kresge in the living room of Bill Scully ’s residence. Det. Kresge informed Agt. Scully that three large bank deposits in the amount of $30,000 each had been made in the last eighteen months in the name of Mrs. Sim by a pharmaceutical company identified as Transgen Pharmaceuticals. Agt. Scully and Det. Kresge proceeded to the Transgen Pharmaceuticals complex in Chula Vista, California. There they interviewed a man identified as Dr. Ernest Calderon. Dr. Calderon described an experimental drug treatment program of which Emily Sim was a subject. He further revealed that Mrs. Sim had wanted to withdraw Emily Sim from the program, and that the payments by check had been intended to induce her to allow Emily Sim to remain in the program. Dr. Calderon stated that he had prescribed doritriptan to Mr. Sim.

Agt. Scully, Det. Kresge, and uniformed officers proceeded to the Sim residence, where they arrested Mr. Sim for the murder of Mrs. Sim. Agt. Scully and a social worker identified as Susan Chambliss escorted Emily Sim to the Children’s Services van. In the van, Agt. Scully spoke to Emily Sim, who appeared drawn to the gold crucifix Agt. Scully wore around her neck. Agt. Scully took the necklace off, and put it around Emily Sim’s neck.

During a Christmas Eve party at Bill Scully’s residence, Bill Scully and Agt. Scully privately discussed Agt. Scully’s belief that Emily Sim was their niece. Bill Scully suggested that Agt. Scully was using that belief to fill an emotional void. Det. Kresge called Agt. Scully on the phone and informed her that Mr. Sim had confessed. Agt. Scully now expressed skepticism as to the veracity of Sim’s confession. She and Det. Kresge proceeded to the San Diego County jail. Outside the jail, Agt. Scully observed the two unidentified, dark-suited men whom she had observed twice previously with Mr. Sim. The two men drove away. Inside the jail, a guard informed Agt. Scully and Det. Kresge that the two men had claimed to be Mr. Sim’s lawyers and had been with him for ten or fifteen minutes. Agt. Scully and Det. Kresge discovered Mr. Sim hanged by the neck in his cell, close to death. He died shortly afterward.

At Bill Scully’s residence, Agt. Scully and Bill Scully discussed the murder of Mr. Sim and the attempt to make it appear to be a suicide; much like the circumstances surrounding Mrs. Sim's death. Bill Scully showed Agt. Scully a photograph of Melissa Scully dated four weeks before the birth of Emily Sim: in the photograph, Melissa Scully did not appear to be pregnant. Bill Scully suggested that Agt. Scully's mistake had something to do with her desire to have a child and her inability to conceive. Susan Chambliss then arrived to discuss Agt. Scully’s petition to adopt Emily Sim. Privately, Chambliss informed Agt. Scully that she was inclined to recommend to the court that Agt. Scully’s application be rejected. Agt. Scully and Chambliss discussed Agt. Scully’s emotional and professional priorities, and the extent of Emily Sim’s grave illness. Remaining noncommittal, Chambliss wished Agt. Scully luck at the adoption hearing.

After Chambliss left Bill Scully’s residence, Agt. Scully dreamed about herself and Melissa Scully conversing in 1991. In the dream, Agt. Scully and Melissa Scully discussed Agt. Scully’s decision to accept employment at the Bureau and their father’s opposition to that plan. Agt. Scully was awakened by Tara Scully and the Scully family, preparing to celebrate Christmas. The family’s opening of presents was interrupted by the arrival of a Bureau courier, who delivered Bureau medical reports to Agt. Scully. After reviewing the reports, Agt. Scully informed her family that DNA test results revealed not Melissa Scully but Agt. Scully herself to be Emily Sim’s mother.

At Agt. Scully’s request, Agt. Mulder traveled to San Diego to appear as a witness in support of Agt. Scully’s petition to adopt Emily Sim. Agt. Mulder and Agt. Scully met in the Special Needs ward of the San Diego County Children’s Center, where they discussed the risks Agt. Scully might encounter as Emily Sim’s parent. Agt. Mulder reminded Agt. Scully that certain unidentified parties had murdered Emily Sim’s adoptive parents. Agt. Mulder also informed Agt. Scully that Emily Sim’s surrogate mother was listed in a California Social Services database as a woman identified as Anna Fugazzi. He described that record as likely to be false. He also admitted that he possessed information regarding Agt. Scully that he had not revealed to her.

At the San Diego County courthouse, Agt. Mulder was interviewed by Judge Richard Agt. Maibaum in the presence of Agt. Scully. Agt. Mulder revealed to Judge Maibaum and to Agt. Scully his belief that during her abduction in 1994, Agt. Scully had been subjected to a procedure in which her ova had been extracted, as described in Bureau case files. Agt. Mulder believed those ova had been used experimentally to conceive Emily Sim. Agt. Mulder urged Judge Maibaum to grant Agt. Scully custody of Emily Sim.

At Bill Scully’s residence, Agts. Mulder and Scully discussed Agt. Scully’s 1994 abduction and the fact that Agt. Mulder had been aware of what he believed to be genetic experiments conducted on Agt. Scully, but had not informed her of those beliefs until now. The phone rang; when Agt. Scully answered it, there was no caller on the line. While Agt. Scully held the receiver, Agt. Mulder used his cell phone to request a Bureau trace on the call. The call was traced to the San Diego County Children’s Center, to which Agts. Mulder and Scully immediately proceeded. In the Special Needs ward, they discovered Emily Sim exhibiting symptoms of high fever. They also observed a greenish cyst on the back of Emily Sim’s neck.

Emily Sim was examined by Doctor Vinet at St. Clair Catholic Hospital. Interviewed by Agts. Mulder and Scully, Dr. Vinet expressed his uncertainty as to the nature of the cyst. Informed by Agt. Scully of Emily Sim’s anemia and its treatment, Dr. Vinet also noted that he did not know Dr. Calderon. While an unidentified emergency room doctor was attempting to perform a biopsy on the cyst, the cyst burst, emitting a greenish bubbling fluid from Emily Sim’s neck. The unidentified doctor reacted violently to the presence of the fluid and fell to the floor. Emily Sim appeared to be unhurt. After Emily Sim was transferred to a hospital quarantine room, Agts. Mulder and Scully discussed the condition of the unidentified doctor, whose symptoms Agt. Mulder described as similar to his own when similarly exposed. Dr. Vinet then informed the agents that Dr. Calderon had refused to transfer Emily Sim’s records to him.

Agt. Mulder proceeded to Transgen Pharmaceuticals, where he interviewed Dr. Calderon. After Dr. Calderon refused to release Emily Sim’s records, Agt. Mulder applied physical pressure and threatened the doctor, drawing his weapon. Leaving the office, Agt. Mulder promised to return. Waiting in his vehicle in the facility’s parking lot, Agt. Mulder observed Dr. Calderon leave the facility, enter his own vehicle, and drive away. Agt. Mulder followed Dr. Calderon to a large residential building, later identified as a residential hotel and nursing home. Agt. Mulder remained in his vehicle while Dr. Calderon entered the building and met with the two unidentified dark-suited men whom Agt. Scully had previously observed with Mr. Sim . The two men murdered Dr. Calderon, by sticking a stiletto in the back of his neck, apparently releasing a green, bubbling fluid; the two men then both appeared to take on the form of Dr. Calderon. Agt. Mulder observed one of the men, whom he mistook for Dr. Calderon, exit the building and drive away in Dr. Calderon’s vehicle. Agt. Mulder followed the man to Transgen Pharmaceuticals.

Meanwhile, in the hospital quarantine room, Agt. Scully spoke to Emily Sim, who objected to undergoing another medical test, referring to her adoptive mother’s promise that she would have no further tests. Emily Sim was then given an MRI exam. Agt. Scully, Dr. Vinet, and Chambliss discussed the MRI results, which revealed the cyst to be an inoperable tumerous infection that would soon kill all surrounding tissue. Dr. Vinet and Agt. Scully agreed that treatment was problematic.

Shortly afterward, one of the two unidentified dark-suited men entered the hospital in the form of Dr. Calderon. He entered Emily Sim’s quarantine room and apparently injected her with an unidentified substance. Observed by Agt. Scully leaving Emily Sim’s room, Dr. Calderon hurried toward the hospital exit. Agt. Scully first checked Emily Sim and then pursued him, drawing her weapon, announcing herself as a Bureau agent, and demanding that he halt. When a hospital orderly stopped the man Agt. Scully was pursuing, however, he appeared to be not Dr. Calderon but an unidentified male. Agts. Mulder and Scully conferred via cell phone. Both agents described having observed Dr. Calderon. Agt. Mulder suggested that unidentified parties were attempting to keep Emily Sim alive. Det. Kresge, having posted uniformed officers outside the door of Emily Sim’s room, met with Agt. Scully, who explained to him her belief that unidentified parties were keeping Emily Sim alive in order to continue experiments.

Later that night, Dr. Vinet informed Agt. Scully that Emily Sim’s tumor was spreading. After Dr. Vinet left the room, Chambliss entered and noted that the court was becoming highly concerned about Agt. Scully’s decisions regarding Emily Sim. Emily Sim was then placed in a hyperbaric oxygen therapy chamber. As oxygen pressure was increased, Agt. Scully observed Emily Sim to be in considerable pain and to have thick, ropy veins on her arms. Agt. Scully aborted the test.

Agt. Mulder meanwhile returned to the retirement hotel and entered the building. On the door to one of the rooms, he observed the name A. Fugazzi. Agt. Mulder entered the room and interviewed an elderly woman identified as Anna Fugazzi. Agt. Mulder then conferred via cell phone with Melvin Frohike, who used a computer to enter a California Social Services database. Agt. Mulder read to Mr. Frohike the names of female residents of the retirement hotel; Mr. Frohike reviewed database records for each name and informed Agt. Mulder that each was listed as having recently given birth, despite their advanced age. Agt. Mulder noted the fact that all the women were being regularly medicated with estrogen and progesterone. Under questioning by Agt. Mulder, Ms. Fugazzi alluded to Dr. Calderon’s frequent visits to her and mentioned a procedure she referred to as "beauty sleep."

Later that night, Agt. Mulder observed sleeping female patients receiving hormones through intravenous drips. In a refrigerated cabinet, Agt. Mulder discovered a packing list, which contained the names of Agt. Scully and one of the sleeping women. The cabinet also contained a cylinder containing an embryo, apparently human and alive. He also discovered ampoules containing a greenish fluid. Observing the approach of a man appearing to be Dr. Calderon, Agt. Mulder removed some of the ampules and left the room. In the hallway, he encountered Det. Kresge, who had drawn his weapon, ordered Agt. Mulder to halt, and began to frisk him, removing the ampoules. Agt. Mulder informed Det. Kresge that he is with the FBI. At Agt. Mulder’s instruction, Det. Kresge pointed his weapon at the unidentified man appearing to be Dr. Calderon, who threw Det. Kresge to the floor. Ignoring Agt. Mulder’s warning, Det. Kresge shot the unidentified man. Agt. Mulder quickly left the building and called for an ambulance and backup. Reacting violently to an unidentified substance released by the wounds of the unidentified man, Det. Kresge fell to the floor. The unidentified man appeared to take on the form of Det. Kresge and left the building. He informed Agt. Mulder that he had handcuffed Dr. Calderon inside. When the man left in Dr. Calderon’s vehicle, Agt. Mulder then realized that the man was not Det. Kresge.

Agt. Mulder proceeded to the hospital, where Agt. Scully informed him that Emily Sim had gone into a coma. Agts. Mulder and Scully discussed the probable benefit to Emily Sim of allowing her to die. Agt. Mulder left the room; Agt. Scully remained at Emily Sim’s bedside. As Agt. Mulder left the hospital, he discovered an ampoule of the green fluid in his pocket that had not been taken by Det. Kresge. Despite this discovery, he did not return to share this information with Agt. Scully.

After Emily Sim’s funeral, Agt. Scully exchanged good-byes with her family, including her newborn nephew Matthew Scully. Agt. Mulder arrived and placed flowers on Emily Sim’s coffin. The agents discussed the genetic experiment that had created Emily Sim, the recovery of Det. Kresge, the disposal of evidence at the nursing home, and the recent placement of the nursing home residents in new homes. Agt. Scully opened Emily Sim’s casket and discovered Emily Sim's body missing, and sandbags put in its place. Atop the sand was the gold crucifix Agt. Scully had given Emily Sim.