>>24939492Season 3 and 4: Johto or Sinnoh. Doesn't matter which is first. The events transpire around the same time.
Johto season: Ethan and Silver's rivalry plotline is Ethan hunting down Silver after he stole a starter pokemon (this should be kind of impossible, Silver is some sort of master criminal in the making or some shit). Ethan starts out with no clear goal in mind, other than helping Professor Elm's pokemon evolution research. But he soon develops into a very powerful trainer and dreams of collecting all 16 badges of Johto and Kanto.
After Giovanni left, some upper level Rocket executives took Rocket Corp's security branch and degenerated it into a ruthless organization. Behind the scenes, a masked man aspires to discover one of Johto's ancient legends and using it for his own gain. The masked man is a more savage and ruthless version of Giovanni.
Silver and Ethan both tries to take on this organization, but for different reasons.
Sinnoh: Rival trio of trainers all wanting to become champion. Cyrus wanting to destroy the world in order to create "perfection" in his own image.
Season 5: pick up the pieces from other seasons. Some characters go to other regions, meet up, battle it out and shit. Climax: Ethan vs Red, Blue and Silver join forces to help the professors (after a Silver redemption arc) discover a pokemon evolution mystery in Sinnoh.
Then we're moving on to BW.