MewTwo's War, Part One:

Rise of Giovanni.

Prolog

The land had once been green, abundant with lush grass, fragrant trees, and aromatic flowers. The sky had once been as clear as the sea, allowing the beauty of the sun to reach down and touch the earth. The water had once been cool, and refreshing. Now the mountain road, known as Route 26, was a dead, burning place.

It had taken nearly a year, but Route 26 was now, once again, firmly under the control of the Kanto region. They first captured Victory Road, the mountain pass that protected the Indigo Plateau. Then the Kantonian Army drove the Elite Four form the Indigo Plateau, before finally starting their siege on Route 26.

The war had cost the Johto region more than they could afford. Nearly half of the Johto Infantry had been lost, trying to stop the Kanto advance. Thousands of Pokémon had been sacrificed to try and keep Route 26 in Johto's possession. Worst of all, as Giovanni pushed his forces closer to New Bark Town, the government of Johto began to lose the faith of its people; the Johto Republic collapsed, and the Elite Four had no choice but to seize control.

The northeastern and eastern parts of Johto were protected by Mt. Silver, a vast hollowed mountain. It was nearly impassable in the best of conditions, and the few pathways were blocked by what remained of the Johto Infantry. What ships belonged to Johto were deployed to protect New Bark Town and the Gulf of Cherrygrove. Volunteers, lead by the Gym Leader Falkner, patrolled the skies over Mt. Silver, and the Charizard Valley was prepared to help intercept any air invasion made by Kanto.

Johto was safe so long as Giovanni, the "President" of the Kanto region, didn't launch a joint assault by land, air, and sea. For his part, Giovanni wasn't willing to risk devoting all of his forces to an attack on Johto, for the Sinnoh and Hoenn regions, islands that resided close to one another, had entered into a military alliance; Giovanni couldn't take the gamble that as he invaded Johto, Kanto wouldn't be attacked by the joint force of Sinnoh and Hoenn.

So it was that, tentatively, the Johto region was able to keep its sovereignty. Yet the fighting continued. The Kantonian Army sustained its assault on the passes through Mt. Silver, and it was only a matter of time before the Johto Infantry would run out of men. As more and more men, and women, enlisted to protect Johto, there were fewer and fewer people left to produce food, and military equipment, thus depriving soldiers of vitally needed supplies. Johto had, at best, another fifteen months.

Lance, Champion of the Elite Four, was growing desperate. His own legion was slowly being eroded, and not even his great dragons could keep the generals of Kanto at bay. So, in a despite attempt to save his new nation, Lance, Champion of the Elite Four, sent out for help.

To Sinnoh he sent an envoy asking for any Onix trainers that could be spared, to help prevent new tunnels from being formed through Mount Silver. To Hoenn he sent an ambassador begging for naval support. To Dared Isle, where all Ghost Pokémon had fled, he sent Morty, to try and reason with the dead. And to the Island of the Psychics he sent his colleague, Will, to seek aid.

And throughout the Johto region, Lance, Champion of the Elite Four, send out messengers to every city under his protection; he wanted the best trainers, with the strongest Pokémon, to enlist, with the intent of using them to launch a desperate attack on Kanto.

And so, as Lance, Champion of the Elite Four, failed again and again and again to attain his needed help, our story begins.