A/N: Hey, everyone! Back and ready to go with a new story! I'm sorry this took so long, but I wanted to wait until I had at least five chapters of it done. To be honest, I've been planning this thing since late last summer; making out lines and time lines and all that jazz, but since this one is going to be rather long, I decided to put it on hold and get my other ideas out there. (Some of you may remember this story being an option in a poll I had on my profile quite a while ago as well) But okay, this is very important to take note of before you begin reading this sucker. This story is AU: Very AU. It is only fair that I tell you beforehand that this will not be your everyday Scrubs story. For example: some ages and phrases will be changed to fit in with the time period and what not, since having a thirty year old cabin boy wouldn't make a lot of sense. Anyway, I'm pretty nervous about this one, I'll admit, so I'll just leave it at that and leave you guys alone to read. Hope you enjoy it!

Disclaimer: I own a very large nothing.

Chapter I:

"I don't want to be a soldier who the captain of some sinking ship would stow, far below."

-Violet Hill, by Coldplay-

Jonathan lay still, giving his vision the time it needed to adjust to the ever present darkness that was his sleeping arrangements. Every night for the past month, he would drag his battered feet to the deck below, doing his best to remember where objects were so that he would not, once again, stub his toe in the dark. Of course, loose items scarcely remain in one place on a ship, as the waves that rock the vessel make sure to send them flying about. Hence, the kid would always manage to stumble over a lone barrel, tattered nets, or anything else that seemed insistent upon blocking his path.

That, and the small fact that the boy was simply clumsy.

Even so, when he did finally make it to his hammock, he would never go to sleep; just lay still and wait for his eyes to adjust to the shadows, and only when he could see the hand in front of his face did he allow himself to drift.

It's not that he was afraid of the dark; he just liked to know where he was. Because really, it wasn't very logical to float off into your own imaginary dream world without knowing where you currently were in reality. Unfortunately for Jonathan, he had, had to learn that the hard way.

It was about a month ago when they came; the Pirates, or as his mother liked to call them, Cut Throats. It was in the middle of the night when they entered their small town. Whoever had been on duty had fallen asleep, very unaware of the large ship that made port and the mass of pirates that followed after.

They bombarded their homes; crashing through windows, banging down doors, and filling their hands with whatever seemingly valuable item their eyes landed on.

If you got in their way, you were dead.

Yes, these pirates were undoubtedly cut throats. No mercy. No compassion. They were in and out with what they wanted, no looking back.

Villagers scattered as they continued to break down their homes, setting fires to the ones whose owners had fought against them. Jonathan's mother snuck out as the first loud crash echoed through their small living arrangements, her older son Daniel right behind her.

And right behind him, Jonathan.

The three curved and bent and twisted their way through the masses, trying to reach the town's "Safe Place." Through the confusion and the chaos, John decided to do what he always did to slip away from the pressures of reality: day dream. It wasn't supposed to make things worse, honest to God it wasn't. He was just imagining; pretending the current situation wasn't as bad as it really was. Perhaps they were on a quest; some massive group outing in which he and his town were about to embark on a magical adventure. Something. Anything other than what was taking place.

But he had let his mind wander just a little too far, and by the time he had brought himself back to reality, it was too late. He had lost hold of his older brother's hand, and even worse, he had lost sight of where his family members had gone amongst the crowd.

Before he could take in where he was, before he could even attempt to relocate them, rusty metal met his throat in one ragged motion, pressing against his skin as hard as it possibly could without making an incision. "Follow quietly or die," the voice whispered dangerously against his ear.

He obeyed.

Through screaming crowds and weeping children, he followed the man who reeked of old fish and grimy sea water to the very place he and the rest of the town had been avoiding: The pirate ship.

It was nothing magnificent, nothing like the ones that had been described to him through story books. In fact, if pirates and the adventures that followed were any thing like the stories he had been led to believe, then this really wouldn't be too bad. He had dreamt of some grand adventure for years; something to come and remove him from his small and desolate town, but this…this wasn't what he dreamt of at all.

The ship looked old, too old to be out at sea. It smelled of the man he currently followed, and its sails were tattered beyond the point of repair. How was the ship even sailing?

The soiled man was suddenly behind him, urging him forward. While the man's nudging was surprisingly not too forceful, Jonathan still managed to stumble, landing with a small thump on his knees. The splinting wood grated his tender skin, causing him to let out a small hiss of pain.

"He's a good age, right?"

The brown haired boy looked up then, instantly brought back to the moment by the very same voice who had threatened to kill him only…how many minutes ago? Perhaps not minutes. Perhaps hours. He could no longer tell.

But his eyes did not meet the pirate who had brought him here, but another pirate. He was small in stature, and while Jonathan was still a young lad, he was sure that if he were not on his knees, he'd be taller than him. The man wore a very large tricorn hat, and the little hair that peeked its way through was undoubtedly gray. He had a bit of a belly on him, but Jonathan had seen bigger. The word Captain rang through the boy's mind, as this man in front of him was undoubtedly the pirate in charge.

Very suddenly, he smirked, and Jonathan had to look back down at the wooden planks, unable to avoid the slight shiver that ran up his spine from the evil that came off of this so called captain before him.

"For once, Theodore, you managed to not screw up. Yes, he's the perfect age."

Jonathan kept his gaze steady on the planks, knees shaking ever so slightly against the wood they were pressed upon. He stayed like that until a hand from behind took hold of his shoulder, hoisting him up onto his feet. The young man stiffened, though inwardly congratulated himself for guessing correctly. Now that he was standing face to face with the captain, he could say for sure he was taller.

"What is your name?"

A demand, not a question. The boy swallowed. "Jonathan Michael Dorian, sir."

"And how old are you?"

"Eleven, sir."

The captain's eyes actually widened some at this. He looked to the man behind Jonathan, who backed up a step. The brunet boy turned to look at him too, and instead of feeling a swell of fear for the man who had earlier threatened to kill him, he felt something remotely close to pity

The poor guy, Theodore if he remembered correctly, looked just as shaken to be on the ship as he did. Balding and covered in sweat, he gave the captain what could only be described as "sad eyes," before replying to the unspoken question that lingered in the air around them. "Captain, please. You said yourself he was the perfect age, so surely you can see why I mistook him for younger than he appears…?"

"Enough of your excuses, Theodore! No woman or man ever cared."

The balding man openly deflated, but not before giving Jonathan a quick and apologetic look.

The captain cleared his throat loudly, bringing the two before him back to attention. "Eleven…is that right, boy?"

"Y-Yes, sir."

"You look no more than eight, but you'll do fine, I suppose."

"I'll do fine for what, sir?"

"It's Captain, not 'sir,' and you'll do whatever I ask of you, are we clear?"

Jonathan wasn't, but he nodded anyway.

"As I was saying," the captain continued. "We're in need of a new cabin boy, and guess what? You get the job. And in case you're wondering what this new position of yours entails, allow me to elaborate: Cleaning the ship, listening to every order that comes from my mouth, and my favorite part of all: Absolutely no pay. Keep this in mind; you are not a crew member, just a cabin boy. Are we clear?"

This time he was. More than clear actually, as the rules were sounding all too familiar to the jobs he had back home.

"Wonderful," the captain responded sarcastically.

So for the next very long, very tiring month, Jonathan did all that was told of him. It wasn't like he had to do it all by himself, as each and every crew member were required to clean the ship, but he definitely got the brunt of the work, not to mention the poor boy was never paid for all the hard labor. And because Jonathan was indeed a growing young man, he needed the right nutrients, the right food. But all that was remotely edible was given to the crew members, while the Captain dined on the finest in his cabin. So John made do with the leftovers, closing his eyes and swallowing hard as the dreaded food (if you could even call it that) made it's slimy, lumpy way down his throat.

And here he was now, at the end of his first month aboard the rotting vessel that was The Fractured Enid, lying alone, cold and sore in his too small hammock – praying, wishing – for something or someone to come and take him away.

Jonathan immediately regretted that desire.

A very abrupt, very loud crash awoke him from his half asleep state. The ship rocked forcefully, and John was able to manage a deep breath before his body freed itself from the hammock, colliding against the far off wall.

Ignoring the strong ache the collision had left pounding against his ribs, Jonathan scrambled to his feet and ran to the upper deck. The sight that awaited him made him wish he had stayed right where he was.

A storm raged over them, chaotic and violent. Lightening had struck the main mast, which was now lying haphazardly across the ship. Crew members were scattering, and no matter how hard he tried, John could not get a one of them to stop. He just wanted to know what was going on, what it was he should do. Were they fleeing? Were they leaving the already broken down vessel to be swallowed by the waves? Were they aiming to repair the damage? To fight against the storm and make their way to safety?

But not one of his unspoken questions received an answer, for just at that very moment, another ferocious bolt of lightening came crashing into the ship, mere inches from where Jonathan stood standing. While he narrowly avoided nature's attack, he was unable to avoid what followed after.

Literally half of the ship, the very half he'd been standing on, separated itself from the rest of the vessel, falling hopelessly into the water below. John couldn't tell if time had slowed, or if things were progressing too quickly. All he knew for sure was this: He was going to die.

He'd never be able to see his mother and brother. He'd never be able to tell them how much he really loved them; that he was safe. A little beat up, but safe. He'd never be able to fulfill the one dream he had clung to for years; to go on a real adventure. Pirates or no, he never cared. But he had craved for so long a chance to break free of his village; to see new wonders, to meet new people. And ironically enough, the very thing that had taken him away from his home (much darker and lonelier than he'd ever imagined) would now be the cause of his death.

Jonathan took one final breath, bracing himself for the icy cold water that was about to engulf him. He felt his body hit something hard and rugged, and then felt the sting and force behind the water that surrounded him almost immediately.

He was done. He was undoubtedly going to die.

--

Calloused hands brushed away loose strands of curly hair, letting out an aggravated sigh at the sea before him. The last month had been completely uneventful, and Percival found himself beyond bored.

"C-Captain?"

The man let out a small growl before turning to look at their newest crew member. "What is it nervous guy?"

"I-It's Douglas, sir. Douglas Murphy."

Was this kid for real? Percival turned his attention back towards the ocean, closing his eyes in quiet frustration. "I know your name, kid, I just don't care. Now tell me what you have to tell me or leave."

"I-I, um…"

Percival let out a warning growl, much louder than his last. He could feel rather than see the kid jump, and was instantly rewarded with the boy's explanation, even if it was said in a rather panicked tone. "I-I was up in the crow's nest like you instructed, and-and I saw s-some things…"

"What 'things?'" he asked annoyed, still not turning to face him.

"W-Wreckage, Captain. A ship that looks like it may have e-exploded. And I, um…should we pass it? Or should w-we anchor, to take a look...? Could be some valuables floating around in the f-flotsam."

A ship that appeared to have exploded, huh? Could be a number of things. Gun powder accident, an attack (though by pirates, bounty hunters, or the navy, he wasn't sure) or even a storm. But still, if the ship was nothing more than floating heaps of wood, why stop to look? Still, Percival was bored. Even if they didn't find anything of value, maybe they could find some needed necessities. God knows they could use it, what with not having made port in three or so months.

"And where is this so called wreckage?"

"N-Not too far from here, Captain. A little ways east."

Percival turned his gaze to the pointed direction and squinted. Well whaddya know? Nervous guy was right. Far up ahead, he was just barely able to make out what was once a ship; clouds of smoke and patches of fire circling the area. Turning his attention to the sky, he noticed a mass of gray clouds, slowly rolling away from the disastrous scene before them. Storm then, Percival noted to himself. Walking towards the edge of his own vessel, the red headed man peered over. Chunks of wood and soiled sails floated along the water; ragged and worn. The captain looked up again at the approaching scene, slowly becoming clearer and clearer. No way anyone survived that, he thought grimly. Then again, he should probably consider himself lucky, right? Storms out here were devastating, and they had managed to avoid what appeared to be a fierce one. And who's to say the ship that got torched would have passed them without any problems if all were still alive and well? Even if the vessel had been sailing under the Jolly Roger, it still could've been a problem.

The Navy had a bad habit of assuming that all pirates got along, most likely under the impression that all were set out solely to destroy their "peaceful," civilization, but that was one hundred percent untrue. Sure, almost every ship, pirate or no, had comrades out there on the sea, but that didn't mean every captain under the same flag would automatically be of the same mind…

"C-Captain?"

Percival turned around sharply, crossing his arms and flicking his nose in the process. The new crew member jumped again, but the curly haired captain ignored it. "Listen here, nervous guy. I need you to climb up to the crow's nest – yes, again – and make sure no one else is sailing towards that wreckage. Tell the others what we're aiming for, and try not to piss yourself on the way, understand?"

As Douglas scurried away to do as he was told, a loud, well toned laughter filled the captain's ears. He bit back a grin, pretending not to be grateful for the sudden appearance of his first mate. "What're you laughing at Benjamin?"

He watched from the corner of his eye as the only person he ever called "friend" took hold of the wheel, aiming towards the broken down ship with much more enthusiasm than necessary. "You! You and the whole, 'Grr, I'm the Captain!' thing you got going on."

"I am the captain, Benji."

"Aw, see? Now that's just cold. Why hurt me?"

Percival snorted. His friend almost had the whole puppy dog guilt thing mastered, if it wasn't for the small fact that he could just barely keep a straight face while doing so. "You're not hurt, and you know it."

"Okay, so I'm not upset. But still…Benji? What if I started calling you 'Captain Cox?'

"That's Captain Percival."

"What about Captain Perry?"

"No."

"Captain Per-Per?"

"No. Now why are you over here again?"

"To take the wheel, obviously. And to lecture you about being mean to the new kid."

"Nervous guy?"

"Yeah, that's the one. Poor kid looks like he's about ready to piss his pants."

Percival snickered. "Called that one, didn't I?"

"Listen, Captain, I get it. I always have. You need to show them you're in charge. But do you honestly think they don't know that by now? Why do you think almost everyone who turns pirate, either willingly or unwillingly, searches high and low until they find you?"

"Because the Sacred Heart is the finest vessel to ever sail these waters?"

"Maybe, but no. You're legend, my friend! The pirate who never kills, but somehow still manages to get the gold. Captain Percival, leader of the underdogs! Turning boys into men! Fierce, but loyal! Strong! Brave! Completely - !"

"Okay, I get it!"

Benjamin watched with suppressed laughter as a small grin made its way across his captain's face. If there was one sure fire way to get Percival to listen, it was to feed that super sized ego of his. Not that any of what he said was untrue, but still… "So do you get it? You don't have to be mean and domineering just to prove you're in charge. Everybody already knows!"

The grin his captain wore vanished almost immediately, and Benjamin inwardly sighed, knowing that Percival was gearing up for a rant. "Listen, Ben – there are certain aspects to my so called 'legend,' that give me all the more reason to bite down and bite down hard on all the quivering little peons that come aboard this ship. Because it's very well known that I almost always get what I'm after, the new crew members come on this vessel thinking it'll be all fun and games; that they can sit back and down rum and not do a damn thing to help, yet somehow, magically, will still be rewarded with piles of gold and rubies. Nee-hot how it works. They need to get their asses in gear and pull their weight. And you know that whole, 'The Pirate Who Doesn't Kill' bit? I'm proud of that, I am, but these morons get it in their head that, that means I'm some frilly wearing, flower giving captain who will let any and everyone cross me without a second thought. Which is a ra-heely dangerous assumption. For them of course, not me. So you see, Benji, I really have no choice in the matter. And if they don't like my leadership, then they are more than welcome to leave when we next make port, but until then, they better suck it up and deal."

Benjamin sighed, knowing very well he had lost this round. "Okay, okay. I see your point. But, and I know this is going to sound crazy, but maybe once in a while, you could be nice to someone other than me?"

"We'll see," Percival mumbled, and Ben couldn't help but smile. Even if it wasn't one hundred percent sincere, it was the closest thing he had ever gotten to a yes.

It was only a matter of minutes after the exchange that the ship reached the wreckage. Benjamin openly flinched at the site, while Percival's brows furrowed in an attempt to keep his emotions in check.

It was much worse than he had previously imagined.

The storm had destroyed everything. There was no site of anything valuable; not even a few barrels of rum bobbing up and down in the waves. And as he guessed, but secretly hoped he'd be proven wrong, there was not a single sign of life.

"Uh…Perry?"

Percival turned, taken aback and a little offended that his friend would forgo his title and stick to the nickname he hated at a time like this. "What?" he asked sharply.

Slowly, he followed his first mate's gaze. About twenty yards away from the burnt down ship itself, something – someone – was just barely holding on to a scrap of wood, the waves pushing him further and further away. Dead or alive, he couldn't tell, but there was just no way he was going to sail in the other direction.

Percival immediately began barking orders, and Ben didn't need to be told more than once to make his way towards the body.

"Christopher!"

"Captain?"

"Go down to the hold and grab the box of drugs. In fact, grab the surgical instruments while you're down there too.

"Right away."

"You! Big guy!"

"My name is -"

"Be quiet and listen! You and I are to go overboard and get the body. Is the long boat ready to be lowered?"

"Yes, Captain."

"Good. Now come on."

Percival and No-Name climbed onto the boat and were quickly lowered down into the waters. They paddled to the body in a hurry, making it in record time. The person in question hadn't been holding onto the plank, just simply slouched over it. The red headed captain reached out and grabbed him by the collar, pulling him carefully into the boat. The taller man, a crew member of only a few weeks, watched on, curious. He had never seen his captain act so…hurried. He seemed almost frazzled now, but was handling the body with a gentleness he didn't even know his superior possessed.

Once they were back onto the Sacred Heart, Percival laid the boy down on his back, inwardly wincing. The kid was so damn young. He looked so…so fragile. Quickly, he searched for a pulse. His own heart began to race when he felt nothing.

Why was he acting so bewildered, so distraught? Upon entering the life of piracy, he had seen more than his fair share of death, but at least he had never caused it. And the lives he did see destroyed, well…there was no way he could've saved them, nothing he could've done. But now? Now he was being given a chance to help, to save; much like the life he was a part of before all of this…

The older man's lips met the boys cold ones as he bent over, willing the battered young lad to breathe. "C'mon kid, c'mon!"

Nothing.

Percival pushed on the young man's chest, cursing and praying all the while. "Breathe – for – me – damn it!"

And he did.

The boy's eyes shot open, wide and frightened, yet clearly unseeing. Percival rolled him onto his side, allowing the ice cold water to pour from his lungs. He patted the kids back, willing all the water to escape, repeating over and over for him to cough and breathe, cough and breathe. The child obeyed, and by the time the water had left his lungs, he was once again unconscious, but at least this time, he was breathing.

"Captain?"

Percival closed his eyes. He was too relieved at the living body before him to be annoyed. "What is it, Christopher?"

"I have the drugs and the tools."

"Go into my cabin and put the drugs on my desk. The tools we won't be needing."

Christopher nodded, and while the captain hadn't told him to do so, he left the cabin door wide open. It made things much easier when both Percival and Benjamin carried the boy's body to place him gently on the bed.

--

Nautical terms:

Cut Throats – Ruthless pirates.

Cabin Boy – A young boy who worked aboard pirate ships as a servant. Many cabin boys made their way aboard ships by being kidnapped by pirates or were runaways looking for means of escape.

The Main Mast – The highest point of the ship; where the Jolly Roger flag flies.

The Crow's Nest – A lookout. Someone can see enemy ships from twice as far away as a sailor can from the deck below.

The Hold – Where supplies are kept, such as food, water, extra sails and ropes, spare lumber for making repairs to the ship, gunpowder and ammunition. Also kept in the hold is a chest of drugs and surgeon's instruments to treat the wounded.

--

A/N: Well…what do you guys think? I know, I know. Definitely a little strange, but hopefully it was good enough (or at least interesting enough) to grab your attention. Oh, and I know Dr. Cox hates the name Percival even more than he does Perry on the show, but back then, that name wouldn't have been so odd. And "Captain Cox," reminded me way too much of the cereal "Captain Crunch." lol Anyway, don't hesitate to tell me what you think, though I do hope you stick with me on this one. Until next time!