AN: Howdy, Kats and Kittens! How're things, eh? Well, I haven't posted a new Scrubs fic in a while and decided to get this one up. The original version is actually with Perry and JD's positions reversed, and when I wrote this one as a challenge for sickscrubs over on LiveJournal, I knew I had to keep going and make this into a full-fledged fic. So here it is!

Some notes: It's an AU, obviously. I s'pose they all met the same way in the past, but the plot line sort of drifted when a civil war began. It's all very vague (sorry about that ... not good with describing government disputes and all that), but the real story lies with JD, Perry, and the rest, so I guess that's sort of an out, right?

Enjoy, Ladies and Gents! And have a fabulous day/afternoon/evening/night!

My Soul to Keep

Perry greedily gulps in lungful after lungful of cold, burning air, coughing violently between each breath.

"Tell us where he is!" An angry voice yells into his ear, and someone tugs mercilessly on his hair, pulling his head back at a sharp angle. Perry grits his teeth and grimaces, growling low in his throat in defiance.

He is thrust forward once again, his head shoved deeply into a basin of water and held there. He struggles, knowing it does nothing but waste energy he'll need for later. And when his lungs can't take it anymore, when the fight is slowly leaving him and a grogginess starts to pull him towards unconsciousness, only then does his captor pull him out and watch him cough and sputter all over again.

"Where is he?" The voice shouts again, causing him to wince. "Where is Dorian?"

"He . . . He . . ." Perry pants, his chest heaving painfully and his throat hoarse from all the coughing and choking on dirty water. "He's . . . dead." He doubles over as a coughing fit takes him. "He's dead. He's dead."

"He's not!" The man above him argues, forcing Perry up. "He's alive! We have eye-witness accounts of him all over the grid!"

"He's dead," Perry repeats. "He's been dead. There was . . . an accident."

"Yes, this so-called 'mysterious explosion,'" the man sneers, sitting the doctor down roughly in a metal chair. Perry is grateful for the reprieve from the basin, but he knows that the onslaught is far from over. "We had our finest team examine the site, and they concluded the explosion was staged."

"There were bodies," Perry points out, shivering. The room is freezing, and he sits in only a thin t-shirt and a pair of boxer shorts, soaked from head to foot.

"Burned beyond recognition," the other counters, slamming a fist on the table in the center of the room. "There is still no proof that John Dorian is dead."

"Trust me," the doctor whispers, swallowing hard and lowering his head. "He died."

"He must have been planning this," the man says absently, standing and slowly pacing the room. "He trained you to say these things."

"Trained me?" Perry asks in confusion. "Nobody trained me, especially not him. He's just a-" A look of understanding dawns on the doctor's face, and his blue-tinted lips quirk into a smile. "You don't know anything about him." At the other man's pointed look, Perry lets loose a harsh bark of laughter, nearly falling out of the chair. "You probably don't even know what he looks like. God! And here we were worried to let him onto the surface! He could have walked right past you, and you wouldn't have given him a second glance!"

"Be quiet!" The other's face turns red with anger and embarrassment.

But Perry continues to laugh until his sides ache, unable to stop himself. "Do you . . . Do you even know how old he is?"

"That's enough! Guard!" A burly man in a military uniform enters the room and grabs Perry's arms roughly, hauling him to his feet. The doctor leans towards the other man with a sadistic grin.

"Do you even know if he's real or not?" He grinds out. "What makes you think he's anything more than a figment of someone's imagination?" He watches the other squirm with satisfaction and leans in even further to whisper. "What if you're chasing a ghost?" Perry receives a backhand across the cheek, but the look of doubt that takes the military man's face makes it all worth it.

"Take him to his cell," the man seethes, and Perry is roughly removed from the room.

"They'll be coming soon," the doctor taunts as the over-sized man leads him down the hallway, the soldier from the room following them closely. "They're probably already here."

"What makes you think they'll come for you?" The man walking behind them demands incredulously. Perry, suddenly, spins around, his face mere inches from the other man's as the burly guard holds him at bay.

"You don't have any idea who I am," he laughs breathlessly, his eyes searching the soldier's wildly.

The man clears his throat, straightening his jacket and giving the doctor an acidic look. "You're Doctor Percival Cox, former employee of Sacred Heart medical facility, and traitor to your country for harboring and aiding the enemy."

Perry leans in further, their noses almost touching as he takes a shallow breath and whispers, "You forgot something."

The soldier swallows nervously and cautiously leans in so that his ear is close to the other's mouth. The doctor airily breathes his secret to the soldier, causing the man's eyes to widen and his head to snap back. He searches Perry's face for doubt, for any sign that what the man has said is not true.

The doctor's face is dead-set.

Something over Perry's right shoulder catches his attention, and he glances down the corridor, his jaw going slack and a gasp escaping before a bullet finds his eye, and he limply crumples to the ground.

The burly man reaches for his gun, beginning to turn, but he barely shifts his weight before he, too, falls dead. Perry stands stock-still between the two bodies, their blood pooling around his bare feet. The harsh sound of boots against concrete pulls him from his stupor, and he turns to find two familiar faces. The figures stop beside him, guns trained on the dead soldiers.

"Doctor Cox?"

"Gandhi," Perry greets rather breathlessly, shivering as the cold returns. He nods to the other man. "Dan."

"Having a bit of trouble, Coxy?" Dan shifts the P-90 in his hands as he gives the man a funny grin and chomps down on the wad of pink bubble gum in his mouth. If anyone has adapted to their new life, it's Dan. He's always wanted to be in the military, but his friends and family warned him of the discipline and hard work. He supposes this is just as good. And at least he gets to carry around a big-ass gun.

The doctor grimaces absently as Turk searches the guard for the key to his handcuffs. He rubs at his wrists when he is finally released, staring down at the dead men.

"Hey," Dan snaps his fingers in front of Perry's face. "You with us, buddy?"

"Yea," he huffs, rubbing at his face and stringing his fingers through his wet curls. "Yea."

"Did you get what you came for?" The surgeon asks, looking down both ways of the corridor. He looks nervous. And he should be. It's not often that they have to go out into the field.

Perry nods, releasing a sound somewhere between a bark of laughter and a sob. "Yea," he says huskily, his red, puffy eyes shifting. "Doug's computer virus worked. They, uh . . . They don't know anything."

"Nothing?" Dan asks skeptically, his eyebrows knitting. The doctor shakes his head.

"They've got nothing. His information was removed from the system before they could get to it."

Turk and Dan share a look before the surgeon nods, saying, "All right. Let's get out of here. Can you make it all right?" As Perry nods, Dan pulls out an extra set of clothes from his pack and hands them to the older man. The doctor accepts them gratefully, pulling them on with some difficulty but quickly nonetheless.

"Let's go," Perry demands almost desperately, taking the hand gun that Turk offers him and following both men down the corridor.

0 o 0 o 0

Several hours later finds all three safely back at the base.

"Arrangements have been made?" Perry asks as they make their way through the crowded, underground space.

"We're shipping him out tonight to the new location," Turk confirms. "The equipment and everyone else leave early tomorrow morning." Perry nods.

"Dad!"

The doctor turns to see his son, Jack, running towards him, smiling from ear to ear. The young man has come a long way, and at age thirteen, he has already seen far more than Perry would ever have wanted him to. Jennifer, Sam, and Isabelle are right at his heels, squealing and waving in delight. Jack and Jennifer run into Perry's waiting arms, Sam to Dan's and Isabelle to Turk's.

"Hey, Sammy," Dan smiles widely. "How's Daddy doing?" The boy shrugs.

"Same as when you left," he says. "Is Perry okay?"

"Fine, kiddo," Perry replies, kissing the top of Sam's head and ruffling his hair. "How're things holding up?"

"They were fine until a couple of days ago," Jack says accusingly. "You were supposed to be back the day before yesterday."

"Yea," the doctor nods with a wince, giving his son a look of apology. "Things didn't . . . move as quickly as I'd hoped."

"Did they hurt you, Daddy?" Jennifer asks in a small voice.

"I'm okay, Sweetie." Perry smiles wanly, looking up as another familiar figure approaches.

"We'll see about that."

"Carla," he breathes in relief at the sight of her. "Am I ever glad to be back to you and your needles."

"Come on, Per," the nurse laughs, leading him back to a curtained-off area. As soon as they're out of sight of the others, Perry lets loose a pained grunt.

Carla sighs. "They were pretty rough, huh?"

"They always are." The doctor attempts a chuckle, grimacing as it jostles his sore ribs.

"You've got to stop doing this, Perry. One of these days, something's going to happen before we can get to you."

"I have to keep him safe. He's the only reason we're all still alive, why we're still fighting." The nurse says nothing, gathering the medical supplies she needs onto a tray and setting them beside the other on the make-shift hospital bed – it's more of a cot, really, but it's the best they can do, considering.

"How is he?" Perry asks quietly, his voice heavy with exhaustion.

"His vitals are stable," Carla replies softly, absently arranging the items on the tray. "He started breathing on his own yesterday. We took him off the respirator."

"That's good." The doctor smiles. "Do you mind if I . . ." He gestures outside the curtain, and the nurse sighs.

"Five minutes," she warns, "then I want you back in here for a checkup."

Perry nods and stands, determinedly making his way towards another curtained-off area, this one with a guard standing outside the entrance.

"James," he greets as he nears the soldier.

"Doctor Cox," James returns with a smile. "Good to see you back, Sir."

"Thank you. Any news on your family?"

"They arrived safe and sound in San Francisco last week. They'll be transported to the new base site in a couple of days," the guard says with much relief in his voice and on his face.

"That's good to hear," Perry grins, clapping the man on the shoulder. "I'm happy for you, James."

"Thank you, Sir."

Perry enters the small room just as he always does – hands shoved deeply into his pockets and breath held tight in his chest. He expels a gust of air and quirks one side of his mouth when he sees the absence of the ventilator tube.

It's the first time he's been able to see JD's face clearly since the accident.

Perry had not been lying about the explosion. There had been bodies, most of them planted, but some deaths had not been planned. And JD had gotten caught in the blast and had died in Perry's arms . . . only to be resuscitated with minor brain damage and no telling when he would awaken from his coma-like state.

Even if JD wakes up, there is no way to know if he will still be the same JD who they all remember, who started this resistance, and who has paid far too much to go out like this.

"Carol," Perry says quietly as he sits beside the bed and takes the younger man's hand in his own. "I see Jennifer's been greasing your hair up again." He stares with amusement at JD's dark, styled locks. "I, uh . . . I just got back from another one, if you couldn't tell." He gives a nervous chuckle. "Think I'm still shivering. Not sure if it's because I'm cold or if it's just nerves." Perry plays with the other's fingers absently. "I actually thought . . . I didn't think I'd make it out of that one. They had me pretty scared for a while."

He tries to keep the tears at bay, but somehow they slip down his cheeks as he releases a pent-up sob. He swallows and clears his throat, trying to compose himself as quickly as possible.

"Um," he stammers, trying to find the right words. "They don't know anything. Not even what you look like. So when you wake up, you'll have nothing to worry about." He brings the fingers in his hand to his lips and closes his eyes. "You have to wake up, JD. I can't . . . You were so good at this." He laughs hysterically for a moment. "I don't know how or why, but you always knew what to do . . . And now that you . . . Now that you're not here, they're looking to me for answers." More tears fall from his eyes, but he does nothing to stop them. "I can't do this. I'm not as strong as you . . . There, I admitted it. You happy?"

Perry sniffs and stands, leaning over and kissing JD's forehead.

"Our secret is still safe," he whispers before wiping his face as best he can and heading towards the curtain entrance.

0 o 0 o 0

Far away in a dark room, several men stand around a computer consul watching a security tape recording of their enemies' latest escape from one of their facilities.

"There," one man points to the screen as the figure known as Doctor Percival Cox leans in towards one of their men, whispering something mere seconds before the soldier is shot and killed. "Zoom in on his mouth. I want to know what he's saying."

The tech sitting in front of the screen complies, tapping furiously at his keyboard until the image is zoomed and sharpened. The video plays.

"You forgot something," the Perry image whispers, and the soldier image leans forward. The rest of the conversation is inaudible, but the man standing over the computer screen is no stranger to lip reading, and as he realizes what has been said, his eyes widen.

He spins on his heels to the men murmuring behind him and yells, "How did we miss this?" Some of the soldiers shift uncomfortably. "I want all available resources on this. I want this man." His bony finger roughly raps on the computer monitor.

"Sir," a timid voice ventures from the small crowd, "all of our resources are being devoted to finding Dorian."

"I want this man, Lieutenant," the other spits. "You get me Percival Cox, and he will deliver Dorian to us."

"Sir?"

"Now!"

The men snap a sharp salute and scatter before their commanding officer becomes even angrier. He turns back to the screen.

"Rewind it."

The tech complies, playing the small video stream several times in a row. Perry's lips repeat the condemning information over and over again.

"My name is Doctor Percival Dorian-Cox."

AN: Questions? Comments? Vague disregard for any or all words written and established in the mind of one who has no sanity?

Hope you guys liked this one! I should have the second chapter up pretty soon. It's almost done, promise! Just a few details to fill in. Later, Gators! Catch you on the flip side. :)