There is a very simple explanation for this, and it's very close to the explanation for Mark of the Master - After winding up RP'ing Featherboy for a short period, he decided to move into my skull and settle, redecorate a little, and generally park. Now, having a long history of various D&D characters and such doing this to me, this did not bother me so much. Hell, it wasn't even that much of a surprise when Featherboy decided to rattle off his life story. It was when he insisted on having it written down that I realized things had gotten a little out of hand, and in his usual "reach exceeding grasp by 2.5 meters" way, had pushed me over a barrel. It was also, of a sort, a way of poking through exactly what was going on in his feathery little skull, and how he got to where he was during the game.
Ergo, this fic.

(If you read this before I reposted it – there's not really much change in the first chapter besides grammar edits.  I largely did the repost game because I got frustrated with ff.net not *updating* pages when I tried to update them; it'd still show the old page no matter how much time I gave it to register or how many times I tried to update it.  I don't know if that's fixed now or not, but I'm in the middle of this anyway, so *shrug*.)
*****
A creature's reach should exceed its grasp
What else is Heaven...or Hell? - Lucifer, Leslie Fish
*****

            Garland shifted the mechanisms; the tube slid down, cables snaking into the walls, leaving a small, six-year-old equivalent form curled on the pad, as the Genomes went about the business of running the lab, paying no mind to the child; it was not part of their programmed task.

            The genomes had originally been meant to have been created and left in stasis, empty vessels for the stored souls of Terra when the world was stable enough to be inhabitable.  However, a lack of resources on the restoration project had made it necessary to activate them as little more than biological automatons; this also gave Garland chances to test the design that was the continuing project of centuries. 

            This new one looked different from the others; the tail - a genetic side effect of the hybridization that had been necessary to make them capable of surviving on Terra as it was now - was covered in soft opal-silver fuzz instead of the golden tan of the others; instead of blonde hair, this one had a similar opal-silver shade of fine, soft, slender feathers.  Bone structure was lighter, almost fragile looking even at this young age.  It seemed the addition of draconic DNA and energy structures to the mix had affected things more than he'd expected. 

            He turned off the "sleep" switch, then waited for the new Genome to stir. 

            The small creature pulled up into a sitting ball, looking up at Garland wide-eyed; there was something off about this one compared to the others, something he couldn't put his finger on. 

            "I don't like it here."

            This was odd - the genomes did not speak until spoken to, unless it came up as part of their program to do so, and certainly were not sentient enough to have opinions.  "What was that?" 

            "I don't like it here.  It's creepy."  The child cocked his head, looking at Garland.  "You're creepy."

            "I am Garland - your creator."  Most irregular indeed, this one.

           "You're still creepy."  A pause as his attention wandered off Garland.  "Who am I?"  He looked back up, expectantly.

            Was this creature asking for a name?  The genomes didn't have, or need, names.  They were automatons.  This one was supposed to be, as well. 

            "Well?  Who am I?"  The child was getting impatient.  There was a spark in this one, a spark that had never been allowed into the genomes, that wasn't supposed to be in this new design either; this one had a soul, right down to variations in his energy pattern telegraphing emotions.  The creature wasn't supposed to have a name, or a soul, or a mind of its own, but it quite clearly did.  "You...are the prototype of the Kuja template Genome, and you - are a glitch."

            The child squinted up at him, a mix of confusion and wounded pride.  "Kuja?"  

            What was he supposed to do?  The creature insisted on having a name, and until Garland figured out what went wrong, he wasn't using that template, so in the meantime he decided to leave it be.  "Yes.  Kuja."  Old Terran for 'archangel'.

            "What's a glitch?" 

            "A mistake.  Something that was not supposed to happen, that crept into the sytem in spite of tests and plans."  His tone was calm, level, graven, almost mechanical; no malice, although there was a hint of irritated bewilderment.

            Kuja edged further back, towards the wall.  "I'm a mistake?"

            "You are a machine, meant to work on programming; a vessel for another soul.  You are not supposed to have opinions or emotions, yet you have demonstrated that you do; therefore, yes, you are a mistake."

            The child followed Garland around; he wasn't willing to assign a task to the creature yet, so he simply ignored the boy.  Kuja was quiet and curious, watching everything he did with occasional questions about the things that were not included in his programming; odd, that he could ignore all the behavioral programming yet maintain the information stores.  Garland answered the questions offhand, with the same semi-mechanical tone, barely even noticing the child.  Toward the end of the day, the boy started trailing off, then finally asked where he was going to sleep. 

            "What?"  Garland stopped, looking back over his shoulder.

            "I know the genome barracks is thatway, but I'm not like them."

            Garland stared down at the child; it probably would be better to isolate the glitch so he didn't disrupt the others.  He swiftly ran over the maps of Pandemonium kept on file.  "This way." 

            He led the child to a mostly unused storage room, empty except for a pile of blankets and pillows in the corner.  The boy peeked around metal ankles, then scrabbled in, climbing right into the pile of bedding. 

            "I'll bring a cot in."

            "No."

            "What?"  Highly irregular.

            "I like this; it's a nest, and it's softer than the cots."  A feathered head popped up just far enough to peer over the edge at him. 

            This was strange, but it saved Garland the trouble of rearranging the room, and the pile was all unused stuff anyway.  He turned, the biomechanical door mechanisms moving shut behind him.

            He stuck close to Garland, never really keeping the old man's attention beyond quizzical, ruffled looks whenever he did something particularly odd.  For all that he had more information to work with than any normal creature his biological age, he was an awkward mix; a computer's intellect in a six-year-old body with no actual personal experience.  He went through things learning the difference between data and knowledge - between Odonata, four winged nonvenomous predatory insect, and the bright green dragonfly that had somehow survived and gotten into Pandemonium, which he first saw as a bright, swift flash and a whir low over his head.  He had access to an entire database on it, but that didn't stop him from reacting like any small child that had never seen a dragonfly before.  He watched it hover, then fell over tracking it as it zipped back over his head; it stopped again, as if waiting for him to stand back up.  As soon as he had his feet again, it zipped off, and he chased it, urge to try and catch it bolstered by the instincts of a small predator with canine, feline, and draconian in him - it was pretty and it moved just out of reach, so he tried to catch it. 

            It passed through one of the archways to the catwalks over Pandemonium, out into the area surrounding the Bran Bal complex, Kuja chasing it with all the grace, dignity, and coordination of a still-bony kitten.  It skirted Bran Bal village itself, bound out into the buffer areas between it and the poisoned rest of the world; a fragment of his mind knew where the boundaries were and how far he could go before he left inhabitable territory, although he wasn't really listening to it.  He proved he was ignoring it when he charged after the dragonfly - right off a ledge. 

            There was a brief second as the computer and six-year-old snapped into sync, the computer just finishing confirming that he'd run straight into one of the blue patches on the map while the six-year-old felt the sickening lurch of gravity kicking in now that his feet weren't touching ground.  The computer calculated a nine-point-four-six meter drop between the ledge and the water below while the child yelped and clawed wildly to try and catch the wall that was approximately fifty centimeters out of reach by the computer's reckoning. 

            He hit the water with a thick 'bloosh', the waves on the surface of the ten meter deep pool slurping thickly back into place slower than water was supposed to move, due to the odd static energy fields used to keep the buffer area from deteriorating as he sank slower than a rock, to be sure, but faster than the boy wanted to go under.  His reflexes lagged behind his mind as he tried to gasp in a breath before remembering that his lungs, while tweaked to handle poisonous atmospheres, could not process water.  It was thicker than air, seemed thicker than water should be, and the choking reflex that kicked in made it impossible to hold his breath.  He knew in the back of his mind that slashing at the water and struggling wouldn't do much, the same way he'd known that the path ended when he'd run off the cliff; the more he continued sinking, the more he panicked. 

            As his lungs struggled to process the water, his nervous system set off alarms that were picked up by the Pandemonium tracking computers, alerting Garland that not only had the Kuja template prototype moved outside of where he was supposed to be, but that he was three meters underwater off a short cliff and that his respiratory system was flooded and unable to function properly. 

            Garland sighed, setting the system he'd been repairing to pause function, and sent a signal to the computer to have two genomes meet him at the gates with ropes, poles, and a net; there was no real rescue gear, it hadn't been needed in centuries, and Garland's mechanical logic was running in exasperated circles trying to figure out what the Hell had possessed the boy to run off a cliff, as the tracking system had reported; it didn't make any sense.

            Kuja was still slowly sinking, madly trying to flail back to the surface, choking with no air to take in, only more water to replace the water his system was trying to purge.  His vision was blurring around the edges even more than was explained by the water, dark bits creeping in as he was losing what little coordination he had. 

            Something caught the back of his collar, and he felt a sharp prick on the back of his neck, causing him to panic more.  Another something caught his wrist, and he realized how much he'd weakened as he couldn't move his wrist out of the hook.  He then found himself hoisted out of the water, held above it in the loose grip of two hooked poles.  Once he was out of the pool, he quit struggling, too tired to do more than cough up water until he was afraid he'd cough up a lung with it.  He was brought back to the ledge and dropped; somewhere in his spasms of choking it registered that he was in front of a black, bootlike mechanical foot. 

            Garland dismissed the two genomes back to their work.  The child was too busy emptying his lungs to move; much longer and he wouldn't have survived.  When he could breath again, he stayed sprawled, panting, too weak to move.  Garland gave the boy enough time to recover breathing fairly normally, then picked him up by the back of his collar.

            "How did you get here?"

            The boy feebly waved off over the water.  "D...drag....dragonfly..."

            "How did a dragonfly cause you to almost drown?"  Mechanical thinking still wasn't finding the logic behind what happened.

            "Was...was trying...catchit..."  Purple eyes blinked innocently; he was regaining his energy, but was still not feeling up to more than dangling from Garland's clawed hand. 

            "Why?"  The odd exasperated glimmer was showing in force.

            The wind whistling through the child's skull as he tried to find the answer himself was almost audible.  A few more broad, blank blinks passed before he found a semblance of an answer.  "It was pretty, and shiny."

            The exasperation settled out of confusion, into the dry realization that efficiency, logic, and necessity had yet to penetrate the child's feathered skull, and a good explanation was too much to ask.  His claw snapped open, dropping the boy with a brief squall.  As Garland turned to walk away, Kuja paused in a moment of bruised feline dignity, then tried to shake off the water on an odd animalistic flash of instinct; he was on his feet scampering after the edge of Garland's cloak, as if nothing had happened.

            He got into real trouble for the first time another month after that.  Garland left him alone in Pandemonium, traveling to Gaea to check on the Iifa system.  It didn't even occur to him to spare a thought that the boy might get into trouble if left by himself. 

            The first thing to catch his attention was one of the systems running the pathways, platforms, doors and bridges over western Pandemonium.  That the computer in him understood how the system worked only increased the chaos he was capable of.  He set to rewiring it, changing all the passwords, the patterns of the platforms, the activation for the bridges, the on-off times for the barrier shields, and the locks on the doors. 

            Then he got bored with the computer and wandered off, looking for something else to do.  He found one of the genomes repairing an outer wall with a sort of dark blue enamel; the stuff was painted over the biomechanical walls to protect them while they healed.  It also refracted any light that hit it, shimmering like an oil slick on a bright day.  He wandered over, standing under the sweep of the older genome's brush, watching.

            Then he noticed a second brush in the enamel bucket.  He picked it up, watching it drip, then started painting the bottom of the wall haphazardly, leaving long streaks of color.

            "What are you doing?"  The genome had paused in its work to look down at the interference.

            "Helping.", he said simply, still painting the wall.

            "That area is not damaged."

            He paused, staring at the wall.  "It looks pretty now."

            The genome cocked his head, uncomprehending.  Kuja ran down the wall with the brush, then pointed at the shining line.  "See?  Pretty.  Pretty is good.  It's too dark around here."  The genome scanned it.  "Pretty is good?"  Kuja nodded.  The genome, with no further questions, started adding further sections of the wall to his work, the new descriptor somehow getting worked into his task programming. 

            Kuja ran off with the spare brush and the spare enamel bucket, setting to painting things on the walls all over Pandemonium, making haphazard designs and doodles in dripping enamel, writing scrambled bits of verse and graffiti everywhere. 

            He accidentally dumped the bucket off one of the catwalks, spattering enamel everywhere, dripping off walls and railings, spotting his own clothing, face, and feathers.  He could feel the weight on its plumage; it made him itch.  He scrabbled out of that area, looking for something else. 

            In the basement there was a locked door; he'd never paid attention to it before, but now he was bored.  He knew the password after his earlier hacking, so he creaked it open easily, heading into the dark complex.  He wandered in the dank silence for a long time, before he ran into something - a big greenish something that didn't seem to be a part of the wall.  He craned up, finding a huge thing with filmy wings and huge pincers, a big insect.  The data library part of him quipped in that it was a monstrous thing called an Abadon, highly dangerous; it was looking down at him as if he would make a nice snack.  He turned and ran, shrieking, the Abadon chasing him the whole way, tearing through the door into the rest of Pandemonium; he didn't loose it until he slipped into a narrow duct to another part of the fortress.  He climbed from there to one of the upper spires, watching the Abadon take an erratic and frustrated course through the fortress.

            Garland heard the chaos with a sense of dread as he returned; all the computer found out of place was the loose Abadon and the broken door, which the security system was handling.  The genome he'd left fixing cracks in one wall was painting across the wall of the fortress in long stripes with the enamel, and there were huge swathes that were far too erratic to be the work of the genome.  "What are you doing?"

            The genome paused, logic only halfway making connections.  "Making the wall 'pretty'."  The tone suggested that he really didn't understand the word.

            "Why?"

            "Pretty is good."  Again with the vague, hazy sense and the lack of understanding.

            "Who gave you this instruction?"  He already knew.

            "...it was added to my task by Kuja."  Great; the genomes were affording the glitch the same accord they gave him. 

            "Kuja is not fit to give instructions."  Blank response; a mechanical blink.  "He is only a child."  Blink.  "He is reckless and ignores logic and efficiency."  Blink.  Still no understanding.  "He is a glitch in the system."  The genome nodded.  "Clean all of this off the wall except what was put there to repair damage."  The genome padded off to follow his new instructions.

            Then Garland reached the front door, and learned about the hacking and the true extent of the graffiti.

            Kuja had gotten distracted again by how much he could see from the spire, the distant mountains, the stretch of the pale sky, how small Bran Bal village looked.  He could see all the way outside the buffer area. 

            The main Pandemonium computer tugged on his mind, a summons to meet Garland at the door.  He realized how much chaos he'd caused, and when he didn't come to the summons, he heard clanking footsteps in the passage. 

            His main train of thought, as he dove back into the ductwork looking for a hiding place, was a repetition of "Garland's-Going-To-Kill-Me" over and over as he squirmed into a narrow duct in one of the walls.  The side of the wall opened, and a clawed hand caught the back of his shirt, dragging him out despite his best efforts to cling on with all four limbs and his tail.  He was squealing, with an occasional "Please-don't-kill-me" becoming intelligible in the stream.  Garland held him up to eye level in a cold, inorganic frustration, still struggling and squalling.  Then, he blacked out.

            He woke up in his nest of bedding, in his makeshift room, with Garland standing over him.  His back hurt and he had no clue why, and everything seemed disorienting. 

           "It..took...three days...to repair the damage you did.  Four of the genomes were injured by the Abadon you let loose; one almost died.  The computer began crashing due to the confusion you made in its programming, and it is still glitching occasionally.  The enamel requires a special solvent to remove when it's not placed over a damaged wall.  And it added to the annoyance that I had to chase you down.  Why did you do any of this?"

            The wind was whistling through his skull again.  "...I was bored." 

            Garland stared down.  Kuja stared up, as if that was all the explanation he needed.  "You were bored."  The child nodded.  "And that is your whole reason."  Another nod.  "You cannot make disruptions like this."

            "Why?"

            "It disrupts everything; Pandemonium is a delicately balanced system, and is the only reason this area is inhabitable."

            "Why?"

            "Because it runs the systems that control everything; disturbances could destroy everything we work for."

            "Why?"

            "Because all the main controls are centered here; it is because of these systems that this valley is the only inhabitable area on this planet."

            "Why?"

            "Because a disaster a long time ago destroyed the environment, making this planet a wasteland."

            "Why?"  A positively bouncy look was coming over the child.

            It slowly crept into his train of logic that he had just been put over a barrel with an absolute minimum of effort, and that the boy was asking purely to string him along.  He levelled a cold glare at Kuja, who winced with a yelp; there was an actual jab of pain.

            "Because no logic seems to work, I altered your implants; perhaps a deterrent will curb your behavior." 

            A small, puppyish growl started, his tail lashing. 

            "If you don't wish to deal with the pain, then do not cause trouble.", he stated matter-of-factly, almost smug. 

            He tried to act out a few more times; finding the enamel again and painting walls in little-used corridors, trying to confuse the genomes, taking apart things and leaving them - trying to make it look like it had been done by a rat.  Every time, the sharp pain kicked in, letting him know that Garland knew.  He finally trailed off, finding quiet ways to keep busy while casting glares Garland's direction.

*****
A few mutters from the author...
I'm not particularly siding either way at this point.  ^_^; Garland, in the game, never seemed as...malicious as he's often written; more apathetic, mechanical, not even recognizing emotions. That's bad enough in its own right. Chibi-Kuja, cute as the little fluffball can be, is a class-one-grade-A amoral *Demon Chibi*; I would not want him in my house. (I can say that I hadn't entirely anticipated how much FUZZ there was in his skull as a kid.)   
That having been said, Garland falling prey to the "Why?" game was just too damn amusing not to include.   The first chapter prob'ly coulda been lighter rated than the rest of the story, but this does get darker kinda fast.