When Scully is about to tell Mulder about William right before the trial in The Truth, he tells her that Skinner has already told him. This is my take on that conversation. Comments are love.
Helpless
He would have to tell Mulder himself.
The thought ate at him, filled him with dread, but there was no escaping it. He forced himself to take active part in the conversation, to not let his agents notice how preoccupied he had become, to answer or ask a question when expected from him, when all the while this single thought distracted and tormented him. He would have to be the one telling Mulder about William.
He glanced at Scully whenever he was sure she wasn't looking, which was pretty much the whole time they were inside the cell. Mulder was cautious at first, pulling off his stoic act from before, but once he decided it was safe enough... The way they kissed, without giving two hoots about the fact that he, their superior for all intents and purposes, was standing right there... Afterwards, throughout their brief stay, she was clinging to Mulder's side in helplessness he would never have associated with her, her eyes never leaving him. Not that Mulder would have let her go far; he didn't let go of her hand since he'd taken it earlier, brushing it against his lips every now and again, kissing, sniffing.
He looked away when they kissed, mostly to give them what little privacy he could, but that didn't mean he didn't see. There was desperation to the kiss, their first in a long time, and quite possibly their last in an even longer time. It was heart-wrenching. It was in that moment he knew he had no choice. It wouldn't be right to keep Mulder in the dark for long; there was no way they'd be able to get away with it anyway. And Scully had been through so much already – enduring his absence after the abduction, thinking he was dead, suffering through his recovery, then his exile, learning of his imprisonment, and in the midst of all that, William... An emotional rollercoaster didn't even begin to cover it. There was no way he could let her be the one to tell Mulder that his son had been sent away.
A guard came to order them out of the cell eventually. Doggett and Reyes murmured a goodbye and began to shuffle towards the exit. Mulder and Scully exchanged frantic looks but eventually, reluctantly, Mulder let her go with another kiss to her knuckles. He seemed embarrassed to properly kiss her again, with Doggett and Reyes lingering by the door. Or maybe it is because of the guard. He remained behind Scully as she unwillingly turned away from Mulder, gently leading her outside. She seemed composed enough, but as he touched the small of her back ever so slightly, he thought he felt her shivering.
While observing the two newer agents who walked ahead of them down the dim corridor, the idea struck. Once they all arrived at the foyer, he pretended to receive a text message on his phone, then asked Doggett if they'd be able to drive Agent Scully back to DC, that there was an urgent matter in Maryland he had to attend to. They all seemed to believe him, even Scully who had initially eyed him with suspicion, but eventually yielded and followed her colleagues to their car.
He lingered in the foyer a moment longer, making sure they weren't coming back. Then, reassured that the coast was clear, he turned on his heel, meaning to do all in his power to regain access into Mulder's cell.
Once inside he allowed himself the closer look he had avoided earlier for Scully's sake. He eyed the tiny space in dismay; the cell was bare with hardly any light. There wasn't a chair, not even a cot. There was no knowing how many days Mulder had already spent there; no one was telling them anything. Worse yet, there was no knowing how long he might remain imprisoned. He shook the grim thought away. That certainly didn't alleviate his helplessness. He must focus.
Mulder was sitting on the floor in the corner when the guard showed him in. He squinted, then his eyes widened ever so slightly with recognition as he stood up. The guard glared at him menacingly before he left them alone.
"Skinman," said Mulder. The amusement that momentarily lit a spark in his eyes was the only reason he let the nickname slide. "Did you forget something?"
"No, I... I needed to speak to you. Alone."
Haggard. That was the only way to describe him. An old man trapped in this young, lean body. Even when he was back from the dead, he didn't look as bad. On the surface he might seem vital, invigorated by the reunion with the woman he loved, but it was easy to read beyond it. And he really didn't want to know what affect his cruel words would soon have on this already broken man.
"Where are the others?" He said others but he obviously meant Dana.
"On their way back to DC."
"The workers are going back in the factory, huh?"
He couldn't bring himself to crack a smile. "Yeah, something like that."
One could say many things about Fox Mulder; stupid was definitely not one of them. His former agent eyed him warily. "Is something wrong, Sir?"
"Let's sit down," he said, stalling. Mulder nodded towards the floor, somewhat embarrassed by his circumstances, it seemed. He shook his head dismissively and followed suit. But even sitting facing one another, he still couldn't find the words. He pondered the sharp contrast between his immaculate suit and Mulder's orange overalls, was somewhat embarrassed by how overdressed he was.
"I'm all ears, Sir," Mulder reminded him, flashing that tiny grin once more.
He nodded, then cleared his throat. Nothing. His brain remained blank. "It's not easy," he said.
"Well, while I have you alone, I wanted to thank you. For keeping Scully safe while I... couldn't. Not just now, but when I was taken. I've never properly thanked you back then." Unbeknownst to Mulder, him being here instead of Scully was just another way to keep her safe. Still, he felt like a traitor. He could barely meet Mulder's gaze. "Honestly, it means the world to me that you would care for them this way."
He meant William as well; his heart skipped a beat at the realization. He nodded, struggling to appear cool and collected. "I wouldn't have it any other way. You two saved my life more times than I can count. It only seemed fair to return the gesture."
"I didn't want to say it next to Scully, but I'm not optimistic about all this. I doubt we could win either way, even with you defending me." He couldn't argue with that; it did seem rather hopeless. "So I wanted you to know... no hard feelings if we lose." His tone was easy, but not without pain. It was as though he was accepting the inevitable. "But there's one thing I'd like to ask you to do for me." He was almost afraid to ask; before he had a chance to, Mulder's eyes was on his, intent and imploring. "I want to get out of here for a few hours, to see William."
He should have seen this coming, and yet the request stunned him into silence. All of a sudden his mission became ten times harder. Mulder must have misinterpreted his hesitation, for he continued with fervor. "I'll take any punishment, whatever they say. I'll go quietly, I promise. As long as I can be with him for a few hours. It kills me to know I've missed on so much already. I know that if you try to pull some strings, you'll be able to make it happen."
He had to put them both out of their misery. He couldn't let Mulder keep doing this; the more he spoke, the more it would hurt when he knew the truth.
Before he even managed to open his mouth, Mulder blinked, then stopped speaking. His heart began to beat just a tad faster when the younger man's gaze bore into his. "You... wanted to tell me something," he said slowly. It was as though he was putting two and two together very slowly in his head. "Sir – "
"Mulder, there's no easy way to say this." He took a deep breath and steeled himself. "William is... gone."
There was barely any light in the cell, but he could see very clearly how Mulder's face drained of color. "W–what do you mean gone?" he asked, his voice barely a whisper. "Skinner? What do you mean gone?"
He closed his eyes, opened them. Shook his head. This was worse than he thought it would be; worse than when he had to tell Scully about losing Mulder in the woods, or when they found his body in a field. He cursed himself for having to do this, yet at the same time thanked his lucky stars he had spared Scully this misery. This would have been the final straw for sure. "I mean... He's been put to adoption, just a few weeks ago."
Mulder got impossibly paler. "What?"
"William was... special. He had special abilities, none of which any of us has ever seen." Mulder just stared at him incredulously. He wasn't even sure he had heard a word he said, but there was no stopping him now. He spoke about the baby moving objects with his mind, about Josepho and the cult, about Jeffrey Spender. He left out the more painful details, like the various attempts on William's life, or how Scully couldn't stop crying when they all packed the nursery after the papers were signed and the social worker left.
"Scully had no choice," he said in conclusion, peeking at Mulder, who was staring at nothing on the opposite wall. "The boy was in grave danger time and time again and not even she could keep him safe. She did it in order to protect him, to protect both of you."
Finally, he dared to look up. Mulder was still not looking at him. His eyes were filled with tears, spilling soundlessly down his cheeks. His lips were trembling ever so slightly. "I'm so sorry, Mulder," he whispered.
"But he's not dead," said Mulder, his voice breaking on a sob he held back. This was when he realized his mistake. He shouldn't have used the word gone. No wonder Mulder looked so shaken. He wanted to kick himself for his own stupidity, wished he could start over.
"No. He's safe. The adoption records are sealed; no one will ever find him."
"Is Scully – "
"She was devastated. Still is. I didn't want to put her through telling you this, she's been through enough," he said, as if that was an excuse.
"Thank you," Mulder nodded somberly, then shook his head. "I didn't even know – she never mentioned it in any of her – "
"She didn't want you to worry. Those people were looking for you as well."
"The reason I left in the first place was to keep him safe." He was speaking through tears now, slowly unraveling. "If I'd known... I shouldn't have left her here, I should have..."
He wasn't sure which of them moved first, but suddenly Mulder was weeping against his shoulder. Slowly, hesitantly, he wrapped his arms around his former agent as he slumped against him, defeated. He couldn't even imagine how it felt; he had never been a father himself. But letting Mulder cry it out, offering him comfort, waiting for his sobs to become soft whimpers, he sort of got a glimpse into that foreign sentiment.
"There was no other choice," he said again, quietly. "She believed she could keep him safe. Please don't resent her for her decision."
Mulder shook his head, finally meeting his gaze. He looked a mess. "I know she would never have done it unless she absolutely had to. But there was another choice." He recognized that stubborn, tormented gaze; had known it for years. "I could have stayed here. Then she wouldn't have done this alone, I would have watched him grow, and all of it wouldn't have happened."
He couldn't let Mulder do that; carrying the blame for the rest of his life, like he had done with his sister. "You can't know that, Mulder. There are too many forces at play here which are beyond your control. There was nothing you could do." It felt as though Mulder wanted to protest, but he was too overwhelmed by grief. He spoke again before he had a chance to. "Look, just think of a way to get yourself out of here, because I don't think Scully will be able to handle losing you, too. You owe it to her."
"Does she know you're here?"
"No. She would probably be furious I told you. But how could I possibly..."
"It was the right call. Thanks for looking out for her. Again."
"Of course," he murmured. Finally composed, Mulder slid further away, leaned against the wall, pressed his knees to his chest and sighed. "What?"
"I began to accept the fact I would never leave here. I figured she would have William and so she'd be okay. But now... I honestly don't know if there's a way out of this, Skinner."
"We'll find a way." Honestly, his own words sounded like a hollow promise, but with Mulder so helpless, he felt the need to be the one pushing forward, towards a resolution, whatever it is. "Put that belief of yours to good use for a change," he tried to joke, thinking a second too late it sounded like a telling off.
Luckily Mulder let out a dark chuckle. "Other than constantly pissing you off with it, you mean?" They shared a nostalgic smile before he shook his head sadly. "I don't know if I can count on my belief anymore. Not with all I know, not with what you just told me."
His thoughts wandered to the kiss he witnessed less than two hours before, to the way they were clinging to one another. The answer seemed obvious. "You believe in Scully, don't you?"
"She's the only truth I have left."
"Well, there you have it."
"Is that enough?"
"It will have to be, for the time being." He searched for Mulder's eyes, then said, "You can't let them win, Mulder. You deserve a happy ending."
Mulder let out another bitter chuckle. "I believe in many things, Sir. Too many, some would say. A happy ending has never been one of them."
He thought of the many times he had observed them over the years, getting closer together as the years wore on. Over time, against all odds and yet as inevitably as can possibly be, they had almost become one being. The most beautiful love story he had ever known. "I believe in you two. And Scully does too."
Mulder smiled sadly. "She once told me she had the strength my beliefs."
"Well, isn't it time to try and do the same?"
Mulder considered it. Then, when he shook his head, he was relieved to find resolution in his eyes. "It will have to do... for the time being."
When he left a short while later, he was feeling carefully optimistic. Perhaps they were all helpless at the moment, but maybe there was a sliver of hope. They could still make their way out of the darkness. At least, he wanted to believe it was so.
