I have never wrote a story before but wanted to take a stab at it. First of all let me just say that I do not own any of the xfiles material it all belongs to Chris Carter and the several writers that have spent tireless hours writing the brilliant episodes of the xfiles. Having stated this, my story will take place after the end of Season 8 where Scully and Mulder have had their baby and will be told from Scullys point of view with some Mulder thoughts in it too. Some of the details have been changed but basically the same story. This is my take on how Scully got Mulder to leave for his own safety.
Scullys Voice: It was the most beautiful site I had ever seen in my whole life. To know that all that I had went through with Mulder, and the emotional roller coaster that I had endured in the last eight years of my life on the xfiles; had led up to this incredible Mulder and I have our baby boy William and we now know that he as at least in some part alien. Now we start a new adventure as parents and go down a whole new road in life.
"Mulder, I just received word from Skinner that those who are buried deep within the FBI want to kill you, they will not stop until they do". "Scully, mulder replied;I don't care what happens to me as long as I can be with you and our son". "I care Mulder, I did not get you back just to lose you all over again. You can hide out for awhile and then when it is safe, I will call for you but you have to leave now" scully said with heated resolve. She was scared for Mulders life and he didn't seem to be taking it very seriously. She loved his sense of humor but wished with all of her heart that he would take this matter to heart.
All of the years she had spent working with Mulder she had always conceded and given into what he wanted…this was one time she was not willing to do so. She knew if she did, that she would have to raise her son without Mulder and she would not have the life she had always dreamed of. But instead would be a single mom, mourning the man that had become her whole world. "Mulder, you have to leave now and I am not discussing it with you any longer. Please Mulder, please go, please save yourself", Scully pleaded with Mulder. "No Scully I won't do it I won't leave my family behind", Mulder replied determinedly. "If you care for us at all Mulder, then you will." "You will leave us and let us have the comfort of knowing that you are still out there somewhere alive instead of having to bury and mourn you."
Alright Scully, Mulder conceded and he hopped in the shower, packed a bag, called some connections and prepared to leave his family not knowing when he would see them again.
Mulder got out of the shower and dressed in a casual white t shirt and jeans. As he was leaning over his and Scullys bed he began to realize that this was the last time he would be waking up here and getting dressed, the last time he would be able to hold his son and kiss Scully. He began to realize that he may miss a lot of milestones in little Williams's life like his fist word, his first step, and his first laugh. Would he have my sense of humor Mulder wondered?
Mulder rose from the bed after tying his shoes and picked up William and embraced him. He held him for a few moments savoring every second of his time with his son. Then he grabbed his bag and headed towards the door where Scully stood waiting to send him off into the night. He grabbed Scully in a tight embrace and then kissed her slowly and passionately as if he would never get to kiss her again. Then he headed out into the night. Scully waved goodbye and then very slowly closed the door and then collapsed against it in a fit of tears. This was her worst nightmare come true; she had got the life she had always wanted only to have it ripped away once again by those who meant them harm. She pulled herself up and walked over to the crib where William was laying, she picked him up and cradled him in her arms and sang a sweet lullaby to him until he fell sound asleep. Once the baby was asleep she laid him back in the crib and crawled into her bed. As she lay there, she turned over to find the empty spot where Mulder had lied the night before and the pain of this moment began to rip at her heart and she began to sob softly until she finally fell asleep.
The morning sun began to peek through Scullys window and after waking up several times during the night to the empty bed and a newborn hungry baby Scully was not eager to get up out of bed. She turned over and pulled the covers over her head in hopes that the sun would just go away. After a few minutes she gave up the fight and got up out of bed and went to check on William who was fast asleep in his bed. Scully decided to take advantage of this moment and ran into the bathroom to get a quick shower. Now showered and dressed Scully sat down on her couch in the living room and began to remember the night before, the passionate kiss and the heartbreaking goodbye she had said to Mulder. She did not want to dwell on this moment for long and decided instead to make some coffee and check in with Skinner and let him know that Mulder was gone.
Agent Doggett had some questions for Mulder regarding all the information that he had just learned and knew he needed to go see him in person. He first went to see Skinner to find out where Mulder was and when he was told that Mulder was not in the office, he headed over to Scullys place. He knocked on Scullys door quietly because he was not aware of if the baby was awake or asleep at this time. Scully answered the door in a sweatshirt and jeans. "Scully are you alright", Doggett asked. "I am a little tired, long night with William, but I am okay", she replied. "Scully I need to speak with Agent Mulder can you get him for me please?" Scully looked down at the floor as if her whole world was crumbling down around her. "No, he is not here", she replied. "Well when will he back, and where is he?""He is just gone, please do not ask me any more questions about Mulder, please just let it go." What do you mean don't ask any more questions and let it go? "No I won't just let it go someone needs to tell me what is going on here, he demanded a reply. " Agent Doggett I want you to leave please, do not come back and leave me alone. Just forget about us. Scully showed him to the door and then shut the door after he stepped out to leave, clearly this was going to be more difficult than she had imagined. She needed Skinner's help to keep Agent Doggett from digging into this and therefore endangering Mulder's life even further than it already was endangered.