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He was promoted to a Master Poison-type Trainer, and became a member of the Johto Elite Four, at some time after the events of Generation I and its remakes, but before the events of Generation II and its remakes, thus leaving his daughter, Janine, in charge of the Fuchsia Gym.
While he has a neutral role in the games and anime, in the Pokémon Adventures manga, Koga is a villain during the first main chapter Red, Green, and Blue as he is a member of Team Rocket in that version.
In the games
Koga, known as the Poisonous Ninja Master, serves two roles in the Pokémon games. In Pokémon Red, Blue, Yellow, FireRed, and LeafGreen he is the Leader of the Fuchsia Gym, but is promoted to a member of the Elite Four in Pokémon Gold, Silver, Crystal, HeartGold, and SoulSilver. Koga is a user of the Poison-type; he likes the despair and horror that Poison-type Pokémon can inflict on others.
Koga has studied medicine and antidotes; he makes his own potions to heal his Pokémon. He also serves as a teacher. Many students come to him to be trained in the arts of Ninjutsu and Pokémon. One of his students is his own daughter, Janine, who takes over his Gym in the Generation II/IV storyline. In addition to these roles, Koga also patrols the grounds of the Kanto Safari Zone, to ensure that the players of the Safari Game are safe from the wild Pokémon within.
In Generation I/III, Koga's Gym is typically the fifth to be challenged. He has built invisible walls in the Fuchsia City Gym, constructing a confusing maze out of them. Koga awaits challengers in the center of the maze, clearly visible, but a group of Jugglers and Tamers—Koga's students—must be fought first. Defeating him will earn the successful Trainer TM06 (Toxic) and the Soul Badge.
With the future of the Gym in his daughter's hands, Koga advances to a role in the Pokémon League of Kanto and Johto before the events of Generation II/IV. In these games, he is the second member of the Elite Four to be faced. The team he uses in this role is similar to his Gym Leader's teams; the main difference is the introduction of Pokémon not native to Kanto. Koga's battle style as an Elite Four member is designed to confound and destroy his opponent in battle. Rather than using brute force, Koga attempts to confuse, put to sleep, and poison his opponent.
In the anime
Koga's only anime appearance was in the episode The Ninja Poké-Showdown.
Koga is a ninja who trains in an old mansion, the Fuchsia City Gym, in the woods outside Fuchsia City. The Gym is filled with traps such as fake mirrors, invisible walls, pits, and many Voltorb. Aya, Koga's younger sister, is one of his students.
Ash, Misty, and Brock managed to overcome the traps in the Gym and Ash was finally able to challenge Koga. Although Ash's Pidgeotto initially lost to Koga's newly-evolved Venomoth, prompting Ash to call out Charmander, their match was interrupted when Team Rocket tried to steal Koga's large supply of Voltorb, although they had raided the Gym with the intent of getting Poison-type Pokémon. Team Rocket was stopped by Psyduck, allowing Ash and Koga to have a rematch. Pitting Charmander against Koga's Golbat, Ash triumphed and won the Soul Badge.
Pokémon Adventures manga
Koga debuts in the Red, Green & Blue chapter in Raging Rhydon searching the Moon Stone in Mt. Moon, here Koga fights with Red and Misty and forces his Rhyhorn to evolve with a mysterious injection, revealing what happened to Misty's Gyarados when it was kidnapped, however the mission fails. Koga later tries to bump off Red in Lavender Town's Pokémon Tower, where he uses a Gastly to reanimate the corpses of dead Pokémon buried there. He also attacks Red with his Arbok. However, Blue has his Charmeleon slice Arbok in half. Under his boss's orders, he captures Articuno and brings it to Saffron City. He is once again defeated by Blue at Silph Co., albeit that he almost killed both him and Red by not allowing them to reach their Poké Balls by using his Muk, then almost freezing them to death with his Articuno. After he is defeated and knocked out Red gets Koga's Soul Badge and Blue uses his special Golbat to find out where Team Rocket is holding his grandfather.
Later, Koga helps the Pallet Town Trainers in the fight against the Elite Four at Cerise Island. Koga is paired with Blue and battles Agatha, but Blue first returns his Golbat to him. When the two of them finally meet Agatha, she separates them, making Blue and Koga's Golbat that he got paired up with again face Agatha's Golbat. Meanwhile, Koga's Arbok had to face Agatha's Arbok which could change its patterns allowing it to gain the upper hand over Koga. When Blue was paralyzed from a Haunter's Lick, Koga started throwing his shuriken balls. Agatha thought this was a desperate tactic, but in reality they were Pokémon holding Parlyz Heals. Koga was hoping just one of them would get to Blue, which it did. Blue then joins him, and Koga commands his Golbat to use Leech Life on himself. His blood is then put on Arbok's torso to prevent its ability to change its pattern. Without Arbok's ability, Agatha was defeated.
Or so it seemed. In reality,Agatha just pretended to be defeated and had her Gengar masquerade as Koga and Blue's shadow to slowly suck the life out of them hidden due to Koga's quick loss of blood. After traveling through the maze for a while, they found themselves back where they started with Agatha nowhere to be found. They then figured out her plan and defeated the Gengar, but not before Koga is nearly swept in the collapsing terrain of the destroyed battleground. He narrowly escapes using his Muk to defend him in his wounded state.
Unlike the other two Rocket Admins, who were instructed to return and manage their Gyms, Koga was not even reached by Giovanni. He then disappears for a time, leaving his daughter Janine in charge of the Gym. Janine is worried for her father, but opposes his criminal ties. Later in the Gold, Silver & Crystal chapter, Koga reappeared with a new partner, Bruno, who had saved Koga when Cerise was about to collapse. They trained together for a while and both of them later met their former opponents Red and Blue, whose Rhydon was drilling underground towards Ilex Forest. Towards the end of the series, Koga and Bruno found Will and Karen in the Ilex Forest and persuaded them to work together. The new Elite Four was formed, but were not seen in action until the HeartGold & SoulSilver chapter.
Two of Koga's Pokémon have unusual powers: his Arbok can regenerate itself as long as its head remains intact (see above); and his unusually small Golbat's mouth can be used almost like a magic mirror for scrying to see things from a distance, even if walls or land are in the way. Blue takes this Golbat and keeps it for quite some time before returning it to Koga at Cerise Island.
Koga also uses custom-made Poké Balls which can be thrown as shuriken—perhaps an inspiration for Falkner’s later boomerang Poké Balls.