1. She doesn’t tell him right away. She tells herself it’s fear, it’s silly, she’s just distracted by the Boggs case, worry over Mulder or over what her father wanted to tell her. But she can’t stop thinking about it, even after Boggs is dead. She distracts herself by visiting Mulder, trying to entertain him, but it doesn’t work.
Mulder notices. Of course he notices. “Hey, Scully,” he says, chucking her chin gently. “You okay? You seem distracted.” His voice is concerned, and she knows what he’s thinking: he’s worried she’s still stuck on this case.
She picks at a loose thread on her slacks. “I’m fine,” she says quietly. “Do you need anything? Are you in pain?” She reaches out and fluffs his pillows, just to have something to do.
He gives her a look like, I thought we’d gotten past this now. Like he’s going to call her Dana again.
She sighs, looking down at the floor. “You’re going to think I’m crazy.”
He nudges her side. “No, I won’t. Is it the case? Is it Boggs?”
She shakes her head. She feels silly, vulnerable, and she loathes to feel vulnerable. She clears her throat. “It's… my father.”
He touches her hand gently, almost earnestly, and she feels the words bubbling out of her involuntarily. “There’s something strange about the way he died,” she says. “Mom said it was a heart attack, but Dad… as far as I knew, he didn’t have any heart conditions at all.” He’s watching her carefully, listening, and it gives her the courage to keep talking. She says, “I… I just thought it was odd. Dad seemed… distracted at dinner, like his mind was on something else. Almost like he was nervous.”
“Scully,” he starts, uncertainly, but definitely not dismissive, “are you…”
She bites her lower lip, lifts her chin to meet his eyes. “I think… that there’s a possibility my father’s death wasn’t an accident,” she says softly.
2. They start investigating as soon as Mulder’s leg has healed. He insisted. She’d tried to backtrack, insisted she was probably just being paranoid, but he’d insisted. “If you’re having these suspicions, I don’t want you to ignore them,” he’d said. “You deserve to know the truth.” And she’d known he was thinking of his sister.
It’s not an easy process, considering that Scully is trying to hide the investigation from her mother and siblings. There was no autopsy. She’d asked her mother, and her mother had vehemently disagreed. She suspects that if her father’s death was a murder (it hurts to even think it, much less say it), than it was likely some sort of poison used to induce a heart attack. She’s seen it before. But there’s no way to prove it.
She retraces her parents’ steps on the day that he died. They ate breakfast at home, went for a morning walk, cleaned up the house from Christmas. They went to a late Christmas party thrown by one of her father’s Navy friends, people she’s known forever. They spent the afternoon and evening at her place. She considers, briefly, the idea that someone could have tampered with the food at her apartment, but no. No. That’s silly. She’s becoming as paranoid as Mulder. (And it feels unfair to say that, after everything he’s done to help her. God, she never knew her life could go like this. She never thought she’d be investigating her father’s death.)
It’s hard to keep a constant investigation going. There’s an onslaught of cases: Jack Willis’s mental breakdown and her subsequent abduction, the return of John Barnett, the return of Eugene Tooms. They find little times to look into it. Mulder goes with her to talk to her parents’ old friends. They are perfectly sweet, and Scully tries not to show her cards, but she itches under her collar, the back of her neck hot. She feels ashamed for even thinking this, these people who would rent a beach house with her parents. She called them Aunt and Uncle as a child. She leaves blushing madly, feeling as if she’s going to try.
Mulder tells her he thinks they are hiding something. She doesn’t know how to respond.
3. When Mulder had told her about his sister, that she’d been taken when he was twelve, she hadn’t bothered to do the math. She didn’t notice until she read his file: the fall of 1973. The moment when Mulder’s life has been altered forever.
It was a strange thing to reconcile. It was a selfish thing, but it was strange to consider that with her thoughts of what had been happening to her in the fall of 1973. It was the time of the worst fight her parents had ever had. Screaming matches nearly every night for reasons Scully still doesn’t understand, her mother threatening to leave him and take the children—something that none of them had expected, as devoutly Catholic as their mother was. For weeks, tension crackled through the house, so taut they all feared it would snap, until her father went off to sea again. Scully can hardly think of 1973 without thinking of those horrible fights.
She thinks about that sometimes, now. It’s hard not to.
They keep digging. They keep digging even after the X-Files are closed down. Mulder insists. They meet sporadically, he’s trying to be cautious in the wake of Deep Throat’s death, but he keeps digging. Tries to get information on her father’s friend. Scully’s nearly reached the point of letting the whole thing go. The further she digs, the more she regrets it. The more she starts to be scared by what she finds.
Mulder finds her father’s friend in a completely different place. In the files he finds in musty government building, in whispers from his mysterious informants. He tells her about it in soft voices in parking garages, as if it’s bad news. Her head is spinning. She doesn’t understand what he’s saying.
Are you telling me that the people who took your sister killed my father, she whispers, and his face falls. He says he doesn’t know. He says it could be a coincidence, but the guilt on his face seems to say it all. She doesn’t want to hear it, because all she can think is that they’ve pissed off the wrong people, and that her father was killed because of her. Because of her job. It horrifies her.
She spins on her heels and walks away.
4. Dear Dana,
There are a lot of things I’ve never told you, or your siblings, and a lot of reasons why. I think the reason was my shame. I’ve done a lot of things I’m ashamed of, and I didn’t want my children to look at me with hatred in my eyes. But it’s clear that not telling you had made it worse.
There’s a reason that your mother and I disapproved of your new job, and it has nothing to with you. The truth is that I was afraid. I thought they were putting you into a position to fulfill a promise I broke a long time ago. That promise was something I never regretted breaking until now.
I know this isn’t much of an explanation, and you deserve more, and I’m not sure I can give it to you. All I can do is promise you I’ll try and fix this. And reassure you that I won’t break this promise. Like I said, I’ve done a lot of things I regret, but the one thing I never did was you children. I’d do anything for my family.
I’m so sorry for a lot of things I never be able to tell you. But I wanted you to know how sorry I was, and how much I love you, Starbuck.
5. Scully puts some distance between them after Mulder shows her what she found, the breadcrumbs of her father’s murder in dusty old files. He tries not to take it personally. He throws himself into work, into trying to bond with that new partner of his. But something in him won’t let go. He misses Scully. He feels horribly guilty for what he’s done to her. (Because it has to be because of him, right? Dana Scully, spotless record, on the fast track to great things, gets assigned to him, and seven months later, her father mysteriously drops dead? It can’t be a coincidence.)
He thinks things are over between the two of them, and then he is taken hostage by former abductee Duane Barry. And the next thing he knows, her voice is in his ear, telling him what to do. She came for him. She came for him, and the shock of it is almost too much to handle.
He can’t save Duane, and he’s more or less distracted by that. Scully seems lost in her own thoughts as well. They go their separate ways after a little while, quiet and solemn. Scully takes Duane’s implant with her.
Mulder’s head is spinning so badly that he doesn’t even notice when someone rounds a corner and pins him against a wall, hisses a warning in his ear. They’re coming for your partner. They’re going to take her. They’ve been planning this for a long time now. Years and years. And Mulder suddenly realizes that Scully’s father wasn’t killed because of him. And that Scully being assigned to him wasn’t random at all.
Horror cinches through his chest, and he yanks away from the stranger and sprints for his car. He doesn’t stop to think, or do anything but floor the pedal, speed towards Georgetown with everything in him.
He drives straight to her apartment without skipping a beat, his heart thudding hard against his ribs, his breaths coming in shallow panic. He sees the broken window—Scully’s window—and he gasps a little in fear. And then he hears Scully screaming. Screaming his name. He swears, his shoes pounding the pavement; he pushes his way through the shattered window without hesitation.
Duane Barry has Scully pinned on the ground, and Mulder’s stomach drops out from under him. He grabs Barry and wrestles him off of her, shoving him down and cuffing him immediately. Scully scrambles away from him, scuttling backwards across the floor, gasping frantically for breath. “Are you okay?” Mulder rasps, a lump rising in his throat. “Scully, are you okay?”
She nods, her chin trembling. There’s a scrape on her jaw, rug burns on her arms. Her lower lip is split, and it makes him furious. “H-how did you know?” she whispers.
“I… i-it’s a long story,” he stammers. He helps Duane up, shoving him down in one of her chairs, and falls to his knees beside her. He can hear sirens in the distance. “Are you okay?” he asks again, too softly, touching her cheek gently.
She nods, but her chin is still trembling. Her lower lip. “Was it because of my father?” she whispers. Like she’s known all along.
His breath catches in his throat. He nods, gingerly.
She sniffles, caught off guard. Her head drops as she hides her face from view, as she sobs quietly. Her entire body slumping in defeat, tears drip off of her cheek, her nose.
Mulder ignores Duane, ignores the sirens. Draws closer to her and wraps his arms awkwardly around her, one hand cupping the back of her head. He halfway expects her to push him away, but she wraps her arms around him, grips his shirt with a startling strength. She’s shaking, quivering in his arms, and he rocks her back and forth, his cheek against her hair. “It’s okay,” he whispers. “It’s okay.”