Pokémon Adventures: Ruby & Sapphire

This chapter features the journeys of Gold through Johto trying to at first search for the ones who stole his backpack and uncovers that the ones who stole his backpack are planning something. Two other new Trainers come into the plot of the story, Silver, whose life is tied in with the villains of this series, and Crystal, an average Pokémon Trainer with a staggering talent in catching Pokémon who later helps Professor Oak catch all the Pokémon to complete his Pokédex. Along with these three, the original 3 Pokédex holders come back to help these three along with Yellow. With their aid, will Gold be able to stop the reformed Team Rocket and the Masked Man's nefarious schemes?

(Source: Bulbapedia)

This chapter returns to the characters of Red, Green, and Blue, protagonists of the original Red, Green & Blue chapter of Pokémon Adventures. Red and Blue are forced to explore the Sevii Islands to look for Professor Oak who was kidnapped by a Deoxys. Meanwhile, Green has finally located her parents; however, just as she is about to meet them, they are swallowed up by a mysterious black hole. Red, Green, and Blue must locate the missing relatives with the help of a former foe, Lorelei, and Mewtwo while defeating Team Rocket again at the same time. Back in Kanto, Silver is seeking his parents as well, with the help of Yellow.

(Source: Bulbapedia)

Red is just a normal kid living in the rural Pallet Town, when he decides to go out on his own adventure, along with his rival since childhood, Green. In this world of Pokemon, he makes many friends, humans and Pokemon alike. However, all is not well. Team Rocket is trying to capture Mew, a very rare Pokemon, and is performing experiments on other Pokemon, trying to increase their power. Red and his friends must battle against Team Rocket to stop their cruel experiments and unlock the secrets of Pokemon.