With the advent of the Puyo Puyo Circus, Arle and Carbuncle have come to visit and take part in festivities. Arle makes her way to one of the tents to watch a show, led by Satan as the ringmaster. As part of one of the acts, Satan requests a volunteer to come down to the stage. With Carbuncle as said volunteer, he performed a disappearing act, making him vanish before the crowd. After Arle leaves the tent after the show has concluded, she realizes Carbuncle is nowhere to be found. Thus, Arle begins to explore the circus grounds in search of her friend. Puyo Puyo~n features a Beginner and Normal course. The Beginner course features the first three stages and does not play cutscenes. Arle cannot use her personal Super attack in story mode, but can call upon the powers of Draco Centauros, Serilly, Witch, and Chico as the player advances. Unlike previous Puyo Puyo story modes, the gameplay rules drastically change between stages. Due to the length of the Story Mode compared to other Puyo Puyo games, the game saves after every stage. This allows the player to quit and then start back on their current stage without losing progress.

With the advent of the Puyo Puyo Circus, Arle and Carbuncle have come to visit and take part in festivities. Arle makes her way to one of the tents to watch a show, led by Satan as the ringmaster. As part of one of the acts, Satan requests a volunteer to come down to the stage. With Carbuncle as said volunteer, he performed a disappearing act, making him vanish before the crowd. After Arle leaves the tent after the show has concluded, she realizes Carbuncle is nowhere to be found. Thus, Arle begins to explore the circus grounds in search of her friend. Puyo Puyo~n features a Beginner and Normal course. The Beginner course features the first three stages and does not play cutscenes. Arle cannot use her personal Super attack in story mode, but can call upon the powers of Draco Centauros, Serilly, Witch, and Chico as the player advances. Unlike previous Puyo Puyo story modes, the gameplay rules drastically change between stages. Due to the length of the Story Mode compared to other Puyo Puyo games, the game saves after every stage. This allows the player to quit and then start back on their current stage without losing progress.