"The journey ahead promising no more than my past reflected back upon me. Until at last I reach the end. Facing a truth I can no longer deny. Alone as ever." As she lifts the cross in her hand, the image of Scully turns to sand and disperses in the wind. "How did she come into this world?" Scully asks. "Have you asked yourself that?" Mulder wants to know. Scully says there must have been someone she belonged to and Mulder says it's the same people who were willing to kill to protect her. "I can protect her too," Scully claims. He tells the judge that all of Scully's ova were extracted and a look of shock and surprise crosses Dana's face. Mulder says he thinks Emily was conceived as a result of those very experiments and that Dana is the mother. Since she is now sterile as a result of those crimes, he feels she has the legal right of custody to the child. Scully answers the phone, it's an open line but no one speaks. Mulder immediately dials out on his cell phone for a trace and it comes back with the point of origin the County Children's Center. Rushing to the facility to check on Emily, they find her safe in her bed but she's burning up with a fever. Mulder lifts her from the bed and holding her discovers a green cystic mass at the base of her neck. While Scully is talking to the doctor, Mulder watches through the window as an ER doctor preps for the biopsy. Suddenly realizing the potential danger, Mulder begins banging on the glass to stop the procedure but he's too late. As the skin is broken, a green bubbling fluid is released from the cyst. As the doctor falls to the floor, clutching her eyes and coughing, Emily sits up on the exam table, unaffected. Calderon speaks to the suits who arranged Mr. Sim's staged suicide. "He came to see me. He knows I'm involved," he tells them breathlessly. The man behind him pulls out an alien stiletto and stabs Calderon in the base of the neck. He falls dying to the ground as a green fluid bubbles from the wound. The two suits look at each other and suddenly morph into two identical copies of Calderon. Mulder returns to the first location Calderon lead him to and finds that the building is a convalescent home. Once inside, he sees a nameplate on a door that says "A. Fugazzi". Inside is a 71-year old woman who confirms that she is, in fact, Anna Fugazzi. Scully tells the social worker, "I suggest if your job is to do what's best for this child, you do everything in your power to tell the authorities that if they take Emily out of this hospital, they are going to hasten her illness. And I will make it known that all of you are responsible." Mulder gets Frohike on the phone and begins to feed him names from the convalescent home patient list. Frohike finds records of recent deliveries for all of the women despite their advanced age. Frohike wants to know where Mulder is and, when told it's a maternity ward says, "Any fetching young mothers there?" Mulder tells him, "Yeah, I think you might have a shot here, Frohike." One of the charts lists the name of one of the women Mulder just saw on an exam table. But a notation further down the chart lists the name D.K.Scully. Pulling out a core, he finds a glass container filled with green fluid and a live embryo. Still searching, Mulder finds another container which contains multiple vials of green liquid. As Calderon reaches Kresge, he casually swats the gun aside and tosses the detective down the hall behind him. He continues walking toward Mulder. A stunned Kresge manages to get to his gun and aims at Calderon despite further warnings from Mulder. He shoots Calderon and, as the green fluid bubbles out, is assaulted by the gas and falls coughing to the floor. Joining Scully at the hospital, Mulder finds out that Emily has gone into a coma. Without even being prompted, Scully says, "I'm okay, Mulder. It's what's meant to be." Mulder begins, "But if you could treat her...," but is cut off by Scully who says, "I wouldn't. I wouldn't do it to her." Scully sits quietly contemplative following Emily's funeral as those attending file out. Her mother stops, putting her hand on Dana's shoulder. She stands and hugs her mother then turns to her brother Bill and gives him a hug too. Standing just behind him is his wife, Tara, holding their newborn son. "Who are the men who would create a life whose only hope is to die?" Scully wants to know. Mulder tells her he doesn't know, "But that you found her, and had a chance to love her, maybe she was meant for that too." Scully corrects him, saying Emily found her and Mulder adds, "So you could save her." Dana reaches into the casket and removes something half-buried in the sand from one of the broken sand bags. It's her gold cross necklace. Lifting it in her hand, she closes her eyes in pain. We've come full circle to an image from the opening of the episode. Alone as ever.

Emily A poetic voice-over by Scully accompanies a stylistic scene where we see Dana walking through the sand while the wind whips around her. She bends to look at something and we see her gold cross lying half-buried in the sand. "The journey ahead promising no more than my past reflected back upon me. Until at last I reach the end. Facing a truth I can no longer deny. Alone as ever." As she lifts the cross in her hand, the image of Scully turns to sand and disperses in the wind. Mulder arrives at the County Children's Center in San Diego to meet up with Scully. He enters a sunlit room and sees Scully sitting on the floor talking quietly to Emily who is busy coloring. Scully introduces the shy Emily to her friend, Mulder. He notices Scully's gold cross necklace around Emily's neck and looks with some compassion at Dana. Mulder tells her that he had Frohike hack into the California adoption records and he's found out who Emily's surrogate mother is. The name on the record is Anna Fugazzi - fugazzi being another term for fake. Mulder believes a false record has been created because there are no true records. "How did she come into this world?" Scully asks. "Have you asked yourself that?" Mulder wants to know. Scully says there must have been someone she belonged to and Mulder says it's the same people who were willing to kill to protect her. "I can protect her too," Scully claims. Despite the potential danger and life changes she would face, Scully still feels the right thing to do is adopt Emily. Scully finally decided to call Mulder and bring him into this because she needs him to testify on her behalf at the custody hearing. He feels he should decline if only for her own safety. Scully asks, "Then why are you here?" "Because I know something that I haven't said. Something that they'll use against you to jeopardize your custody of Emily. No matter how much you love this little girl, she's a miracle that was never meant to be, Scully." At the hall of justice, Margaret Scully, along with Bill and Tara, emerge from the hearing room. Bill tells Mulder they're ready for him and gives him a poisonous glance as he walks past. No love lost between those two. Mulder explains to the disbelieving judge the circumstances of Scully's abduction and the experimentation by government elements. He tells him that all of Scully's ova were extracted and a look of shock and surprise crosses Dana's face. This is the first she's heard of the news. Mulder says he thinks Emily was conceived as a result of those very experiments and that Dana is the mother. Since she is now sterile as a result of those crimes, he feels she has the legal right of custody to the child who was the product of those experiments. Back at Bill's house, Mulder and Scully sit down for a long overdue conversation. When she asks why he never told her, he says, "I never expected this. I thought I was protecting you." He doesn't know for who or for what reason the experiments were carried out. They are interrupted by a phonecall but, when Scully answers the phone, it's an open line but no one speaks. Mulder immediately dials out on his cell phone for a trace and it comes back with the point of origin the County Children's Center. Rushing to the facility to check on Emily, they find her safe in her bed but she's burning up with a fever. Mulder lifts her from the bed and holding her discovers a green cystic mass at the base of her neck. At the hospital, the doctor says she's dehydrated and suffering from an infection, probably related to the cyst which they are going to biopsy. He asks if they are the parents and Scully tells him she's the mother. When asked for a history, she can only tell him the limited information she has regarding Emily's anemia. While Scully is talking to the doctor, Mulder watches through the window as an ER doctor preps for the biopsy. Suddenly realizing the potential danger, Mulder begins banging on the glass to stop the procedure but he's too late. As the skin is broken, a green bubbling fluid is released from the cyst and the doctor experiences the same symptoms we've become familiar with since "Colony/Endgame". As the doctor falls to the floor, clutching her eyes and coughing, Emily sits up on the exam table, unaffected. With Emily now in a quarantine ward, Scully is torn. Mulder claims she can't protect the girl but she can't allow this to become Emily's life. The doctor returns and tells them Emily's physician, Dr. Calderon, refuses to turn over her medical records and claims Scully has no legal authority over the child. Mulder decides to pay Calderon a visit at the Transgen facility. Calderon offers his condolences on Emily's downturn but he can't release the information about the drug trial. He says it's purely business and they must protect their research. "So I'm wasting your time. This is not worth the life of a 3-year old girl," Mulder inquires. Calderon doesn't like the implication and says there is nothing he can do, as he stands to see Mulder out. Mulder decides on a new tactic and slams Calderon's head down on the desk and proceeds to kick him around the room. With a gun to Calderon's head, he demands any and all information they have on Emily. Before he receives compliance, the door opens to reveal a security guard and some other interested office personnel. Mulder leaves, claiming he'll be back. Figuring Calderon will run to his superiors, Mulder stakes out the parking lot then tails the doctor. He leads Mulder to a building in a residential neighborhood. Rushing inside, Calderon speaks to the suits who arranged Mr. Sim's staged suicide. "He came to see me. He knows I'm involved," he tells them breathlessly. They aren't happy about him leading Mulder right to their doorstep and the doctor is not long for this world. The man behind him pulls out an alien stiletto and stabs Calderon in the base of the neck. He falls dying to the ground as a green fluid bubbles from the wound. The two suits look at each other and suddenly morph into two identical copies of Calderon. One of the Calderons leaves the house, leading Mulder back to Transgen. During Mulder's surveillance, a masked Scully enters the quarantine ward to talk to Emily before she is taken for an MRI. Emily tells Scully, "Mommy said no more tests." "We just want you to get better," Dana says. As Scully watches from outside the procedure room, Emily is placed in the MRI chamber and every sound from the machine causes an empathic Scully to flinch. The results of the test show a neoplastic mass or tumorous infection originating from the cyst in her neck. The doctor says the mass is growing rapidly. As they discuss the results, we see Calderon enter the hospital and walk past, heading to Emily's room. He removes a syringe filled with green fluid and injects it into Emily. As Scully returns to Emily's room, she sees Calderon emerging from the room and, recognizing him, calls after him. But he walks right by, ignoring her. She rushes in to check on Emily then calls for a doctor and security. Running after Calderon, she catches up to him and aims her weapon at his retreating form, telling him to stop but it's no longer Calderon. Scully calls to see where Mulder is and, when he says he's been tailing Calderon, she says it's impossible since he was at the hospital. Mulder tells her he doesn't think Calderon was there to harm Emily; rather, he wanted to treat her. He says these men want Emily alive, but for different reasons. Kresge arrives at the hospital to post guards on Emily's room. Scully tells him she may have been mistaken about Calderon. He's not necessarily a threat to Emily, though he's still dangerous and capable of eliminating anything that gets in the way of the tests. Mulder returns to the first location Calderon lead him to and finds that the building is a convalescent home. Once inside, he sees a nameplate on a door that says "A. Fugazzi". Inside is a 71-year old woman who confirms that she is, in fact, Anna Fugazzi. Back at the hospital, Scully is confused and distressed. She thought the injection given to Emily was helping; her fever was down and her vital signs were almost back to normal. But the doctor says the latest MRI shows the continued spread of the growth. He says it's beginning to necrotize the tissue and is basically causing Emily's body to shut down. Scully is devastated. To add to her distress, the social worker tells her that the courts are concerned about her making decisions for Emily; decisions that are having an affect on her health. She thinks that Scully is incapable of responding with any clinical ability in this situation. Scully responds, "I suggest if your job is to do what's best for this child, you do everything in your power to tell the authorities that if they take Emily out of this hospital, they are going to hasten her illness. And I will make it known that all of you are responsible." Mulder gets Frohike on the phone and begins to feed him names from the convalescent home patient list. Frohike finds records of recent deliveries for all of the women despite their advanced age. Frohike wants to know where Mulder is and, when told it's a maternity ward says, "Any fetching young mothers there?" Mulder tells him, "Yeah, I think you might have a shot here, Frohike." The women's records also indicate they were receiving hormones to help their systems maintain a pregnant state they could no longer achieve on their own. Mulder asks Anna Fugazzi if she knows Dr. Calderon. She says she was expecting him because it's time for her to start her "beauty sleep." Sneaking into some procedural rooms (no security at this place), Mulder finds a room with rows of patients seemingly asleep or unconscious; all with IV drips feeding hormonal treatments into their systems. This must be the "beauty sleep" Anna was looking forward to. Stored in a refrigerator, he finds a sample container with some charts and records. One of the charts lists the name of one of the women Mulder just saw on an exam table. But a notation further down the chart lists the name D.K.Scully. Pulling out a core, he finds a glass container filled with green fluid and a live embryo. Still searching, Mulder finds another container which contains multiple vials of green liquid. Hearing a car approach, Mulder grabs some of the vials and goes to the window and sees Calderon getting out of his car. Mulder tries to leave by a rear entrance but is stopped by Kresge who points a gun at his head. Taking the vials from Mulder's hand, he asks for him to identify himself as he searches him. At this point, Calderon (or one of the Calderons) enters the far end of the hallway and begins walking toward the two men. Mulder tells Kresge to take the gun off him and point it at the approaching man instead. Despite a gun pointing at him, Calderon's pace doesn't slow and Mulder decides it's time to leave. He tells Kresge to run and warns him not to shoot Calderon, knowing he's got the green blood chemistry. Kresge drops the vials and assumes a stance with two-hands on his gun, apparently ignoring Mulder's advice. Mulder takes the opportunity to grab one of the dropped vials. As Calderon reaches Kresge, he casually swats the gun aside and tosses the detective down the hall behind him. He continues walking toward Mulder. A stunned Kresge manages to get to his gun and aims at Calderon despite further warnings from Mulder. He shoots Calderon and, as the green fluid bubbles out, is assaulted by the gas and falls coughing to the floor. Mulder decides to get some fresh air and call for back-up outside. He's surprised to see Kresge emerge, seemingly unharmed. He tells Mulder that he's cuffed Calderon and he'll take care of back-up, leaving Mulder to watch the suspect. Mulder starts inside then realizes it was the morphed suspect when Kresge climbs into Calderon's car and drives away. Joining Scully at the hospital, Mulder finds out that Emily has gone into a coma. Without even being prompted, Scully says, "I'm okay, Mulder. It's what's meant to be." Mulder begins, "But if you could treat her...," but is cut off by Scully who says, "I wouldn't. I wouldn't do it to her." "Are you sure?" Mulder presses. "Mulder, whoever brought this child into the world didn't intend to love her." "She was born to serve an agenda, " Mulder says. "I have a chance to stop that," Scully replies, "You were right. This child was not meant to be." Mulder offers to stay with Scully, putting his arm around her shoulders, but Scully tells him she'd like to be alone. Mulder doesn't menion that his question about a cure for Emily wasn't purely hypothetical. He holds in his hands a potential chance to cure the child; the vial of green fluid. He can't be sure what it is or what it would actually do, but he doesn't share the information with Scully, leaving their conversation to hypothetical speculation. Scully goes into Emily's room and brushes the girl's hair gently from her forehead. Looking down at Emily with a sort of pained compassion, she lays on the hospital bed next to the young child. Putting her head on the pillow next to Emily's, she stays with her as if she just wants or needs to be close to her at the end. The image of Scully and Emily fades and becomes a stained glass image of the Madonna and child in a church. Scully sits quietly contemplative following Emily's funeral as those attending file out. Her mother stops, putting her hand on Dana's shoulder. She stands and hugs her mother then turns to her brother Bill and gives him a hug too. Standing just behind him is his wife, Tara, holding their newborn son. Scully smiles a genuine, but sad, smile at the two then places a kiss on the child's head. Turning back to the front of the church, Scully stands alone and silent as she stares at the small casket. Mulder joins her, placing flowers on the casket. "Who are the men who would create a life whose only hope is to die?" Scully wants to know. Mulder tells her he doesn't know, "But that you found her, and had a chance to love her, maybe she was meant for that too." Scully corrects him, saying Emily found her and Mulder adds, "So you could save her." They stand together, looking at the casket in silence. Scully asks how Detective Kresge is doing and Mulder tells her he's out of ICU. Now that they know to reduce the core body temperature of the alien virus' victims, people like Kresge and the ER doctor are able to survive. Mulder tells her the nursing home has already been sanitized. No evidence is left and no one at Transgen admits to knowing of Dr. Calderon's work. Looking at Emily's casket, Scully says there is evidence of what they did. She prepares to lift the lid of the casket and Mulder turns away, perhaps to give her privacy or because he knows what she will see. A shocked Scully finds no sign of the child's body, only a casket filled with sand. Mulder looks back at his partner with sympathy and compassion. Dana reaches into the casket and removes something half-buried in the sand from one of the broken sand bags. It's her gold cross necklace. Lifting it in her hand, she closes her eyes in pain. We've come full circle to an image from the opening of the episode. Alone as ever.