Agatha's Gastly and Haunter intercepted Professor Oak in the halls before the finals of the Indigo League began. Gastly and Haunter attacked his Kangaskhan and Chansey, who retaliated back and wounded Gastly and Gengar. The two were also sent during the finals, but Oak managed to defeat them and become the Champion of the League.
Agatha was waiting at the power plant with her Ghost-type Pokémon, including Gengar. To scare Blue and Evan away, Agatha sent Gengar to scare them off. It used Night Shade, so Blue had Golduck use Hydro Pump to protect Evan from the attack. Since Blue was Professor Oak's grandson, Agatha wanted Blue to suffer, as her Gengar used Hypnosis to lull Blue to sleep and drain his energy through Dream Eater. Gastly and Gengar emitted fog to drain Blue from his energy. Blue managed to communicate with Evan by having Golduck display Blue's thoughts through the Pokédex he dropped. Agatha saw that and had Gengar use Confuse Ray on Blue. Evan managed to reach his Haunter and distract Agatha, allowing Blue to break free. He had Scyther slash Gastly and Gengar at their cores, defeating them.
Facing Blue and Koga on Cerise Island, Agatha had Gengar use Lick on the former. This caused Blue to be paralyzed. Blue and Koga left after defeating Agatha's Arbok and Golbat. However, Agatha had Gengar hide in their shadows to attack them. Koga felt his energy was being drained; Blue turned around and saw the Gengar. Blue sent Golduck and Koga sent Koffing, but Gengar knoked them out both, then disappeared. To retaliate, Blue had Ninetales use Fire Spin, Charizard to blast Flamethrower out and Scyther to use Slash. Gengar evaded these attacks and used Counter, knocking Ninetales out. Blue sent Porygon, who used Conversion. As Gengar attacked Porygon, the attack had no effect, as Conversion turned Porygon into a Ghost-type Pokémon. Porygon used Sharpen and tried to attack Gengar, who disappeared into the shadows. Blue got attacked again, and realized Gengar was moving through shadows and was attacking if a sound was uttered. Seeing the signal coming out from Koga's Koffing, Blue had an idea. Gengar came out once more, but it encountered the leftover tail from Koga's Arbok. Due to that mistake, Gengar was defeated by Blue's Porygon's Psybeam; Blue and Koga had it lured to the tail, that moved on its own.