After Red sends out Aerodactyl, Giovanni doesn't have the time to retaliate as Aerodactyl unleashes a mighty Hyper Beam attack, instantly defeating Giovanni's Beedrill. This creates a thick fog, shrouding both trainers. However, when the fog begins to clear, the Viridian Gym began falling apart thanks to a mighty quake underground. Red tries saving Poliwrath, and Red almost fails to escape the crumbling gym before its collapse.
Upon getting back up, Red notices the Nidoking responsible for the earthquake. Giovanni praises Red for forcing Giovanni to take him seriously, sending out his true team of specialty ground-type Pokémon. Giovanni's Rhyhorn knocks Aerodactyl out of the air, and then Rhydon uses Fissure on Red, dumping all of Red's pokéballs underground. Red spots two free ones—Venasaur and Gyarados, coincidentally his two Pokémon with type advantages over Giovanni—but Giovanni's Dugtrio gets to them first, damaging the opening mechanism so that Red cannot release them. Giovanni then goes into great detail about just how much influence his criminal organization has, stating that most of the cities that Red has visited have been Team Rocket's to command. He then elaborates further:
- 1. The stolen Pokémon were taken to Celadon City, where they were experimented on via bioengineering.
- 2. The Pokémon were then sent to Saffron City to be trained.
- 3. Afterward, the Pokémon were shipped from Vermillion City to Cinnabar Island through the use of the S.S. Anne, as the good gym leaders made it too tough to use a northern route.
- 4. Finally, the stolen Pokémon were sent to Viridian Forest, a breeding ground where they could learn to be as savage as possible. As Viridian City's gym leader, Giovanni, is "missing," no trainers would bother to traverse Virdian Forest, giving Team Rocket's Pokémon time to be amassed into a veritable army.
As Red is the only good guy who knows the truth, he realizes that he must defeat Giovanni—and thus, more importantly, Team Rocket—right now. Pikachu propels his pokéball into Red's hand. Red shouts that this is no longer a battle between a trainer and a gym leader, but a battle against Team Rocket. Giovanni laughs that it will take Pikachu five seconds to come out of his pokéball, charge an electric attack, and unleash it; by that point, Giovanni's Nidoqueen would already have killed Red with Poison Sting.Red unleashes Pikachu, who lets out devastating Thunderbolt, defeating Giovanni and Nidoqueen. Red reveals that Pikachu was charging inside his pokéball, allowing him to attack more quickly than Giovanni, in his arrogance, had miscalculated. The glove Red wears previously belonged to Lt. Surge, giving Red insulation against Pikachu's energy inside the pokéball.
Giovanni is quick to claim that he was defeat by the technology of his own minion, but Red corrects him, saying Giovanni was defeated by the evil energies he tried to put into his Pokémon; that is, Giovanni's cruelty.Red awakens in a hospital, with Pikachu and the girl he saw earlier by his side. The girl tells him that she found him at the edge of Viridian Forest, and that the townspeople had gone out to the forest to calm the Pokémon there. The girl invites Red to become Viridian's new gym leader, asking if he would teach the townspeople to battle. Red agrees, declaring that when he comes back, he will be the best gym leader of all time.