Zeller first appeared in Besting Buizel I, as one of the many wild Buizel and Floatzel living in Route 213. After the bombing on Lake Valor by Team Galactic, Crasher Wake took Pearl here in order to catch one of them. After failing to get a Floatzel Crasher Wake suggests he go after a Buizel instead. Pearl nods at his suggestion and has Rayler attack Buizel with Shock Wave. Pearl cheers at the hit, and hurriedly tosses out a Poke Ball to capture him, but the ball bounces off his head. Buizel then glares at Pearl, causing him to flinch from the high amount of hostility. Buizel then charges at Pearl and attacks, with Pearl barely dodging. Pearl questions why Buizel would be so furious at him, and Crasher Wake explains that Route 213 is located close to Lake Valor. Due to the bomb that exploded the lake, the destructive energy spread out to the surrounding areas and evaporated all the water, destroying their homes. The Pokémon could not understand the act of terrorism by an evil organization but knew that it was humans that ruined their way of living.
Having a better understanding of what happened Pearl continues his battle against Buizel, who dodges most of his attempts to capture him. After some encouraging words from Crasher Wake, Pearl manages to hit Buizel with a ball, successfully capturing him. Pearl then names him Zeller and promises they will get along. Zeller, however, attacks Pearl from within his ball and rolls away. Crasher Wake picks him up and explains that Zeller is still nervous from the explosion and it will take time for him to accept his Trainer.
In Cleaning Up Grimer, Zeller is used in his first battle with Pearl to battle against a group of Team Galactic Grunts. Upon being sent out he turns around and bites down on Pearl, causing him to cry out in pain. The Team Galactic Grunt's Pokémon soon begin to annoy him and he attacks them by spinning his twin tails to blow up a tornado of dust, blinding them. This allows Digler and Tauler to quickly finish the battle.
In Double Trouble with Dialga and Palkia VI, Zeller was used alongside the other Pokémon to battle against the Legendary Pokémon Dialga and Palkia. With the help of Diamond and Pearl's Pokémon and with a combined technique, they were all able to destroy the Red Chains controlling them.
In The Final Dimensional Duel IV, Pearl intended to use Zeller alongside the rest of his team to fight Charon and his Heatran but Reg showed up with Rotom's appliances, allowing it to defeat him.