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The Truth: Echoes Beneath Shadowlight

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(The Previously on The X-Files portion contains spoilers for the fic, Rooted in Friendship, you can skip to the start of this story, beginning at the the area noted as Chapter 1, at any time.)

Previously, on the X-Files...

Mulder took a deep breath and Scully noticed his hands beginning to shake. Her heart leapt into her throat. "and it would mean everything to me to have the honor to call you my wife.”

Mulder took the ring box from his right pocket and made his way down on one knee, cracking and popping as it bent, irritating scar tissue as it supported his weight at home plate. “Dana Katherine Scully, will you marry me?”

Dana Mulder. If that thought hadn't sent her running... Not that she had to change her name. They didn’t need marriage, didn’t need a ceremony or a piece of paper or fancy nothingness or people to witness. She knew the only meaning was what they decided to put behind it, but she understood why and she understood that they needed to give each other what neither of them had before - simplicity. peace. prolonged happiness. Some color inside the lines.

Scully didn’t realize how much time had past as these thoughts ran through her head until Mulder said, “Scully, my knees aren’t getting any younger.”

A tear ran down her face at the relief, the anxiety, and the honesty that she wanted this as much as he did and much more than she let herself feel. Then she really started to break down which made tears spill from him, and she let out a breathy laugh and said, “Yes Fox William Mulder, I will marry you.”

*****The Wedding*****

It wasn’t until the minister prompted them to read the vows they had prepared for one another that they both snapped back to reality.

“Scully, you have always been my constant and my touchstone. My one in five billion… or whatever it is these days. My light in the darkness that’s always seemed to find you and me, as much it may continue to try, I am choosing you, for better or for worse,” Mulder’s voice started to break as tears fell freely down Scully’s cheeks. “You had me from the moment you first walked into my office twenty-six years ago and now you’ll have all of me, forever.”

It wasn’t just his words that made her a believer, but his actions that truly convinced her they were made for one another. Hearing his love verbalized in this manner was almost foreign to her ears as they almost always communicated wordlessly.

“I once said that the best relationships, the ones that last, are frequently the ones that are rooted in friendship. That one day you look at the person and see something more than you did the night before, like a switch has been flicked somewhere. And the person who was just a friend is suddenly the only person you can ever imagine yourself with.”

Scully paused a moment as Mulder regarded her with a grin, yet his eyes betrayed his emotions.

“That person is you, Mulder. It always has been… even in the moments of most extreme duress and uncertainty, your stubbornness never fails to remind me why I fell in love with you. That’s why I followed you and why I would do it all over again. I don’t want to be married to a brain surgeon or to be Kersh’s boss. I want to be with you, Mulder. For better or for worse.”

Her voice was as steady as she could make it for her own part. Tears ran silently down her cheeks for a lot of it, but Mulder held it together for the most part. That is, right until the end, when the minister was reciting a small part Mulder decided to add. It was a quote from Benediction of the Apaches:

"Now you will feel no rain, for each of you will be shelter to the other. Now you will feel no cold, for each of you will be warmth to the other. Now there is no more loneliness for you."

Mulder’s gaze never wavered from hers, even as they filled with tears, the tears swiftly overflowing, running down his cheeks before the minister had even finished the line. Scully reached up and softly wiped them away with her hands. It was only fair. He had been quietly drying her tears since they met.  

“By the power vested in me, by the American Marriage Ministries and the state of Virginia, I now pronounce you… Husband and Wife!”

*****The Baby*****

Bill’s demeanor transformed instantly, his normal stiff exterior loosening as he held her. “She’s beautiful. She.. she looks a lot like both of you. Even her eyes.. She’s got that shit hazel of Mulder’s mixed with our family’s blue and it created the most beautiful turquoise coloring.” He looked up. “What’s her name?”

Scully rested at Mulder’s arm and he placed it around her. “We named her after our mom and grandmother. Margaret Katherine.”

Monica piped up, “Mulder and Scully together created from an empty darkness, pure light.” 

*****William/Jackson’s Origins*****

Squinting through her glasses Scully read the results. “Well, the first thing that jumps out- you have two distinct genomes. It could be part of your alien DNA not able to attach properly.. Well, now this is interesting...” Scully went through the paperwork and pointed at the values. “This strand.. You see how this matches? It is an obvious link. Your link to Cassandra is undeniable. You have her alien DNA.. but interestingly, I don’t see evidence of that on this strand. Yet, your junk DNA is turned on even on this strand.”

William leaned in closer. “What is junk DNA? Cassandra? The old lady from Thanksgiving? That man’s wife? Jeff’s mother. What in holy fuck?”

“Watch your mouth,” Scully said pointing at him. “You’re not related to her. It’s a lot to explain.”

As Scully spoke she sifted through the papers. Something caught her eye and she stilled. Astonished. “Your junk DNA, is coded.. It’s a direct match to mine. I can see the indicators of a grafting on this strand, but the one that matches mine does not contain indicators.”

William stood beside her and followed her fingers as she pointed and posted each section on the wall, jotting notes as she went. He nodded and frowned. Wrinkled his brow and scratched at his head, she wasn’t certain of his actual understanding. She decided to continue anyway. “Now if you look at Mulder’s DNA.. the percentages are too low.” A lump gathered in Scully’s throat as her chest grew tight. “You two are not a match.” She took a breath and spoke as though she had just been stabbed. “He’s not your father.”

They stood in silence staring at it as though it might change something. Scully picked up the next set and slid it into the long clip beside the first. It was puzzling, but the results were very clear. “If you look at this report, your DNA and Mulder’s...  This is a high percentage. Very interesting. William, Mulder is the father of this genome.”

“What does that mean? I don’t get anything you’re saying.” William spun around in frustration, his hands in his hair. Scully tried her best to explain.

“You’re a chimera William. Made up of several genotypes. DNA code for creating more than one individual.”

“I already know I’m a hybrid.”

“Yes, but what I’m looking at.. The only way this is possible is if I had more than one zygote inside of me during my pregnancy.” Scully walked over to the results posted at the beginning of the wall. “This,” she said pointing at William’s paper deciding to not even touch on percentages with him, “This is one of your complete DNA strands. It would be considered a match for myself and Cassandra with repaired or missing nucleotides from a third.”

“I-I don’t understand,” William said fixing his hair.

“You have DNA working independently from the other. Some chimeras might have two different eye colors or blood types. Organs that normally wouldn’t be able to survive inside a body are able to within these conditions.”

“How did this happen?” William asked, his eyes wide, his arms falling to his side.

“It’s been known to occur with fraternal twins. The fusion of the two usually happen at the blastocyst or zygote stages. It results in the development of an organism with intermingled cell lines.”

“How come I didn’t find this out before? Why didn’t you know about it?”

“That information wouldn’t be detectable in a paternity test. You only have one blood type, so with most exams doctors wouldn't question it.”

“What about the other doctors? With the tests?”

“Well, it’s like you said, they already knew you were an alien/human hybrid, so under that assumption they may have concluded it was intentionally part of your makeup.. Your design...”

“So which am I?”

“Which is your dominant DNA? It depends on a lot of factors, the fittest genes will win out, environment also plays a role…” Scully stopped mid sentence. Through the frosted glass she could see men standing on the other side. They were pressing their luck staying in the lab for such a long time. “William, I think it’s time to leave.”

*****Scully/William’s Connection/The Baby’s Origins*****

William kicked a rock down the sidewalk and pulled at his jacket. “When we had that connection, the visions of the future, could you, could you feel it was me?”

Scully lifted her chin. The sky was clear, the sun warming the cold November day. She grasped his sweaty hand. “I knew.”

He squinted her way. “What did you feel? From me..”

Scully let their arms naturally sway and he returned her smile. “I felt your fears, your terror, stress, frustration, anger.”

William's blue eyes connected with her own and they paused as they reached the car. “I felt you too. Your fears, your frustrations, and what you really wanted. I felt you love me, I know you wanted to raise me.”

Scully tightened her lip. “That’s past us William, but we can have something now, something special. When you’re ready, we can move forward.”

They got in the car and Scully started it up. William put his head in his hands then slapped at the dash. “I’m fucked up. Sometimes I hate myself. I feel like I give misery and pain to everyone I care about, but when I thought… when I felt how much you loved someone you didn’t even know and how much it hurt you..”

Scully was shocked. “That one vision, it had that effect on you?”

“It did. It wasn’t just that is was a bleak future, but you.. And Mulder. How desperate you were to save him. I had other visions. The inside of your house, you and him on the run from some Russian dudes and you two kicking some serious ass.. but I saw and I felt it through your eyes, how you looked at him and I saw the way he looked at you and all the pain I caused..” William’s chin started to quiver, his voice cracking, he ran a finger across his temple, “I felt like I could fix it.. I wanted to give.. wanted to give, something I knew my abilities were capable of. Something good out of all my fucked up destructive bullshit.. I wanted to give my mother a gift.”

“William, I’m not understanding you.”

“I’m the reason you were able… to get pregnant.”

*****The Dyson Clusters*****

A pillar of fiery smoke and dust, still boiling up from where the space shuttle lifted off, impaired The Scientist’s view. A series of new flashes broke out, rising and spreading the incandescent radioactive gasses, and then a great gush of flame rose. A column of pure hydrogen must have rushed up into the vacuum created by the explosion; the next blast of flame, in a lateral sheet, came at nearly ten thousand feet above the ground, great rags of fire, changing from red to violet and back through the spectrum to red again, went soaring away to dissipate in the upper atmosphere. The shuttle already breaking past the Karman line. It carried with it the chosen few to live among the Dyson Sphere. The Scientist pondered what they might be thinking; knowing this was the last time they would step foot on the planet. Was this the 144,000 the book of revelations prophesied or was Lucifer leading this crew?

*****On the Bridge/The My Struggle II Vision coming to Life w/a twist***** 

Barely conscious, using his last bit of energy, Mulder’s eyes rolled open and Scully joined his gaze, directing her own eyes towards the blinding light. An ARV hovered above, a door on the underside retracting, the spotlight closing in on Scully. She stared into it as a single black drop of liquid, perhaps no bigger than ink from a dropper, fell from the ship into Scully's eye, swirling around it, until the sclera, now indistinguishable from her pupil, went completely black.


*****Chapter 1 - Andromeda*****

A shudder ran through Scully as she stared up at the underside of an unidentified aircraft. Fear made her eyesight blur, anger of time lost that could be spent saving Mulder made her chest tight, then everything went fuzzy, her extremities, numb. Then, she saw…. Nothing. 

She felt her inner voice scream as inky tentacles ripped her away from her own physicality, floating her into a thick static. There was nothing to hold onto as she traveled away, the static transforming to stark jagged lines of blood and arced light, forming a bizarre web of overlapping pictures of her life, personal and professional, childhood and those with Mulder, all playing on an ever moving reel.

It was distracting, but her pull to save Mulder was greater. Her heartbeat pounded loudly against the space where she was trapped, the only greater sound resonating from indiscernible machinery coming from unknown directions.

Somehow she knew her body was moving in a forward momentum although not under her control. She could not see her surroundings, smell the air, or taste the saliva in her own mouth. She couldn’t feel herself breathing yet somehow knew it was happening. Something had taken over and all her strength proved futile against this parasite.


72 hours later…


“We’re headed towards a Dyson cluster?” Skinner asked the man who he guessed had to be close to one hundred years old if he truly was who he thought. He was thin, pale, and walked with a slight limp.

“Yes, Mr. Skinner. The Syndicate and all our families will be there.”

“Right, but where do I fit into all this? Why did you take me aboard?”

“Your family is there as well.”

“My family? But how? When?”

“Mr. Skinner. We had to guarantee certain eventualities. We will need your help to police in our new government.”

“And if I don’t?”

“You will Mr. Skinner. It may take some time, but you will come to understand.”

A man dressed in sanitary scrubs, and a mask hung around his neck, excused himself into the room. “You told me to update you on Mulder? His vitals are faltering and he’s currently in the active stages of dying. The antivirals were not effective. If there were plans by Spender to save him, it was from a bounty hunter or a healer.”

“How much longer does he have?” the man asked the medical professional.

“Could be hours. Up to three days possibly, no more,” the doctor replied.

The man looked at Skinner. “Guess it’s time you paid your respects.”

Skinner felt as if a bag of rocks laid in his gut. “I’ll get Agent Scully.”

“Dana?” Skinner asked as he entered her cabin, approaching her delicately. “We need to go see Mulder. It’s time.”

She looked at him with an empty gaze that he interpreted as despair. “You need me to hold Maggie?” he asked, and she blankly shook her head. He knew there was nothing he could do but be there for her yet he couldn’t stand to see her in pain.

They made their way to the quarantine unit, Skinner staying in the hallway to allow Scully her privacy with only Mulder and Maggie. She opened the door slowly and stood by the bed. She squeezed Mulder's hand, her finger stroking his bruised cheek. Maggie shrieked and wriggled, stretching out, reaching for her father.

Scully’s body instinctively brought her child to her chest to comfort her. Maggie didn’t accept it, pushing at her mother’s chest, punching and kicking, until she was free, sliding down to the bed, falling down on what was left of her father’s life. She crawled onto his chest, his heart beating shallowly against her ear. She closed her eyes as if creating the most pleasant of dreams and sucked her thumb, her other arm clinging to his neck. 

Mulder’s pulse grew weaker, his breath shallow. Maggie, in a moment of clarity, started to cry. She gripped her father’s white gown, at the center of his chest, her tiny feet kicking just above his waist. She pulled herself up, her angel hands haphazardly patting at his frosty blue lips, his bruised and battered face. “Dada,” she whined, releasing a tiny cry, her puffy cupid’s bow lips kissing his cold cheek. Mulder remained lifeless, his monitor displaying an even more erratic heartbeat. The graph not mapping days or hours, but minutes, until the finality of his life.

Maggie sat up with her knees on his chest and slapped both his cheeks, her small unlined forehead leaning into his deep creviced one. Mulder’s eyes lifted and stared into his baby girl’s turquoise shine. His lips parted and his throat released a death rattle.

“Dad-dee. Dad-dee.” The child sounded almost annoyed. Maggie squeezed his cheeks tighter, puckering his lips, her tiny nails scratching his cheek. Looking straight into his eyes without blinking, she commanded, “Daddy. Up!” 

Mulder felt a chill as his body numbed. The painful process, the feeling of pins and needles at his extremities, as he lost oxygen while his circulation decreased. Regretting the things he’d never get to do with his family haunted him only briefly, his love for Scully, his children, lingered much longer. His final thought as he grew cold, was that the world would soon follow in his steps, the plague of death and war leaving few to grapple at what was left, if anything, of humanity. When the last spirit’s arm laid outstretched to receive him into the heavens, the bright light grew dim into a final pinprick of light. His hope still strong, his will to live refusing to give up, the white light shifted to a color no less beautiful than the Maldives, slowly growing wider, and more in focus. He bathed in the strength of the hue, the blues and greens of fairytale dreams. When the colors came to focus he knew those open and loving eyes, for they were more familiar than his own, and the door to his very soul. His precious Maggie touched him with those gentle hands and he was made anew, not like sculpting clay, but as if his body was reborn in its most perfect form. What life she was breathing into him, weaved in innocent unadulterated love, he held it in deep gratitude, sensing what she was giving him was sacred and transient, bypassing the eternal cycle of existence.

With his first ounce of restored strength he held his child. “Maggie, my girl. Wh-what have you done?”


Scully had been pushed down deep within herself by the parasite. She was buried in a place with no door or windows and the way out didn’t quite suit her. Every minute hell. Scully heard voices, machines ticking and beeping, penetrating the stillness in the indefinite expansion of internal nothingness. Even with those facts, she got the feeling of suffocation, like her lungs had collapsed, like she could run forever, but get nowhere- no progress, no light, no shadow. No color. Prisoner of her own body. 

She felt a warmth in the void. A voice. Mulder, calling to Maggie. Maggie’s wonderful infectious laugh. Scully strained against the blackness to hear the divine sounds of her true loves.

24 hours later in an undisclosed location...

William tried to move, but the rattling chains held him to the metal chair. He took in a breath, the rancid residue that coated the floor penetrated his nostrils. It smelled like death. The sound of distant footsteps distracted him. The footfalls got louder until the man came into view. He knew this man. The one that identified himself as his creator.  The one that shot him in the head believing he was his father.

“These chains might hold me in place, but they won’t stop me from killing you,” William spat.

CSM smirked as he lit his cigarette. “My boy, you’re not going to kill me. I have something you want.”

“What could I possibly want from you.”

“What does one look for in life? Simple pleasures. Answers, reason, purpose. That’s what I can offer you.”

“Answers? To what?”

“Who your parents are.”

“I know those answers. I have the proof.”

“You know of your human origins, possibly, but I’m talking about the part of you which is what you may call... extraterrestrial.”

“I’m listening,” William hissed.

“There is another father besides myself from which I harvested your alien DNA. It was not from a preserved fetus. He is very much alive and on this ship.” CSM inhaled deeply. “Shall I introduce you?”


“It’s good to have you back, Mulder,” Scully purred, her hand blazing a trail down his bare chest. 

Strange was the word Mulder would use to describe Scully’s current behavior. With a shirt in his hands, he was contemplating putting it on, because where she was leading, he didn’t need it. 

“I’m happy to be missed, but how am I back?”

“Must we always search for an answer, Mulder?” Scully remarked. 

He looked at her curiously. What had gotten into her? With a push of her fingertips he fell backward onto the mattress. Her clothes slithered to the floor right before her smooth legs straddled his hips. Her nails ignited his nerve endings as they scraped his skin like the little magnetic shavings under the plastic toy he’d played with as a kid. When the pen moved, so did the shavings. Her body calling to his, he arched into her when she bent over and kissed him at the base of his neck, her tongue tracing a line across his shoulder. Not a single word left their lips, even when he felt himself growing against the inside of her thigh when her hands moved across his stomach. His erection could feel her heat through his jeans. God, when she touched him like that, and the way she kissed him, her lips were more than lips, they were the physical memory of every time, of who they were. Tonight, her touch and kiss had an edge that bit. 

She kept grinding into him, pinching his nipples, biting at his neck. Scully hadn’t acted this crazed since.. well, it had been some time. Mulder looked down and watched her as her hands freed his cock. The intensity of the lust in her eyes was nearly intimidating. She whispered hotly in his ear. “I hate these jeans. I hate everything between myself and you. I want to feel your cock Mulder, rigid and hot, sliding inside me, your hands at my breasts. I want those hard dry thrusts to have purpose.”

Mulder was not a man that had to be told twice, well, maybe he was, but his pants and underwear were at his ankles before Scully could leave his ear. He turned his head to meet her tongue, to let them tangle, while his fingers worked their way deep into her, grazing her clit with his thumb.

Scully moaned. “They said you were good Agent Mulder, but I underestimated.”

They were role playing. He definitely could get into that. “Who is They?” he asked her.

“The men that watch. They see it all.”

Voyeurism. What brought all this on? She didn’t give him much time to ponder, sitting up and bearing down, lodging his cock, now hard and firm, between her folds without allowing it entrance.  He did a crunch to watch her move against him, and she rubbed the length of him with her clit for the show. His teeth sunk into his bottom lip so hard he tasted blood. “Please, Scully.”

The blue of her eyes were absent in the dark as she growled at him. “Not Scully. Call me, Andromeda. You get so hard, and you’re so very very long. Impressive, Agent Mulder. I’m not used to someone so big, where I’m from.”

“Where is that?” Mulder panted, the tip of his cock tingling as she teased it around her opening. 

“Not yet,” Scully commanded, twisting her hips, sliding his cock up her folds without the ability for him to enter, rubbing the length against her clit, sending waves of pleasure through him. She was so wet, he slid against her easily. Her legs parted farther as she leaned against him tortuously. He wanted to be inside her. She was using his cock to masturbate and it wasn’t like he minded, but his heart yearned for their connection.

“I want you, Scully” he finally admitted. 

“Not until I’m ready, Agent Mulder.”

“Tell me then, please, what will it take?”

“Say my name,” she commanded, leaving a wet trail of arousal along his cock.

Mulder’s eyes closed, the back of his head pushing against the rough fitted sheet of the mattress, absorbing the pleasure. “Andromeda.”