Answer: The plot of each one is the same for Ash to beat the Pokemon League and become the Pokemon Champion, thus becoming a Pokemon Master. This video gives a little about that: Anime 101: Pokemon - The Anime .

But if your speaking of the different VILLAINS, here you go:

Indigo League, ADVENTURES in ORANGE Islands, Battle Frontier, The Johto Journeys, Johto League Champions, and Master Quest: The first three take place in the Kanto region and the last three take place in the Johto region. In all of these you have Team Rocket led by Giovanni. Their main mission was to obtain powerful and rare Pokemon to take over the world.

Advanced, Advanced Challenge, and Advanced Battle: These take place in the Hoenn region where you have Team Aqua and Team Magma led by Archie and Maxie respectively. Team Aqua’s mission was to expand the seas by using Kyogre and flooding the land. Team Magma’s mission was to expand the land using Groudon.

Diamond and Pearl, Diamond and Pearl Battle Dimensions, Diamond and Pearl Galactic Battles, and Diamond and Pearl Sinnoh League Victors: These all take place in the Sinnoh region where you have Team Galactic led by Cyrus. Their main mission, depending on whom you ask, is to rebuild the universe in Cyrus’ image.

Black and White, Black and White Rival Destinies, Black and White Adventures in Unova, and Black and White Adventures in Unova and Beyond: These all take place in the Unova Region where you have Team Plasma led by Ghetsis. This team’s main objective is to liberate all Pokemon from their trainers.

XY, XY Kalos Quest, and XYZ: These take place in the Kalos Region where you have Team Flare led by Lysandre. Their main ideal is to make the world BEAUTIFUL by eliminating all life.

Sun and Moon: This one TAKES place in the new Alola region where you have Team Skull led by Guzma. From what I found Team Skull does not have a true objective other than to cause mischief

Explanation: pokemon story