Banjo Bottom was freed from imprisonment when Donkey Kong Island's Volcano erupted and helped its leader, Tiki Tong, by hypnotizing animals to gather every banana in sight on the island for their evil plot. After this happened, Banjo Bottom began taking control of the cave region of the island. After Donkey Kong and Diddy Kong defeated its siblings Kalimba, the Maraca Gang and Gong-Oh, they reached the caves.
After traversing the dense tunnels of the cave, the two kongs reached the Mole Train where Banjo Bottom resided. When it realized the duo could cause problems, it took control of Mole Miner Max and started the train to escape. The Kongs followed the train on a mine cart, a helpful cart used in other parts of the cave. After defeating Mole Miner Max, the Mole Train came to a halt, just before the end of the tracks, and the Tiki came out of the mole dazed. Seeing his chance, Donkey Kong sent it flying with a powerful punch.
Banjo Bottom later appeared with its other eight instrument-based tikis during the final boss fight to help Tiki Tong combat the Kongs. To do this, it transformed into one of Tong's hands and was used to fight the ape. It was destroyed, though, during battle.