Gengar was sent out to find Ash's Pikachu and Misty's Togepi. Thus, Gengar managed to get a Gastly and a Haunter to find them both. Once Gengar found them taken by Team Rocket, it extended its tongue to make them trip over. Jessie sent Arbok and JamesWeezing, but Gengar disappeared and attacked them from behind. Using Night Shade, Gengar caused Team Rocket to drop Pikachu and Togepi, who were rescued. Arbok and Weezing attacked, but Gengar disappeared, causing Weezing and Arbok to bash into each other. Arbok used Wrap on Gengar, who disappeared and blasted Team Rocket away with Shadow Ball.
Morty had Gengar use Confuse Ray on some Gastly to teach his students, before Ash arrived for his Gym match. Morty later used Gengar as his last Pokémon during his Gym Battle with Ash. Gengar launched Shadow Ball, which collided with Noctowl's Confusion. While Noctowl desperately tried to use Foresight, it was countered by Gengar's Night Shade attack. Thus, Ash came up with an idea and ordered Noctowl to send its newly learned Confusion through the whole gym, which hit Gengar. Noctowl then used Foresight to make Gengar unable to turn itself invisible. Gengar tried to counter with Shadow Ball, but Noctowl was too fast and slammed into the Ghost Pokémon with a Tackle attack, defeating Gengar.
Once the crystal bells atop Tin Tower were stolen, Morty sent Gengar to find them. Eventually, Gengar found them in Team Rocket's possession and Gengar used Confuse Ray to make them confused.
Morty and Gengar, along with Whitney and her Miltank, were mentioned by Lyra, who was unable to decide whom to challenge next for her third Johto badge.