Dark times have fallen on Kanto. It started five years after Ash started his pokemon Journey well technically it started long before he was born but it only came to light shortly after his fifteenth birth day. Vermillion city was attacked by a then unknown army genetically engineered pokemon. Lt. Surge the city's gym leader led a successful defense and saved the city. However, it cost him his life. Lance leader of the elite four started an investigation. A mysterious man who claimed he knew not only who was responsible but also, where the guilty party could be found soon approached him and the rest of the elite four.
Three days later the bodies of Lance, Agatha, Bruno and Lorelei we're all found on route 2 south of Viridian City. Team Rocket claimed responsibility for the murder. Giovanni declared himself ruler of Kanto he unleashed him army of genetically altered pokemon and rocket agents upon the peoples of Kanto. Koga gym leader of Fuchia city tried to infiltrate Team Rocket head quarters and assassinate the self appointed Emperor of Kanto. He was never seen again.
When Team Rocket attacked Celadon city Erica managed to lead many of her students to safety. However, she was captured and Giovanni hand her publicly executed in an attempt to frighten the populace into submission. Misty and her sisters were separated when team rocket set fire to the Cerulean gym. Misty and her Sister Lilly survived. I do not know about the other two. Sabrina with her immense psionic powers easily escaped captures and went underground and started one of the major resistant moments called "The High Guard"
Brock was very fortunate in that he got his entire family to safety before Team Rocket attacked Pewter. He join up with Ash and Gary who had started another major resistance group called "The Son's Of Pallet Town"
I suppose you would like to know what became of the fire gym leader Blaine. Well he did not live to see the dark times. He died laughing. Seriously he chocked to death on his chicken dinner its not funny. I'm sure Blaine would have found it historical.
It took Giovanni little more then a year to conquer Indigo. It took him almost four more years to conquer Johto. Mainly due to the fact, Johto had time to prepare. The eight gym leaders raised an army in defense of Johto planning to finish Giovanni off. It was then Giovanni unleash a new kind of pokemon. It called a "Menace", a genetically engineered pokemon. It was of both psychic and fighting type. On it has large syther like blades on each arm.
Despite there efforts one by one the gym leaders of Johto fell. Only Clair escaped no one knows where.
In just five years from Lance's death Giovanni had become the ruler of Kanto. His army gathered in ships and set sail for the Hoen Region. However, his navy was defeat by a single pokemon. Mewtwo using his powers he created a massive storm and annihilated Giovanni fleet. The storm remained, blocking Giovanni's army from spreading. Mewtwo did not have the power to stop Giovanni with out killing tens of thousands of innocent people but he could stop him from spreading his empire any further.
Five years have past sense Giovanni conquered Kanto. Alternatively, 15 years sense Ash started his journey if you haven't been keeping track. The rebellion has fault a war of harassment over the years, slowly undermining Giovanni's rule. Giovanni believes he will eventually crush the High Guard and the Son's of Pallet Town. He maybe right however he should beware.
A new power has been growing in the darkness of Kanto. "The Black Sword" is its name, years ago when Giovanni's mother Madam Boss was the leader of Team Rocket. The Black Sword led by Drake one of the most sinister men ever to live tried to destroy team rocket. He was defeated and his organization destroyed. However, I have resurrected the order of the Black Sword. My name is Kain, I am the Lord of Darkness, and I have vowed to wipe Team Rocket from the face of the earth. Let the rest of the world burn all I want is my revenge and nothing will stop me from attaining it. Giovanni had best prepare for the Tides of Darkness.