This may be a one shot, not clue, depending on how it turns out. First attempt ever.
PROLOGUE:
Johto was the last mainland which stood strong. Years ago, a war began. All because of the fact the restless Pokémon grew tired of their Pokéballs. The Pokémon had a swift, destructive plan. During the cold, frosty nights, the Pokémon began the plan. They caressed out of the chambers, or “Pokéballs”, and snuck out. Their destination, Mount Silver. From there, the Pokémon with the ability to fly would start the long, treacherous journey to Sinnoh, Kanto, and Hoenn. This plan was to awake the legendary Pokémon, and set terror to their ex-slave masters. Then, the slaughter began. The Legendary Pokémon had woken. They started the plan: Massacre the humans, and send the remaining ones to islands. After years of combat, the Pokémon finally won. Any humans who had not been torn limb-by-limb had been drove to the Sevii Islands, or islands in mid-ocean. Most people fleeted to the mid-ocean islands had drowned due to high tide. Only people at the Sevii Islands survived the brutal war.
Through the rough, long, past years, the people on the Sevii Islands attempted to rebuild the damaged islands. Some tried to flee to the other main lands, which had been demolished by the native legendary Pokémon of the main lands. Some of the stranded tried to get to the mainland of Johto. It was turned out to be the last living mainland, with cool, frosty winds, and flushed green lands. The Pokémon reigned here, and any human who visited Johto was to be tortured until death. Now, what was not expected was the fact that some distressed Pokémon were hiding underground. Now, these Pokémon did not mind the capturing of the Pokéballs. In fact, they often wandered into human territories to be caught. The secret of these Pokémon were attempted to be hidden, and those who found out were hunted and killed, or made to join the C.O.T, or “The Council of Trainers”. Some people who had found out rebelled, and went underground to the Pokémon’s lairs. The rebels later found out a secret: There were four legendaries who had refused to fight. The Regis. The Regis insisted to help the human side, because of all the troubles Pokémon had caused in Medieval times to humans. Now, harnessing the powers of the Regi trio, they attempted to rebel against the Pokémon and re-attain the mainland of Johto. They worshipped Regigigas, and partnered with the remaining Pokémon on the island. Here, two boys start their own journey to Johto, unaware of what lies ahead.
Depending on how this goes, I might continue. I'm also aware of alot of mistakes, so please help me get better.