The Start of a Journey
The first arc of the Pokémon Special manga tells the story of a young trainer named Red as he goes out on a journey to collect all 151 Pokémon, fill his Pokédex, beat all 8 of the gym leaders, and become the Pokémon League Champion. Along the way, Red meets two other trainers Blue and Green and they become rivals and friends as they fight to make their dreams come true.
The story begins when Red, a rookie trainer meets Blue while trying to catch a Mew in Viridian Forest. They meet again when Professor Oak, Blue's grandfather, gives them each a Pokédex and sends them on a journey to learn about Pokémon from across the continent. Red quickly learns that he's a rookie compared to Blue. Blue is able to start out with an early lead and even releases Pokémon that Red hadn't even seen yet because he "already caught them" (Ch. 03). He even manages to beat the first Gym Leader, Brock before Red has even had a chance to get into Pewter City.
As they continue their journey, Red and Blue soon encounter Team Rocket, an evil organization with plans to capture powerful Pokémon for the goal of taking over the world. Team Rocket has questionable morals and does things including (but not limited to): giving a Rhydon steroids, shooting electrodes out of guns, creating Pokémon, kidnapping, bribery, trying to kill children, combining Pokémon into chimeras, and otherwise being evil. Through several intense battles Red and Blue (with some help from Green) are able to take Team Rocket down and return balance to the world.
The Red/Blue/Green Arc ends with Red and Blue fighting it out to see which of them will be named the Pokémon League Champion. During the battle, Oak reflects on how each of the boys acted when they began their journey and how both Blue and Red have learned and grown from their friendship and rivalry with each other. Ultimately, Blue loses and Red becomes the champion. Then the trainers go their separate ways with the goal of improving and training themselves further.
The second arc of the Pokémon Special manga tells the story of Yellow, a girl who Red met in the Viridian forest once. She became a trainer after Red gave her a Rattata. Yellow begins her journey by trying to find Red after his Pikachu turns up injured in front of Professor Oak's Laboratory.
After the Pokémon League Championships, Red, Blue, and Green split up in order to continue their training further. Blue heads up to the mountains to train in solitude. He manages to keep up to date with his friends by sending messages back and forth to his grandfather using his Pidgeot. Blue is the only member of the group who has previously fought the Elite Four, who Yellow suspects is behind Red's disappearance. Yellow asks Blue to train her so she will be able to help Red.
Blue trains her to become stronger and they split up in order to try and find Red. Blue teams up with Blaine and together they find that Lt. Surge, Sabrina, and Koga are still alive. Blue once again finds himself facing Agatha with only Koga (who tried to kill him as a member of Team Rocket) to help him. Together they are able to defeat the lower members of the Elite Four and find Red. When everyone meets back up they go off to defeat Lance, the leader of the Elite Four.