Pokémon Adventures, Vol. 24 by Hidenori Kusaka

Red is downhearted after being defeated by the Mythical Pokémon Deoxys and fears that Professor Oak has given up on him. With the support of Blue and Green and an unexpected powerful Pokémon ally, he continues on his journey. But then he must face a formidable human opponent—Giovanni! Meanwhile, what clues to his past will Silver find in Viridian City...?