Scully just stares at Mulder with no sense of recognition on her face.
"Scully, it's me, Mulder," he says.
Still, Scully gives no response. She clutches the baby closer to her chest. "I don't know you," Scully says with no feeling in her voice.
The glow in Mulder's eyes fade as he realizes she has no idea who he is. "We must take you to a hospital. I don't know how long you've been in there."
"No hospital."
"I know you hate staying in hospitals but you could be really injured and-"
"No hospital."
Seeing the fear that rose to her eyes as he said "hospital," he let it go. "I'll take you to my place. They had to sell your apartment so I have all of your belongings in storage in the basement of my apartment," he explains.
On the plane ride home from Charleston, West Virginia, Scully just sat staring into space. Every so often she would reach over and touch the baby. Mulder still has no idea why she has this baby, but she insisted on not letting it out of her sight.
When they finally got to his apartment four hours later, Mulder asks, "Scully, do you need anything." In response she just stares at him.
He makes up his bed with clean sheets and sifts through his clothes to find her favorite t-shirt, his basketball jersey. He hands it to her and decides to run down to the basement. In his storage compartment, he sifts through her boxes, and brings up two that are full of clothes. When he returns, she is fast asleep on his couch, still holding the baby.
While she sleeps, Mulder decides to clean his apartment. This gives him some time to think. He cannot understand why she seems to have no idea who he is, let alone who she is. He is positive that the baby is not hers, nor is it even human. He pauses and looks at the baby, who looks about six months old. It was the only baby at the run down warehouse back in Parkersburg. He wonders if aliens have stolen information from her mind, and in that process removing her memory. Then he wonders if it were aliens at all. What kind of trauma was she forced to deal with? Could her memory loss be directly connected to her minds attempts to block out the trauma she has just experienced?
He had all these questions and no answers. Mulder picked up the phone and dialed a familiar number.
"The Lone Gunman."
"It's me, Mulder, turn off the machine."
Mulder tells Byers how he found Scully and her strange behavior. He also tells Byers that she refuses to see a doctor or go to the hospital.
"According to my research, alien abduction or not, Scully seems to be suffering from a version of post traumatic stress disorder. Her memory will return, but you just have to coax it a little. Remind her who she is, but don't force it. Forcing it will only make her bury herself more and it will be harder for her to return to her normal self. Are you sure she's actually Scully, and not a shape-shifter?" Byers asked.
"Yeah, I saw Scully in her eyes, even though it was really far away. So, will she stay like she is until she regains her memory?"
"It's a possibility. She may go through different stages though. Just be patient. I'm sure you can make her remember."
"I know. I'll talk to you later. Thanks Byers."
"Anytime."