Once Gastly was defeated, Morty sent Haunter out. Haunter, after dodging Cyndaquil's Flamethrower, affected it with Mean Look. Cyndaquil hit Haunter with Swift and covered itself with Smokescreen to evade Haunter's Hypnosis. However, Haunter was able to use its hands independently from the rest of its body; it was able to reach through Smokescreen and pull Cyndaquil out before using its Lick. Ash tried calling Cyndaquil back, but failed, due to Mean Look, which made Cyndaquil defeated. Ash sent Noctowl back, who used Foresight to detect Haunter. Haunter attempted to attack Noctowl with Lick, but failed. Noctowl used Hypnosis, but failed and got affected by Haunter's Confuse Ray. Haunter attempted to defeat Noctowl with Night Shade, but was eventually knocked out by Noctowl's newly learned Confusion.
When Team Rocket stole Ash's badges, Ash was searching for the lost badges. He also remembered his battles with the Johto Gym Leaders, including Morty and his Haunter, as Ash and his Pokémon won those badges through hard effort.