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Unforeseen Consequences

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Part 3 of a trilogy:

Part 1: Best Intentions

Part 2: Second Chances

Takes place approximately one year and two months after Miranda. Starts approximately five weeks after Second Chances, eight months following Best Intentions.

Synopsis: River's decision to once again be a normal girl has far-reaching consequences that no one can anticipate. Mal and Inara prepare for the arrival of their baby, while Simon and Kaylee are still trying to get pregnant. Simon/Kaylee, Mal/Inara, River/Rafe

Additional Notes: The series is rated PG-13 overall, although for some chapters it will probably go up. Each chapter will be marked as appropriate.

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Chapter 1

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The human brain. Mankind had been studying its mysteries since its inception, trying to determine all this small mass of grayish, wrinkled skin was capable of. Many advances had been made in the understanding of its parts – cerebrum, cerebellum, brain stem. It was considered the seat of all human intelligence and in some cultures, the location of a person's soul.

And River Tam's had been cut to shreds.

Eli had been studying the different readouts and results that Simon had gathered, both from his contacts who had initially helped him free his sister and from his own work. And everyday, Eli was astounded at what he saw.

Gazing at the images now, the latest one from a neural imager on Ariel, he realized his mouth was open, gaping like a fish at the unbelievable information before him. Snapping it closed, he gazed to the man standing beside him, his expression unreadable and said, "Simon, this is truly unreal."

"Don't you mean abhorrent?" Simon commented dryly. Turning away from the screen, he couldn't take the sight of his sister's mangled brain any longer.

"Well, that too," Eli admitted, watching as the man paced across his office. "The fact that River is even walking and talking is a testament to her strength."

"So, I should be thankful they didn't make her a vegetable?" Simon asked, his voice a cross between incredulity and disgust. "I should be glad they decided to carve her brain like a holiday turkey, but were humane enough to leave her a shred of sanity?"

"No," Eli stated firmly. Crossing his arms over his chest, he told him, "But you should be grateful she's alive." Cocking his head back towards the images, he added, "Based on what I've seen here, she could very easily have died during any number of these surgeries."

Swallowing thickly, Simon sighed, releasing his momentary flash of anger with the long breath. "I know," he admitted. Raising tired eyes back to his friend, he added, "I may not understand much about neural trauma, but I know she could have died. And I am thankful she's alive."

"But she's not well," Eli finished for him. Turning again to study the readouts, he waited a few minutes before flipping off the screen. Heading to his desk, he took a seat behind it as Simon sat on the opposite side. "However, based on what I've seen, I think there's a chance I can help her."

"You can't repair her amygdale though, right?" Simon asked, his doctor's curiosity supplanting his brotherly concern.

"No, that's impossible. Once an organ as fragile as the amygdale has been so irrevocably altered, it's just not a good idea to try anything radical. I could remove it all together, but-"

"But then she wouldn't feel anything," Simon finished for him. Shaking his head once, he said, "I know that's not what she wants."

Nodding, Eli agreed. "Precisely, which is why we're going to have to repair the other areas of the brain." Sitting back in his seat, he tented his fingers before his face and explained. "I'll need to do some scans of River's brain now, see how things were affected post the trigger. Also, I'll need to run her through some tests."

"What kind of tests?" Simon could see discomfort in Eli's eyes.

"Unpleasant ones," the man elaborated vaguely. As Simon frowned at him, Eli continued. "I'm going to need to agitate her brain, Simon. We need to see what's firing, where the neurons are going and why. Otherwise, I'll simply be experimenting, just like the Alliance. And I refuse to do that."

"I don't want that either," Simon hastily agreed. His memory flashed images of River's crazed state when he'd first rescued her, and he felt his gut clench involuntarily. "There isn't another way, is there?"

Shaking his head, Eli told him, "No, I'm afraid not." He watched the other man struggle with the realization of what his sister would have to go through. Eli had prayed there would be another way, some other method of examining River's brain. But there wasn't. "You'll be there for her," Eli reminded him, getting a curt nod. "She'll be all right. She's strong."

Sighing, Simon murmured, "I know." He didn't have the heart to tell Eli it wasn't necessarily River he was worried about. He was more concerned with his own reaction at seeing her subjected to mental tests of endurance and sweat-inducing nightmares, just for the good of her health. He vaguely wondered if there wasn't a line between making her well and making her worse.

Releasing one more sigh, Simon did his best to push these thoughts from his mind and met Eli's kind gaze. "I know. She'll be fine. We all will."

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"'Nara, ain't this the cutest thing you ever did see?"

Inara fought the urge to roll her eyes, instead turning to face Kaylee with a grin. The younger woman had said the exact same thing about every item in the current baby store they were in … and the one before it … and the one before that.

Currently, she was referring to an onesie with what appeared to be a duck and its ducklings trailing across the front and around the side. It was yellow and orange, and Inara had to admit, it was actually adorable. "Yes, mei mei, it is." As Kaylee beamed brightly, Inara moved towards her and added, "Although I'm not sure it's any cuter than the other fifty we've looked at today."

Swatting playfully at her friend, Kaylee simply folded the small garment and placed it in the basket Inara was carrying – a basket practically brimming with similar clothing, toys and baby accessories. "You best be careful, 'Nara," Kaylee teased lightly, skipping to the other side of the shop to admire a collection of mobiles. "You're starting to sound like the captain."

"Oh merciful Buddha, protect us," Inara lamented grandly, getting a giggle from her friend. She was silently debating the benefit of clothe to disposable diapers a minute later, turning to Kaylee. "Kaylee, what do you-"

Inara swallowed her statement as she took in the sight of her friend, gently fingering a pink and white baby blanket. Moving to her side, Inara reached out and covered Kaylee's hand with one of her own. "It will happen someday, Kaylee. You know it will."

Sighing heavily, Kaylee placed the soft fabric back on the shelf and blinked quickly, ridding her eyes of any hint of tears. She was through being sad, she'd made that decision the minute her pa's funeral had ended. Forcing another grin to her face, she said, "I know that. Jus' got a bit sentimental is all."

Inara watched as Kaylee bounced to the back of the store, her coos audible as she took in rack after rack of frilly, miniature dresses. She wished, in some small way, that it was Kaylee and Simon's baby they were shopping for now, instead of her own. She wanted the baby, Mal's baby, of course, but it seemed that after all Kaylee had been through, getting her heart's greatest desire was the least bit of kindness the 'verse could show her. But Inara knew everything was meant to be and Kaylee and Simon would get pregnant when it was time.

"Ooh, 'Nara, you gotta see this!"

With a small smile, Inara pulled herself from her thoughts. "Coming, mei mei."

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River took a deep breath, unaccustomed to feeling so uncomfortable. She'd been avoiding this conversation with the captain the entire trip to Harvest, and now that they were just a few days out from returning to Sihnon, she knew she no longer had the luxury of avoidance. But she still wished she did.

Descending the two steps into the galley, she caught Mal in the middle of fixing some kind of lunch. "Can I have some?" she asked airily, sitting easily at her normal seat around the table.

Mal glanced to her over his shoulder and grinned. "Well o' course, lil' one. Though I ain't gonna guarantee it'll taste good."

Shrugging, River waited until he'd joined her, depositing a bowl of tan-colored protein before her. "It's got to be better than Simon's cooking," she commented, taking a spoonful. As the lumpy substance hit her tongue, she amended the statement. "Or maybe not."

Mal's eyes snapped to her face, seeing the tease in her eyes and he returned it with a smile. "You were warned," he chided gently, before scarfing down his own serving. They ate in an amiable silence, River more playing with her food than actually eating it. A fact not lost on Mal.

"You got somethin' on your mind, River?" he asked, sitting back from the table and taking a long drink of water. Watching as she regarded him with those large eyes through her curtain of dark hair, Mal got the distinct impression there were a whole bunch of somethings on her mind.

Swallowing hard, she pushed her bowl away and then turned to face him. "I need to talk with you," she began slowly, wringing her hands in her lap so that she wouldn't nervously grip his. "About taking some time off."

Eyebrows raised in a mixture of curiosity and confusion, Mal asked, "Time off?" As River nodded, her face paling a bit as the silence stretched between them. Sitting forward, he studied her even more intently, his blue eyes boring into her face, looking for answers. "You all right?"

She nodded and sighed softly. "Yes, Captain, I'm fine. I just … There's something I need to do when we get back to Sihnon and it's going to take awhile. I won't be able to fly the ship."

Mal was liking the sound of this self-imposed sabbatical less and less. "Well, then if'n it's that serious, I'm thinkin' I'm gonna need a bit more to go on. Ship can't fly without its pilot." River knew he wasn't trying to be difficult, just trying to get more information by using his authority as an intimidation device. It wouldn't work on her, which he more than likely knew, but it was always worth a try.

"You have to trust me, Captain," she told him softly, forcing herself to meet his gaze. With a firmness in her tone that masked the fear and anticipation she was really feeling, she added, "Besides, you're going to have new responsibilities soon. Can't be worrying about me."

Sitting back, Mal wondered why it surprised him that River knew of Inara's pregnancy. It wasn't as if the girl wasn't a mind reader. Frowning lightly, he asked, "You tell anybody else?"

Shaking her head once, River rose, taking their bowls to the sink and beginning to wash them. "Not my secret to tell," she explained as she passed him. She stood over the sink, letting the water run as hot as it could. Soaping the sponge, she put the rest of the protein mash down the drain. She could feel Mal's eyes on her – he was unconvinced. He still wanted answers and the fact that she wouldn't share them caused him a level of anxiety he strongly disliked.

Mal approached River as she toweled off the now clean bowls, not missing the way her shoulders tensed at his approach. Resting a light hand to one slim arm, he asked, "River, what's this really all about?" When her only answer was a sigh, Mal added, "You're still my albatross."

Turning to him with a sad smile, River answered quietly, "I know, but you're just going to have to trust me." She held his gaze steadily and counted to five, before imploring, "Please?"

Mal studied her closely, looking for something – anything – that might lead him to a better understanding of what exactly his young, genius pilot was going through. But there was nothing; nothing but a deep need shining in those damn expressive eyes of hers that told him to put his faith in her, again.

So he did. Pressing a kiss to her forehead, Mal told her, "All right, lil' one. You can take some leave, but I hear things are goin' south, I'm gonna be demandin' some answers. Dong ma?"

Smiling, River pressed herself up on her tiptoes and kissed his cheek. "Yes, sir, Captain Daddy." She hugged him, before running back towards the bridge, leaving Mal to wonder what in the hell was happening. As he turned to head towards his bunk, he caught sight of the engine room.

A new and unpleasant theory burning in his gut, he stalked down the corridor and bellowed, "Rafe!"

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Rafe heard the captain's yell and the anger associated with it and groaned. What had he possibly done now to piss off the older man? It seemed if it wasn't one thing it was another; of course, finding Rafe and River in a – compromising position the other day, probably hadn't helped Mal's opinion of him.

Standing from where he'd been examining the engine, he pulled a soiled rag from his pocket and began wiping his hands. Turning in time to catch the captain's angry glower, the next thing Rafe was aware of was Mal's hard fist connecting solidly with the side of his face. Unprepared for the hit, he stumbled back, steadying himself on the room's curved wall as Mal advanced on him fuming.

"What the hell was that for?" Rafe demanded, rubbing his jaw. Damn, the man could hit.

"What'd you do to her?" Mal was in no mood to defend his actions. Not when Rafe had just cost him his pilot.

"To who?" Pure confusion settling on his young features, Rafe straightened and asked again, "To who, Mal? What are you talkin' about?"

"You know damn well," Mal threatened, taking another step forward. "River. You wanna tell me why my genius pilot all o' the sudden wants time off? An' why she won't give me an explanation?"

Concern blooming through his heart at an alarming rate, Rafe asked, "River asked for time off?" When Mal's expression did not change, Rafe breathed, "Why?"

Mal thought about hitting him again, but one glance at the man's already bruising cheek and he knew that was a bad idea. Forcing himself to take deep, even breaths, he stepped back and hooked his thumbs on his gun belt. "You really don't know?"

Shaking his head once, Rafe told him, "I really don't." Wadding up the rag he still held, he threw it violently towards the workbench and told him, "But I aim to find out."

"Not his fault, Captain."

Both men turned at the sound of River's quiet voice. With a frown marring her young features, she moved into the room, easily sidestepping Mal. Turning Rafe's injured cheek towards her with cool fingers, she clucked in disapproval, scowling at Mal. "You didn't have to hit him."

Reaching for the hand that she still held to his cheek, Rafe tugged on it gently to get her attention. "What's goin' on, Riv?" he asked quietly, wishing he had the ability to read her as she did him. "Why're you takin' a break?"

Sighing, River took another step towards him, resting her forehead against his, as he tipped his head down further to meet her. Suddenly feeling like an intruder, Mal all but tiptoed out of the room, hoping to get away unnoticed.

"No more hitting," River scolded him, just as he'd taken his first step back into the hall. She hadn't bothered to face him, but Mal knew he was the one being addressed.

"Yes, ma'am," he murmured before high-tailing it out of there.

Once the captain was gone, Rafe slid a hand under River's chin, tilting her face back towards his. Her eyes were clear, but there was a tightness to the lines around the edges that told him she was keeping a secret. A fact he did not like. "What is it, bao bei?" he asked again. "You all right?"

"I'm fine," she told him firmly, stepping back and holding her arms out to her sides. "The picture of health." As Rafe frowned mightily at her dodge of the question she added, "There's just something I need to do on Sihnon and it's going to keep me from Serenity for a bit."

"What is it though?" He did not like the secretive nature of this conversation. He liked even less knowing that it was his girlfriend, the love of his life who was hesitant to share something with him. "You're scarin' me here," he admitted.

"There's nothing to worry about." River was lying now and she knew it. But she'd have to. No one, but Simon could know until they were ready to begin whatever treatments Eli felt were necessary. Besides if Rafe knew, he would talk her out of it. And she would listen to him, because the last thing she wanted was to hurt him. So, she would just have to wait until it was too late to stop her plan. "It's really not that big of a deal." Another lie.

"Then why can't you tell me?" Rafe demanded, stepping towards her. As she crossed her arms defiantly over her chest, Rafe watched her expression set and he knew he'd already lost this battle. Her face, eyes and body language all conveyed to him that she'd dug her feet in, and no matter what argument or logic or reasoning he used now, she would not give him the answers he wanted. "C'mon, River. This isn't fair."

"You have to trust me," she told him simply. As she felt a pang of hurt stab his heart, she softened her expression just a bit and added, "I'm sorry, but you do."

Rafe wondered if he could push. He wanted to, but he also knew there was no point in starting a fight. Either she would tell him or she wouldn't; either he would accept that or he wouldn't. She had placed them at a convenient impasse. Sighing heavily, he gave in - reluctantly. "I do trust you, you already know that." Meeting her brown eyes with an intense gaze, he asked again, "You're sure you're all right?"

Moving towards him, River held his face in her hands and said, "Yes. I'm fine."

Holding her, Rafe decided her assurances were enough – for now.

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"Did you and Inara have fun today?" Simon questioned, shrugging out of his shirt and pants, and reaching for the pajama bottoms on the end of the bed.

"Yeah," Kaylee answered, her voice muffled from where she stood before the bathroom mirror. "Shiny."

As Simon crawled into bed, more than grateful for the rest, he watched Kaylee exit the bathroom, one of his old t-shirts thrown on as a nightshirt. She still preferred to sleep naked, but after Simon had made an absentminded comment about the sexiness of seeing her in his clothes, she'd made it a point to indulge him.

Smiling faintly at him as he snagged her hand as she passed, Kaylee came easily to his side as Simon tugged her down next to him. Holding her cheeks in his hands, he gently lowered her lips to his and kissed her, tasting the cinnamon of her toothpaste and the light flower scent of her face soap. She was so beautiful.

Sighing against him, Kaylee easily stretched out beside him, forcing Simon over onto her normal side of the bed, so she had room. With her head pillowed on his shoulder, she found her mind wandering back to those adorable boutiques she and Inara had visited all day. Each store filled to the brim with all kinds of baby things in blues and pinks and yellows. She'd even seen a mobile for a baby's crib made of different models of spaceships. She sighed wistfully thinking of the day when she might be able to hang something similar over her child's crib.

"You sure you had fun?" Simon asked softly, his lips whispering against her forehead.

Nodding, Kaylee propped her head up on one hand and looked down at him. Her fingers rested absently on the top of his chest, lightly caressing the skin there. "Yeah, it was nice. 'Nara bought all this stuff for the baby. It was all so cute, we could hardly pick."

Simon smiled softly at her, but did not miss the flash of sadness in her eyes. "It'll be us someday too, bao bei," he assured, his hand brushing along her shoulder and cupping her cheek. "You know it will."

Offering him a weak smile, she said, "I know. It's jus' takin' a lot longer than I'd like."

"Well, maybe," Simon said wryly, dropping his hand from her face and instead running it up her smooth thigh from where she had draped it over his leg. "But the practicing is a lot of fun."

Kaylee let out the smallest moan as his hand found its way up and under her shirt, his smooth fingers fluttering across the skin of her belly, before slowly working their way downward. Her eyes now lit with desire, she leaned towards him and whispered, "You do have a point there."

Covering her lips with his own, Kaylee and Simon found themselves practicing until the early morning hours.