Special Saga Chapter 1
Red: Listen up. What you must do now to take over the rest of the world is…
What Red doesn't know is that one of his subordinates is a spy. The spy, a ninja under Koga's command, leaves Red's base, ninja style. The ninja steals a boat and rides to Fuchsia City.
Meanwhile, Blue (remember: Blue is Gary look-alike and the two are not the same person) thinks his group, which is larger than the other groups, should split up and look for clues to find Red.
Blue: I wonder what that Koga is up to.
Yellow: Blue, I want to see Blaine.
Blue: Why?
Yellow: Maybe he knows where Red might be.
Blue: Alright, but someone has to come with you.
Green (Green is the female character) and her old friend Silver (he and Giovanni will not meet, so don't ask anything related to the manga) travels with Blue while Gold and Crystal travels with Yellow.
In Fuchsia City, Blue, Green, and Silver meet Koga. Koga told them that a spy has last seen Red in Seafoam Islands. In Cinnabar Island, Yellow, Gold, and Crystal meet Blaine (Blaine looks like the Blaine from the games AKA the true Blaine). He tells a riddle about Red's whereabouts, in which Gold solved.
In Seafoam Islands, the group reunites and sees a tower that Righty mentioned. They go inside, but Red isn't there. There is a note from Red about his whereabouts. But it's in riddle form. Gold answered it and everyone takes their bikes and Pokémon to Indigo Plateau.