Giovanni in the first chapter
Giovanni is first seen traveling with Red under the guise of a friendly researcher off to study Fossils. As they leave the Diglett's Cave after a search for Fossils they find that the Pewter Museum of Science has been set ablaze by two wild Magmar. It is here that Giovanni's true agenda is revealed, to investigate Red and find out how he defeated his subordinates Lt. Surge and Koga. Giovanni watches Red defeat the Magmar in his unorthodox way and gives him an Old Amber as thanks while saying goodbye to him. The two Magmar then wake up from their sand prison and attack him; Giovanni has his Cloyster freeze and kill them. Giovanni laughs at the fact that someone like Red could defeat Team Rocket.
It is later revealed that he is attempting to capture the Legendary Pokémon Articuno, Zapdos, and Moltres and fuse them into a single, powerful weapon. He leaves this plan in the hands of his top subordinates Lt. Surge, Koga, and Sabrina, but with the combined strength of the Kanto Pokédex holders, Red, Blue, and Green, the plan is destroyed.
When Red goes to the Viridian City Gym to find out what had happened to its missing Gym Leader, he finds Giovanni waiting inside for him. There, Giovanni reveals to Red that he is, in fact, the Viridian City Gym Leader and also the Leader of Team Rocket. Giovanni challenges the boy to a battle with a special condition: if Giovanni wins then Red will fight by his side as a member of Team Rocket. Red accepts the challenge and the two begin battling. In the end, Giovanni is defeated after an intense battle after Red uses techniques involving the Trainer and not just the Pokémon battling.
Giovanni later appears at the summit of Cerise Island when Yellow is battling the leader of the Elite Four, Lance. It is revealed that he was the one who had freed Red from his icy prison created by Lorelei and gave him the evolutionary stones of the Vermilion Bay that would allow him to evolve his Eevee multiple times. Giovanni does battle with Lance and uses his Pokémon to destroy the giant bubble that he was using to attack Yellow and protect himself from attacks. Just as it seems that Giovanni has the upper hand, Lance reveals that he had planned for this and that Giovanni had fallen into his trap. Lance reveals that Cerise Island is one giant Gym Badge amplification device and with Giovanni's Earth Badge, he can finally summon the giant bird Pokémon. Seeing what Lance has summoned, Giovanni immediately takes off and leaves Yellow to fight him alone. He is seen witnessing Lance's defeat at the hands of Yellow. His subordinates, Sabrina and Lt. Surge, meet up with him in hopes of starting up Team Rocket again. Giovanni dismisses them, realizing that they are not ready to revive Team Rocket because they required the help of children when battling the Elite Four. He tells them to lay low and go to their Gyms until a more suitable time to revive Team Rocket comes.
Giovanni makes a brief cameo at the end of the fourth chapter where he finds the Ruby and Sapphire on a beach. He reveals that the gems are in fact the true forms of the Red Orb and Blue Orb that have taken their forms after being broken by Ruby's Celebi. He takes the gems and sets off with his mysterious henchmen to start a then unknown plan.
Giovanni resurfaces in the Sevii Islands, where he witnesses the mysterious Deoxys attack a gang of bikers that were planning to raid Three Island. When the leader tries to ask Giovanni to save him from the "monster", Giovanni answers by swatting him away and having his Nidoking send the biker flying with Rock Tomb. He states that Deoxys isn't a monster; instead, it is the strongest Pokémon that ever existed.
He sends his newest group of henchmen, The Three Beasts, to cause trouble on the Sevii Islands and distract the Kanto Pokédex holders while he finishes polishing the Ruby and Sapphire; once he is done, he gives the gems to Sird so that Deoxys can finish its transformations. After Deoxys returns to Birth Island to heal the injuries it received in its battle with Red; here, Giovanni reveals his plan, to capture Deoxys and find his missing son. He sets off for Birth Island where he finds the resting Deoxys, battles with, and successfully captures it.
Giovanni makes his next appearance at Trainer Tower where he confronts the Kanto Pokédex holders while they try to fend off Deoxys's Duplicates. He is attacked by Mewtwo, who is angry at him for creating it to be a weapon. Giovanni responds by trapping Mewtwo in a binding set of armor called the "M2 Bind" and leaves the Pokédex holders to be defeated by Deoxys's duplicates. Later, Giovanni uses Deoxys to search for his son; Deoxys locates him at Viridian City and Giovanni sets course for that location.
Giovanni in the ninth chapter
Giovanni eventually lands near the Viridian City Gym and sends Sird and Orm to find and retrieve his son. As he recuperates from the pain of his disease, Giovanni finds that Red and Mewtwo are flying towards him; he decides to get Red back for his previous defeat at the Viridian Gym and prepares for battle. Red eventually arrives on the Team Rocket airship and Giovanni issues a challenge; one-on-one, Mewtwo versus Deoxys; Red accepts and they begin battling each other.
Mewtwo and Deoxys each manage to get the upper hand on each other throughout the match but it seems like Mewtwo has won once it has attacked Deoxys's core. Deoxys eventually recovers and severely injures Mewtwo by stabbing it in the back with its tentacles. Despite Mewtwo being heavily injured, it manages to recover and defeats Deoxys with a powerful attack, making Red the winner of the battle.
Giovanni collapses from his disease and is carried away by Orm so that he can finally meet his son, Silver. As he rests in bed, Silver finds his father and sulks with disappointment because of the fact that no matter how hard he tries, the side of evil is always associated with him. Silver refuses to accept Giovanni as his father and attempts to leave, but Giovanni quickly stops him but before he can say anything, a power-hungry Carr hijacks the ship and attempts to crash it into Vermilion City. Red has Deoxys use its power to create black holes to suck Silver, his Sneasel, and Giovanni to safety.
Giovanni and Silver eventually exit the black hole, but, instead of a safe location like Red expected, Giovanni instead finds that they have landed near a flaming piece of wreckage from the airship. Giovanni holds Silver up to protect him from the flames; he comments about how proud he is of how he had grown. They are eventually saved by Blue's Rhydon; Silver still refuses to acknowledge Giovanni, a criminal, as his father and states that he should've left Giovanni to die in the flames. Blue reveals to Silver about how he was once like him and manages to convince him to accept his father; Silver then breaks down crying over Giovanni's unconscious body. Giovanni is taken away by Silver's Ursaring to Silver's eighteenth Secret Base on Route 6 to rest from his injuries.
Giovanni in the thirteenth chapter
For the most of this chapter, Giovanni's whereabouts were unknown as he had gone missing after Silver returned to his secret hideout.
When Archer succeeds in having Arceus absorb all 16 of its Plates and has it create the Creation trio, he boasts about Team Rocket's control over the Creation trio and mentions Giovanni, causing Silver to react with surprise. Archer wishes for Giovanni to know, if he's still alive, that Team Rocket has succeeded in becoming the most powerful organization in the world. Falling to his hands and knees, he begs for Giovanni to return to Team Rocket. Shortly after, Petrel approaches Silver from behind, asking why Silver looks so shocked and if it's because he heard a familiar name. Petrel then asks Silver outright if he's Giovanni's son.
During the battle with Arceus afterward, Petrel attempts to escape from an insane Archer. When he does, he disguises himself as the Team Rocket leader, only to be attacked by an Ursaring. There, the real Giovanni, along with Pryce and Lance, appear in order to combat Dialga, Palkia, and Giratina, a trio that would threaten the Johto region. While Pryce goes after Dialga and Lance faces Palkia, Giovanni battles Giratina with his son's Ursaring.
Pryce reveals that after he returned from the crack in time, he encountered Giovanni at the Ilex Forest, who was looking for Celebi so that he could get a cure for his disease. When Giovanni saw Pryce, he immediately attacked Pryce and would have killed him if it weren't for the intervention of Lance, who told them of the events going on at the Sinjoh Ruins. Although reluctant, Giovanni agrees to help and has Ken, Al, and Harry guard the Ilex Forest while Celebi searches for the herbs for his cure.
Eventually, his disease gets the better of him, preventing Giovanni from continuing the battle against Giratina. Immediately, Silver steps in and attacks Giratina to defend his ailing father. After Arceus is calmed down and the three Pokémon leave, Ken, Al, Harry, and Celebi arrive with the cure to Giovanni's disease. The cure works, and Giovanni becomes completely healthy again. Now cured, Giovanni decides to lead Team Rocket once more, as he still has some evil in his heart.
He offers Silver a position in Team Rocket, but Silver declines and promises to change his father's evil ways one day. Giovanni accepts his son's decision and tells him to grow stronger under Lance and Pryce's teaching in the hopes that they will battle someday.
Giovanni is first seen in Blaise's flashback explaining what happened to the Red and Blue Orbs. It is revealed that when Giovanni discovered the shards that would be used to power up Organisms No. 1 and 2, Blaise was there watching him. Giovanni senses him, and sends out his Beedrill, but doesn't give the command to attack.
Giovanni later appears in person, where he travels to Hoenn. There, he finds an unconscious Red, Green, Blaise, and Amber after they were defeated by an enemy. He takes the four aboard the Team Rocket airship, heals their injuries, and takes their possessions in order to prevent a fight. When they awake, Giovanni reveals himself and explains that he wishes to help stop the meteoroid threatening to destroy the world.
Later, Giovanni, Red, Green, Blaise, and Amber head to Sootopolis City, where they meet with Ruby, Sapphire, and Emerald, discussing a plan to stop the meteoroid. Giovanni reveals that he possesses a Key Stone and proceeds to Mega Evolve his Beedrill. Red and the others follow suit by Mega Evolving their Pokémon as well. Giovanni points out that if he was able to use Mega Evolution, which is normally impossible outside of battle, then it suggests that the meteoroid may actually be a Pokémon itself. When Ruby and Sapphire later ride Rayquaza into space and successfully destroy the meteoroid, a Deoxys emerges from inside of it and attacks them. Down on the ground, Giovanni confirms that this Deoxys is Organism No. 1, which Team Rocket had disposed of after it had outlived its usefulness to them.