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I know, I know. It's long and sort of goes against exactly what you just said, but before it all becomes irrelevant, I'm just going to throw my concept out here in full. The episodic nature of Kamen Rider would likely result in most of this information being divulged slowly, but here goes.

THE ORIGIN OF THE VILLAINS:

Humans were not the first super intelligent race on earth. In prehistoric times lived the (for lack of a better name) Dinosaur Lords: Kaijin-like humanoid dinosaur creatures who possessed immense power, ruled the prehistoric beasts, and lived an extremely long lifespan. Toward the end of the Cretaceous period, the most powerful shaman of the race looked to the stars and predicted the doom of their world. Without telling the others of his findings, he tricked them into traveling far below the earth. Once to safety, he sealed the rest of his kind away in a binding stasis until the world was livable and ready for their return. Curious as to where their leaders had gone, many dinosaurs roamed right above ground and waited for them to return to the surface. As predicted, an asteroid fell from the sky and eradicated them all. The last of his people still conscious, the powerful shaman fell into a slumber guarding the gate of their underground "tomb" for millions of years, unaware that new life began to develop on the surface.

Finally, the shaman awoke much later than planned and traveled up to the ground above to scout out the world that awaited his people. The races and civilizations that had emerged during his hibernation surprised and fascinated him, but he knew his brothers and sisters all too well. Unlike him, they would not take kindly to these "invaders" of their world. They would accuse him for treason before eradicating all unidentifiable life on the planet and humanity would not be ready to fight back. He believed his people had already had their chance and were meant to have gone extinct millions of years ago; he felt it would be selfish to take this world away from those who had inherited it. He had also come to the realization that because he had not been in stasis himself for these long years, his body was beginning to give out. His lifespan had finally come to it's fateful end and his death would vanquish the seal that had kept the Dinosaur Lords at bay. He was the only thing between humanity and their extinction. There was nothing he could do to stop this from happening, but in the meantime he would find a way to help the humans help themselves. He disguised himself and studied this new world in secrecy for as long as he had left.

RAY, PALEONTOLOGY, AND A DRIVER:

Both Ray Kaseki's mother and father were Paleontologists who traveled the world. In his young life, they took their son along with them on expeditions allowing him to become enthralled with Dinosaurs himself (so much so that his American mother nicknamed him "her little Rex.") Ray aspired to become a great Paleontologist himself one day, and he tried to learn as much as he could from his parents when he accompanied them to dig sites. Then everything changed.

Ray's Father (I'll call HIM Junoichi for the time being) had hit the jackpot. He had made the discovery of his life: a dense mass of diverse dinosaur fossils piled up in a single area below the earth somewhere in Japan (these fossils of course belonging to the Dinosaurs who waited for their leaders.) Junoichi and his wife conducted a large scale dig which would surely define their careers. Well in to the excavation, the bottom of the site began to shift. Many of the workers chose to evacuate, and though ill advised, Ray's parents were determined to discover the source of the disruption. Soon the ground beneath them gave way and they fell deep in to a stretch of winding tunnels that traveled down further still. Ray's mother insisted they wait for help, but there was no stopping Junoichi from exploring as far as he could go, so she had no choice but to follow. Far below, they finally approached the gateway the Lords had been sealed behind. While excited by the mystery of this find, the two agreed that this dead end was a sign they should turn back. Just as they began to retrace their steps, the powerful old shaman revealed himself to them.

He knew the curiosity of man would unveil his secrets in due time and that curiosity was precisely what he had been searching for. After observing human kind for a long while, he began to develop a system that would allow a representative of their race to become more powerful than the rest. This chosen warrior would be able to defend all life on earth from extinction. He had created a belt that would allow this transformation, and while the basis of his design was mostly there and it had been imbued with his knowledge and power, with tired breath, heavy hands and death awaiting him, the shaman was unable to complete it. He spoke of everything he knew, warned them of catastrophy, and passed along his project to the couple with a heavy heart and bated breath. He assured them he would devote the rest of his willpower to staying alive for as long as he possibly could, provided they were able to complete what he could not before doomsday arrived. The shaman guided them out of the cavern and whisked them away to safety before the tunnels began to crumble and collapse.

REX KASEKI AND THE RETURN OF "THE EXTINCT":

Ray's parents never told him about this incident, believing that keeping him as far away from their new life consuming project would protect him. They didn't want the burden they had been left with to weigh down their son's goals in life, so they sent him away to live with his grandfather in America, allowing him room to pursue his own dreams. The two of them went off the radar completely and disappeared from the world. While it was not their intention, Ray began to resent his parents and believed they abandoned him because he was getting in the way of their work. He tossed out his dream of becoming a great paleontologist to spite them and grew up a bad egg in his neighborhood, despite being extremely intelligent, strong and kind at heart. The "Motorcycle Riding American Bad-Boy Rex Kaseki" lifestyle he'd adopted never worked out for him professionally, as he could never seem to find work beyond "low paying store clerk" or "delivery boy" anywhere he went. His grandfather suggested this was the universe telling him he should move back to Japan because that's where he'll be needed. Rex was reluctant at first, but soon became motivated by the idea that he could also look for his parents there, as well. Once he had found them, he'd give those two a piece of his mind.

Back in Japan, Rex fell victim to cruel irony and he was only able to secure a job as a delivery boy here, too. That didn't matter to him now, though. He had a mission to find his parents, although something else found him first. Not long after he'd moved into his apartment, he received a mysterious package from an all too familiar name, "Junoichi Kaseki." He tore open the box and was surprised to discover a strange looking belt inside along with a set of instructions. Rex's parents had not been fast enough in their development of the Paleo Driver, and while Junoichi had planned to don the belt himself, he was now lacking the youthful strength he once had. Regretfully, he had no choice but to contact his father-in-law and finally involve Rex in this mess. Their son was the only one they knew they could trust anymore. Rex however was shocked, confused, and furious.

Deep in the caverns below, the old shaman gives his final breath and the seal is broken. As expected, the Lords felt betrayed and confused. Their prolonged stasis had transformed them in to skeletal creatures and they soon found their world had been taken from them. After discovering the corpse of the shaman who doomed them, they wanted someone to pay for his crimes. Considering themselves walking dead, the self proclaimed leader of the group christened them "The Extinct" and began plotting a violent revenge.