MSR sometime between the 6th and 7th Seasons I think.
Scully sighed and rubbed the bridge of her nose. She'd been staring at the same paragraph of the case file she was holding for at least 30 minutes. Instead of actually reading it she found she was replaying over and over again in her mind Mulder's latest attack on her sanity. Flipping the case file down on her motel bed she reached for her wine glass and took a sip. There was a time in her life when Friday night didn't always mean drinking bathtime wine alone. There was a time in her life, she reflected, where work stayed at work and her free time was her own. There was a time she pretended to be able to have a personal life.
Sighing again, she glanced at the wall separating their rooms. She heard the faint drone of his TV and wondered what the big oaf was doing. Today, in a stunning display of unprofessionalism, he had mockingly harassed that local police officer who had taken an interest in being "helpful" to the FBI, and Scully specifically. In the sanctity of her own bureau-funded motel room, Scully allowed herself and private smile at the memory. Duane, the cop, seemed a bit pompous but generally nice enough. She honestly had a hard time concentrating on anything he said as Mulder had taken to positioning himself behind the officer but in her eye line and rolling his eyes and making faces while Duane talked. After Duane had actually offered to help her with the autopsy, she had to work very hard to avoid Mulder's shining eyes. That infuriating way he had of smiling without smiling. She always felt it like a bubble in her throat, her own giggle about to escape. Scully smiled down at her bedspread. He was unique, her Mulder.
She had given him piece of her mind in the car back to the motel, but Mulder just grinned quietly at his hands on the steering wheel and agreed with everything she could find to scold him with. Which frankly was worse than if he had yelled back at her. By the end of the ride she was seriously fighting to restrain her wild irritation and retain her composure. It was shades of Arcadia all over again.
Leaning back against the headboard, Scully pulled a pillow onto her stomach and crossed her arms over it. The digital clock on the bedside table read 9pm. She was normally lights out around 930, but she still felt awake from the emotional upheaval of the day.
Mulder had always flirted with her, she knew that. In the beginning she very much enjoyed shooting him down when he made off-color jokes or innuendos, it was like a battle of wits between them. She had suspected in the beginning Mulder's flirting had to do with a certain amount of immaturity on his part. A teenaged response to the fact he found her at least physically attractive. As their partnership had deepened over the years, the flirting had changed. Now it felt a lot more like he was trying to get her to laugh along with him.
Scully took another sip of wine. She thought about the near-kiss in his hallway before she was stung by that damn bee. About the time in the hospital after she had desperately tracked him down from the Bermuda Triangle and he had told her he loved her. At the time she had been so angrily relieved that he was back and safe and relatively unharmed, she had played his ramblings as a joke. Thinking back on it now, Scully felt a twinge of uncertainty.
Her mind slipped back over some of the events of the previous year. There had been a lightness to his flirting. She thought about the Rain King case file, of going under cover as a married couple in Arcadia, of the time he called her out of the blue to take batting practice with him. She shivered involuntarily at the memory of his arms around her holding the bat. He had put his hand on her hip as they rotated awkwardly with the bat. It was a detail she had mostly banished from her mind, except when it presented itself at odd moments and she felt a bit shocked it had happened.
Then there was the whole Padgett case file. After that case Mulder had been a bit brooding around the office. Scully frequently felt his gaze on the side of her face as heavy as a physical touch. She had refused to read the relevant pages of the novel where Padgett wrote of an imaginary explicit encounter between them. She didn't know if she liked to think Mulder ever thought about those pages more than once or not. She didn't think Padgett with his self-involved pompousness, would have written anything even close to a realistic depiction, but rather something a lot more glamorized. Something that made her seem like an unattainable sexual goddess who had her crown knocked askew. Mulder better not have thought whatever stylized filth Padgett wrote was an accurate depiction. Scully rolled her eyes. She had thought at the time that it was more likely Mulder was maybe disturbed by the idea she could be so vulnerable to someone paying her that kind of attention, but hoped it was more to do with finding her bloody, shirt unbuttoned, and unconscious on his floor, and thinking she was possibly dead. She had put it out of her mind at the time. Yet another unexamined, unresolved notch on the belt of their relationship.
Together they had faced so much trauma it was laughable. At some point she went from being someone who was marking time in a less favorable assignment on her way up the ladder, to someone who was legitimately working the X-Files with her partner. She almost didn't recognize herself at times. She knew Mulder thought he was someone who put work above any need for a personal life. He had long ago abdicated any hope of a normal personal life or significant personal relationships. It used to be a bit of a badge he wore proudly when he was younger. She also suspected he thought she was too good for a similar fate.
As if, Scully thought, the choice in that matter was up to him. Hell, it wasn't really up to her either. After that first case seven years ago she'd been completely hooked.
Her mind drifted back over a more recent conversation, yet again in his doorway. Another big emotional moment that she had shut away. Something too painful to fully explore until sometime later. Well, Scully supposed, now was later. She had gone to him to bring him sad news that she felt deeply conflicted about. She shivered, recalling the intensity of his gaze as he looked down at her sadly. She had expected something else than his reaction. Something more grief-stricken or him shutting her out. Instead he had gathered her to him in comfort, and rumbled a story to her about how she was his "touchstone." Scully flushed at the word. She wasn't sure why. She recalled her heart was racing and she was also slightly crying and she thought he was going to confess his feelings, or kiss her on the mouth or something. When he didn't she found she was unable to muster the courage to express anything much more back to him, and settled for kissing his forehead. She wasn't embarrassed by it, but sometimes late at night she thought of the ways it could have ended much differently. She actually found herself thinking about his words quite a bit.
Then there was the actual kiss, on New Years. She had thought he was going say something again afterwards, but his face remained inscrutable. It had been sweet, but hardly a breathless confession of undying love.
Now, as she thought about these times, and about Mulder quietly making fun of the officer today, she felt another twinge in her secret soul. Something slid into focus. Scully covered her burning face with her hands.
He wasn't perfect, her Mulder. Their communication actually wasn't that great either. But what they did have was trust and respect. Scully sighed heavily and felt a heavy weight on her chest disappear. She supposed that over the past year or so, all his open flirting with her, and those big moments she had thought were incomplete, might have been Mulder's best efforts to show her his feelings and he was waiting for her to either make up her mind or find the something better he always thought she deserved and put him out of his misery.
Scully cursed softly. She was slow with emotional things. She knew that. It took her a long time to face and resolve emotional issues. She tended to lock things away and deal with them far past the fact. She thought about the almost kiss in the hallway outside his apartment. She thought about what she had told the vapid rain king prom queen about friendship and switches being flipped and not being able to imagine yourself with anyone else. She also thought about how important he was in her life, and acknowledged that all her general irritation with him was probably, at least a little, based in her unresolved feelings for him.
Scully sighed and felt tears crowd the corners of her eyes as she realized she no longer saw the stereotypical career and family path for herself she had always assumed she would have. She hadn't thought about her future 2.5 kids for a long time now. Frankly it seemed beige and foreign, like a stranger's life from a magazine. She realized she wasn't holding out for something better, for a long time now, she'd been holding out for what she didn't realize she already had. Scully thought about the intensity of his eyes and bit her lip.
Of all the nights to realize your partner was in love with you and had been showing you as openly as he could, why did it have to be one when she had just been flagrantly irritated at him? Scully cursed again and finished her wine.
For a long moment she looked at her fingers on the wine glass and considered the big lunk behind the door in the next room. It was only fair, she supposed, the ball was in her court. Standing, she brushed her hair behind her ears and looked down at her pajamas. Mulder had seen her in these a million times before. Scully bit her lip and took a deep breath before knocking on their adjoining door.
"Mulder?" She whispered. The TV muted and there was the sound of creaking bed springs then his bare feet padding on the carpet. He swung the door open and she felt her tension dissolve at the sight of his quiet grin.
"Yes ma'am?"
He was wearing a knicks t-shirt and cotton pajama pants. He leaned against the doorway, looming over her in the way he liked to encroach on her personal space. Scully felt her heart beating faster. She was very short next to him in her bare feet. She bit her bottom lip, trying to ignore the shape his shoulders made against the fabric of his shirt. He really was very a good-looking man.
"I just wanted to-" she suddenly found it hard to proceed.
"-thank me for saving you from Officer Goober's attention today?" Mulder helpfully finished for her. She fixed him with her best unamused look. Mulder steadfastly met her eyes. He truly seemed still annoyed with the man. Scully felt her defenses crumbling and smiled in spite of herself around her bit lip. Mulder rubbed his face.
"You know Scully, sometimes I hear those local guys talk behind your back on cases. I know how they think. That pissant officer is just another yokel trying to show off by trying to get in the FBI's pants." He sounded a bit plaintive, a bit envious.
"And does that make you jealous?" Scully found herself smiling. Mulder's eyes narrowed. He seemed a bit taken aback by her directness. Steeling herself, Scully willed herself to step forward, into his space, almost against him. She saw his pupils dilate and he straightened in the doorway, hands fidgeting at his sides.
"No, of course not- it's just, you know, disrespectful-" He mumbled, cutting off suddenly when Scully absentmindedly pulled one of his arms around her and stepped fully against him. She pushed her arms around his back, pulled him against her, burying her nose into his chest, inhaling his scent. The one that washed over her from time to time in the car or when his suit jacket swing open in close proximity. She could hear his heart thumping wildly, matching her own. His arms tightened around her, one of his hands resting on her waist. Her hearing turned to a dull roar. She opened her mouth to confess, cheek pressed against his chest. To tell him he never needed to be jealous, that even when she was royally irritated with him she secretly craved his touch. To tell him about all the times in the car or motel, or the office she had wondered about him, about them. To confess how devastating, it felt when he was lost from her, and what a revelation it was when he was miraculously restored. To assure him she saw her future in their basement office and nowhere else. But she found it was difficult to say out loud. To a certain extent she thought, it was almost redundant at this point.
Mulder's hands were making big lazy circles against her back and she felt excitement flare in her stomach. Leaning back a little, she looked up at him and saw the tension had left his face. She felt his quiet smile mirrored on her own features. Something like joy welled out of her. It was the most obscenely easy thing she'd ever done, to reach up, grab the back of his neck, and pull his mouth to hers.
She felt his awkwardness at first, but she willed every ounce of sexual frustration into pulling him against her and was rewarded when he capitulated with a deep sigh. Then his body moved to push hers against the doorframe and Scully felt her stomach explode with heat at the warmth and force of his response. Jarred from his lips she opened her eyes. His eyes were shining at her again, bright and mirthful, but this time he was smiling with them, a small vulnerable smile. Her breath caught as one of his big hands touched her cheek, and she thought for a moment she saw a glimmer of tears in his eyes. He exhaled and she felt him steadying himself. She grasped his hand on her cheek and pulled it to her lips. Cheeks flushing she pressed a kiss on his palm. A silent admission and reassurance. She felt his eyes burning through hers and he rapidly closed the distance between their bodies and she was pressed against the door frame once more. Heat consumed her and she found herself clinging to and moving against him in the most regrettably obvious way. Not that he appeared to mind, she thought wryly, judging by the activities of his hands under her pajama top, circling her back, moving up the sides of her ribs, stopping just short of well, other physical attributes. Scully found his mix of plain eagerness and deferential awkwardness endearingly humorous. She had long suspected he was more bark than bite. Without overthinking the movement, she caught his hand on her side and shifted it blatantly onto her, making her intentions clear. He stilled for a moment, seemingly stunned. She found herself smiling and then a bubble of laughter bounced up from her throat, and then she heard him laughing too. Shoving against his shoulders, Scully pulled him into her room and down onto her bed.
That was the first time they became physically involved. It became a feature of their field work, away from prying eyes. Gradually they began spending nights at each other's apartments, waking together in the morning, spending weekends together. True to form, they never really truly discussed the new aspect of their relationship, but to Scully's mind, everything had kind of already been said and the path forward was obvious. She supposed it had been obvious for a long time.