As he flies on Blue's Charizard, Red looks back at the Trainer Tower. Blue looks back at Red and tells him to go on ahead in his mind. Red realizes that Blue gave Charizard to him because Aero's wings are still pierced from the battle with Deoxys. Mewtwo confirms Red's theory by informing him of what Blue told it earlier. Red puts his Pokédex in his pocket and tells Blue and Saur that he won't let their efforts be in vain.
Back inside the Trainer Tower, Blue tells Professor Oak that Red has already left. Green tells him that Blasty managed to give Red his new Pokédex. Blue notes that he was lucky that he was able to get through the hole Blasty made with Hydro Cannon and not get trapped with the Deoxys duplicates. Since Green's Pokémon have immobilized the other duplicates that aren't trapped, they won't be causing trouble. Blue thanks Green for her help, while Green notes that since she had the hardest time, she was the most valuable person in the plan. She tries to give Blue his new Pokédex while he attempts to call her obnoxious as usual, but he falls to the ground in exhaustion. Since they're too tired to help, Blue states that everything is all up to Red.
Back in the Viridian Gym, Yellow asks Silver's Sneasel why the statue of Giovanni is in its memories. Silver states that although he hasn't been there, he has memories of Viridian City buried into his heart. Recalling the moment when Green had her Abrateleport him to safety, Silver remembered a city surrounded by a forest. He reveals that he later found out that Green's intention was to use her Abra's Psychic abilities to pry through Silver's mind and send him to his birthplace. After doing some research on what he saw, Silver decided to come to Viridian. Silver expresses delight at seeing that his assumptions were correct. He asks Yellow who the person on the bust is. Yellow tells him that it belongs to Giovanni, the original Gym Leader of the Viridian Gym and leader of Team Rocket.
Yellow hears rustling coming from the Viridian Forest and goes outside to investigate. She calls out to Dody, who brings Yellow her straw hat. Silver asks Yellow what's about to happen. When Yellow asks what Silver will do know that he knows that he has a connection to Team Rocket, Silver states that he will ask Giovanni what their relation to each other is. Although he knows that he will be facing the boss of Team Rocket, Silver decides that he will fight him. They hear a sound in the air, so Silver puts on his Silph Scope to see it closer. He sees the Team Rocket airship, which he notes saves him the trouble of finding Giovanni. Noting that this isn't the same group he fought in Johto, Silver guesses that the group must be Team Rocket's elite.
On the Team Rocket airship, Giovanni asks Deoxys that it found his son near the Viridian Gym. Although Deoxys remains silent, Giovanni decides to trust in its skills. Giovanni decides to go down and meet his son himself, but he suddenly collapses in pain. As he cannot go down at the moment, Giovanni tells Sird and Orm to go in his stead. They exit the airship through a small pod, causing Silver to note that they can't avoid a fight.
Silver sends out his Gyarados and has him fire off a Fire Blast. The pod dodges the attack and sends out a Banette, which attacks Gyarados with a Shadow Ball. Silver tries to have Gyarados heal its injuries with Rest, but Banette steals the move with Snatch. Silver tells Sird and Orm to come out of the pod and face him in person. Inside the pod, Sird uses a machine to determine that Giovanni's son is actually Silver. Sird and Orm exit the pod and tell Silver that they are there to pick him up.
Silver demands to know where Giovanni is. Sird simply responds by introducing herself and Orm to Silver. Silver tells them that his business is with Giovanni alone and tells them to get him down there. Sird notes that Silver is stubborn like Giovanni, which is uncalled for as a leader. Confused at what Sird is talking about, Silver sends his Murkrow to attack, only for it to be easily tossed aside by Sird's Banette. Sird tells Silver to calm down, or else they will have to take him by force. Although Orm notes that Silver is important to Giovanni, Sird tells him that she won't hurt him. Orm sends out his Jumpluff while Sird suggests having a Multi Battle. Much to Yellow's shock, Silver agrees to the battle.