Thank you, GayRon, for giving me a push on this next chapter! –Sci-Fi Nerd

Chapter 1- Cortex

When Thass and Khette arrived at the Hall of Confluence on the equator of Yuuzhan'tar, they discovered that over twelve thousand other Yuuzhan Vong had already arrived to hear whatever Yuuzhan had to tell them of this threat to their peaceful civilization. The call had gone out for listeners yesterday, but Thass knew that many of his friends and their families had stayed behind for fear of the dark battlefleet in the heavens.
The Hall of Confluence was a massive building, a radiant combination of aesthetic and structured order. Huge bone pillars carved with beautiful designs and adorned with flowers spiraled up to a perfumed roof that rained occasional small birds of many colors. Soft fountains bubbled in far corners, and the music of the water echoed from the walls.
In the center of the hall stood a platform of carved bora wood, situated so that the hall's acoustics would enable a person speaking from the platform in a whisper to be heard by anyone in the chamber. At this moment on the tall platform, the gracious form of Yuuzhan stood in his glory, wearing a long loincloth of woven leaves, and a crown of blossoms.
When Thass, Khette, and the others who had arrived late had oozed into the packed chamber, the doors were swung closed, and Yuuzhan began to speak.
"Yuuzhan Vong!" he cried plaintively, clearly aggrieved. "I weep for what we are forced to do to protect our civilization! We have always loved life, and happiness, but now we must learn a new way, one of pain and sadness!"
The world consciousness paused to collect himself, and then raised his hands, and a dark mass shaped like a Yuuzhan Vong's brain free of any concealing material rose out of an opening in the floor. All the assembled Yuuzhan Vong shied back in fear of the strange object.
"Behold!" cried Yuuzhan. "The cortex of the Yuuzhan Vong!"
One brave man dared to step forward and question the world consciousness. "What is this thing for, Yuuzhan?" All twelve thousand others moaned in fear and agreement.
"This is how we will protect ourselves against the machine lords!" Yuuzhan said. "In this is contained the knowledge to grow weapons and ships so that we may fight our enemies; we must, however, be cautious! These are not to be used lightly."
"You intend us to fight?" someone else cried.
Yuuzhan hung his head. "We have no choice!" he declared, "Unless we choose to face extinction!"

Thass found himself assigned to the 'warrior caste'. There were three of these 'castes': warriors, shapers, and priests. The warriors would fight the enemy, while the priests kept the more common people calm through a religion that they could throw together around this 'cortex' that the Yuuzhan Vong had been given; the shapers would be the ones to grow and nurture the organisms that the Yuuzhan Vong would use.
It took four days, using the most dangerous of rapid-growth techniques also gifted to the shapers by Yuuzhan, to grow equipment for one half of the ten thousand warriors assigned at the time of the great conference. Thass then found himself confronting modified breeds of animals he had known, and tended, most of his life.
Vonduun crabs, genetically manipulated to conform to the body shape of its Yuuzhan Vong wearer, stared up at him with blank, armored eye sockets. Mid-stage amphistaff polyps, their energy glands enlarged and accelerated awaited only their owner's command to curl around the vonduun crab bracer. Mutated breeds of Thass' own beloved sparkbees slept in pulsating sacks, now named thud bugs for their armor and explosive reactions.
The first time Thass reached out for his vonduun armor, he twitched back in startlement as the beast latched onto his arm, and fell off as he drew back. He took several deep breaths, realizing that this was all a necessary discomfort, and reached out again.
The modified vonduun crab clamped down hard on Thass' arm, crawling its way up his muscles with astonishing speed. Swiftly, it separated its two massive segments and closed tightly over Thass' midsection, squeezing the breath from him until it fastened itself safely, and then it relaxed enough to allow him to breathe. Next came the bracers, leg plates, and groin panels, in a similar manner, though not as painful in their attachment; perhaps he'd just gotten used to it.
The amphistaff was easier: it simply slithered onto his bracer and coiled protectively on command, then lay quiescent with red eyes glaring up at him. Thass drew in a shuddering breath, then picked up the thud bug bandolier and slung it around his shoulder, and placed the final piece, a helmet, onto his head. The slit eyeholes allowed plenty of peripheral vision, but Thass was forced to fight a thrill of claustrophobia as it closed around him.
"Thass Domain Yenek?" came an imperious voice from behind him.
Before he knew it, perhaps pumped with adrenaline or high-strung from the prospect of impending fighting, Thass had whipped around, slinging his amphistaff into a two handed grip effortlessly and putting all his strength behind the blow.
And found it locked helplessly against another amphistaff, wielded by a shorter but heavyset Yuuzhan Vong who stared up at him with a cocky glint in his eyes.
"Ah, you too wish to test these new weapons?" the other asked knowingly. "I am Yarth Domain Shai. Come, spar with me; we shall see who the better of the two of us is."
Thass opened his mouth to politely refuse, but strangely, he felt a burning sensation arrive in his stomach, and he felt his body tense in anticipation of a fight. It was a... strangely pleasant feeling.
"Very well," he found himself saying, not without anticipation. "I accept."
There was a moment's pause while both of them nodded to each other, and then they sprang into combat.
Yarth led the attack, swinging high and double-handed with his amphistaff, putting as much power as possible behind the blow. Thass thought for a microsecond that neither of them knew anything about fighting, and then his body moved of its own accord to block the strike one- handed. Yarth's weapon crashed down on his with overwhelming power, and even as Thass' amphistaff began to fluctuate backwards, he found that his body was already moving to the right to avoid the downward-falling blade, and his right fist came up to catch the other Yuuzhan Vong in the jaw, making him reel backwards in pain.
As the two stumbled apart, Thass realized with a shock that you didn't have to know how to fight. It was just like wielding an axe or a carpet beater; you only had to calculate force, speed, and distance.
Yarth gave him a challenging nod, and Thass saw the comprehension in his eyes as well. Then, both of them leapt back into the fight with a vengeance.
Thass blocked three successive blows at his midsection with a whirling amphistaff, and then suffered a punishing blow to the shoulder with the flat of the other's blade. He ducked the next strike, lashing out with the amphistaff like a whip, its now flexible form curling around Yarth's shins. A quick yank sent the other Yuuzhan Vong to the floor, and Thass whipped an over-handed blow at the prone warrior with a cry of victory.
Yarth let the amphistaff come down past his guard, twisting away at the last second and hooking his foot around one of Thass' ankles, attempting to pull him down as Thass had done to Yarth.
Thass managed to avoid falling though he stumbled back awkwardly, allowing Yarth to close quickly with him and flail away rapidly with his stiff blade.
This was when Thass caught his ankle on the edge of one of the equipment storage tank's organic legs, sending him to the floor and driving the wind out of him.
Yarth's amphistaff stopped at his neck.
"A good fight," said Yarth after a moment when both of them had gasped for breath; they weren't in the best physical condition they could be, and neither of them, as Thass knew, really knew how to fight.
Then, they realized that all sixty Yuuzhan Vong who were also in the chamber at this time were watching them with open mouths. A gap appeared in their ranks as the two weary Yuuzhan Vong rose to their feet, and Yuuzhan stepped through, still wearing his flower crown, though it had wilted slightly.
"A truly remarkable beginning," he said sorrowfully, as if he truly did not desire any of his children to fight against even a world- threatening force from the skies. "If all the others take to their weapons as easily as you, we will have nothing to fear.
"Come. It is time for you to meet your spacecraft."

The field was speckled with huge gray and blue formations of coralskippers, triangular ships composed of yorik coral and augmented by creatures called dovin basals, which apparently manipulated gravity and propelled the craft.
Thass was led to one of the coralskippers, a very slim type that boasted four small plasma launchers in its nose as well as a belly-mounted dovin basal and a bubble cockpit shield of iron-hard mica. The uneven surface of the living spaceship seemed to radiate peculiar warmth, as if blood flowed beneath the rock of its skin. Thass stroked the side of the vessel almost unconsciously as he walked in a slow circle around it.
"Well?" came the soft voice of Yuuzhan from behind him; Thass turned sharply and looked at the weary, glowing face of the planetary mind. "What do you think?"
"It's... beautiful," Thass said.
"Why don't you get in?" Yuuzhan prompted softly, a flash of sorrow crossing into his eyes as Thass obeyed eagerly.
He found, however, that once he was ensconced in the cockpit, nothing was familiar to him. Strange pulsating organs and devices decorated the instrument panels, and a strangely shaped hood lay on top of it all.
"How do I pilot?" Thass asked, bewildered.
Yuuzhan chuckled, a warm, rich sound that flowed like liquid honey. "Put on the cognition hood, and the ship will instruct you."
"It's... conscious?" Thass asked.
"Of course," said Yuuzhan. "Put on the hood."
Thass reached out for the fleshy device, prodding it fearfully before sweeping it up in one grand motion and slapping it to his face. The warm skin started to slip for a second, and then it contracted, fastening itself to his skin. The sensation of being blind caused a thrill of fear to rise in his breast before an alien mind reached out to his, forming words.
Thass Domain Yenek, it said. Instruct this ship as you wish.
Thass was lost for words.

At the end of the first week of the transformation of the Yuuzhan Vong, Yuuzhan stood on his high balcony above the Hall of Confluence, staring down upon the training warriors with great sadness encompassing him like an aura. Tears slid slowly down his face, and his hands were forced to bear all of his weight as they rested on a railing, his knees giving way beneath him.
In less than a week, the Yuuzhan Vong had adapted from a tranquil, frightened species into a race of warriors taking speedily to the new religion. Skills were honed brutally and fast, and already, talk of glory and death was beginning in the camps.
"We are changed," he whispered softly.