In setting up for IWTB, there are three scenes which need to be slightly changed, thus the epilogue. I have left the confrontation with Christians parents alone, as keeping Mulder's and William's existence from her co-workers/patients/relatives for their safety would lead to this scene and Scully unable or unwilling to correct them.

Part One

'Mulder,' Scully called, listening for the sounds of childish laughter. The house remained quite. Sighing, she walked into the kitchen, only to be assaulted by the smell of dinner baking in the oven.

Giving the vegetable lasagne a look over, Scully immediately checked Mulder's office. Empty, just as she'd expected. He'd taken to cooking lately, thus the reason for the dinner greeting her. Dropping her briefcase on the dinning room table, she removed her gloves. Winter still in full force, her boys could only be out on the small hill behind the house playing toboggan. They'd had inches of powdery snow last nigh.

'Mom's home,' William cried at the sight of his mother exiting the back door. Ignoring his father's protests to slow down, he rushed to her and wrapped his childish arms around Scully.

Sighing in frustration at his son's antics, Mulder pulled the sled to the back porch and put it away, neatly. 'I see I've finally managed to rub off on you, Mulder,' Scully teased.

'Never say never, Scully,' he returned, ushering his family into the warmth of the house.

'Mulder,' just the way she spoke his name, sent a shiver down his spine. Somehow, with these words, he'd given his partner the opening she needed.

'Will, why don't you go and get cleaned up while your mom and I get dinner on the table,' Mulder requested gently.

'OK,' William removed himself from his mother arms and raced up the steps.

'Out with it Scully,' Mulder didn't waist a single second of the two or three minutes they'd have alone.

'I had a visitor today, Mulder. The FBI wants your help finding a missing agent,' she told him. It didn't take long for Scully to repeat the conversation or hear Mulder's expected answer.

'And,' Mulder asked, 'after years together, I can tell when there's something else.'

'I'm pregnant,' she stated (as was GA while filming IWTB) before adding, 'I'll tell then your answer.'

'Shit,' he muttered under his breath. 'OK, I'll go. Under two conditions, you come with me, and William has a nice safe holiday with your Mother while we work on this case.'

Part Two

Scully: Why bring a kid into the world just to make him suffer? I don't know, Mulder, I've got such a connection to this boy.

Mulder: How old is he?

Scully: you think it because of William?

Mulder: I think, even the loss of our son for a short time has left a gaping hole in both of us and a better understanding of how your patients parents must feel. Now with your pregnancy, you're bound to feel the loss of a young patient more acutely. Just go to sleep. Let me curse God for a while

Part Three

'People say I went underground,' Mulder shot at Scully.

'I'm sorry, Mulder,' Scully apologized, 'I had to keep my focus here. It's just as well William is safe with Mom.' They speak about Christian and his treatment for a few minutes, before Scully realizes, 'but that's not what you came to talk about.'

'There's another woman missing,' Mulder starts, telling Scully about the case. 'I need you on this with me.'

'No,' Scully states emphatically, 'no, Mulder.'

'You asked me to get involved, Scully,' he pleads, 'now I'm asking for you stay involved.'

'I'm asking you let it go,' she returns with determination.

'It's not that simple,' he states.

'No,' Scully sighs, 'it's complicated.'

'What's that's supposed to mean?' Mulder demands.

Rolling her eye's as if he doesn't know, Scully turns to face Mulder, before saying, 'something that I knew would happen, that I've been afraid of, that I haven't had to face until now. I can't look into the darkness with you any more, Mulder. I cannot stand what it does to you or to me.'

A slight smile appears, 'I'm fine with it, Scully. I'm actually okay. I'm good.'

'Yeah,' she states, inwardly despairing of their situation, 'that's what scares me. We're not FBI any more, Mulder. We are two people who come home at night, to a family. I don't want that darkness in my life, in the life of my children.'

'Scully,' Mulder pleads, 'this is who I am. It's who I've always been. This is who I was before I met you and we started a family. It's what I do, it's everything I know.'

'I'm asking you to place your family before this. If you feel the need, write it down. Put it in a book. I can't ask you to give up, but I can tell you we won't be coming home.'

'Scully,' he pleads.

'Mulder, I've got my own battles to fight,' she continues, 'and I don't want this life for my children.'

'Don't do this to us,' Mulder looks at her, pleading not to take away all his hard won happiness.

'Please don't argue with me, not about this. I didn't have to choose between my child and you last time,' she reminds him, but turns it into a warning with, 'but I will if you force me.'

'Don't do this now,' Mulder asks, resigned to the fact he knows Scully will.

'I don't know what else to do,' Scully sighs, 'I'm not going to put this child in danger, Mulder. I refuse to let the darkness that influenced William's early years near my daughter.'

'Good luck, then,' Mulder states, hardening his heart he turns and leaves. Stopping by the door, he turns to tell her, 'and it's our daughter, Scully. Nothing can change that.'

Exhausted by the situation, Scully sits and sobs at her sudden losses. She finds this situation as hard as the days spent traveling to gain back their son. Scully never thought Mulder would leave her, not like this and not with their second miracle. The only way she can resolve this situation with Mulder is to prove Father Joe a fraud and try to regain some semblance of normalcy. Her determination becomes paramount when Mrs. Fearon pronounces, 'if you were a mother you'd understand.'

Scully knows it's time to stop hiding. She and Mulder need to come out into the light. They need to do normal. The lives of their children depend on it.