Koga and Muk were waiting for Blue and Blaine, as well as Yellow, Bill and Green on Cerise Island to fight the Elite Four. After obtaining the Spoon of Destiny, Koga went with Muk and Blue to face the Elite Four.
Muk, Koga, Blue and Porygon were searching for their enemy, who was Agatha. To stop Agatha's Arbok, Koga sent Weezing to use Smog and Muk to use Poison Gas. However, Arbok resisted the attacks and retaliated, defeating Koga's Pokémon. As the cave was collapsing, Koga sent Muk to protect him and Golbat from the boulders. Muk took Koga outside, where he met Bruno, his new friend.
Muk appeared with Koga and the rest of the Johto Elite Four to promote the Pokémon League through the Pokéathlon. Later on, it participated in the Circle Push, where it knocked out Exbo, Polibo and Aibo.