Giovanni appears standing outside the Pokémon Tower alongside Lt. Surge. Addressing a large crowd, Giovanni announces that Team Rocket has sided with the effort against Mewthree and that they have arrived to capture Ghost-type Pokémon to use against him. To join Team Rocket, the Player must defeat Giovanni's Persian.
When the Player and Joey return from Celadon City with the Silph Scopes, Giovanni sends them into the tower ahead of the rest of Team Rocket to weaken the ghosts.
At the top of the tower, a Team Rocket grunt tells the Player that Giovanni recommends taking a break on Route 12. At the end of the level, Giovanni appears distraught and tells the Player that Maruto must be rushed to Saffron City for urgent care.
After the Player successfully defends Saffron City, Giovanni again addresses a large crowd to thank the appropriate contributors and clarify the situation. During the discussion, Giovanni claims that Mewthree is heading for Cinnabar Island. He sends the Player, Joey, Erika, and Meowth to Fuchsia City to try and recruit Janine against Mewthree.