- Klonoa and his two newly found buddies, Lolo and Popka, have to foil a sinister force which is causing a mire of gloom to plague the land of Lunatea.
- The game begins with a mysterious figure calling for help. An unconscious Klonoa then falls into the Sea of Tears, during which a ship flown by Leorina and her sidekick Tat appears, attempting to steal the Wind Ring from him. Lolo and her friend Popka appear during this time, and Leorina flies off, not wanting to risk losing the ring. Klonoa soon awakens, and he is greeted by Lolo and Popka, who tell him that his presence was foretold, and that he is now in Lunatea, and must now see the High Priestess.
Before meeting with the High Priestess, Klonoa uses his ring, with Lolo inside it, to ring the Spirit Bell. Believing to have rung it, Lolo thinks she can be a Priestess now. After talking with the High Priestess, Lolo is granted the title of Priestess, and Klonoa is tasked with getting the Elements from the giant bells spread throughout Lunatea, but in every kingdom, the group is confronted by Leorina and Tat, who not only get in their way, but also steal the elements from Klonoa.
The group eventually catches up with Leorina, who plans on using her power to make everyone realize sorrow. However, upon doing so, she ends up being cursed by sorrow and becomes a monster. Klonoa defeats her cursed form in battle and saves her in the process, and ultimately decides to help him. Using the power of the Elements, Klonoa opens a gate leading to the Kingdom of Sorrow, where he has a final confrontation with the King of Sorrow, having been the one who had summoned Klonoa to Lunatea, and now wants to use Klonoa as a vessel for the pain he suffered while in isolation. Eventually, Klonoa defeats the King of Sorrow, and ultimately rings the Bell of Sorrow, promising the King that the world would never forget about sorrow moments before he dies in Klonoa's arms.
In the aftermath, Leorina and Tat decides to restore the Kingdom of Sorrow, and it's also revealed that Lolo had given up her title of Priestess, saying that she'll earn it on her own. With this, Klonoa begins to leave. Realizing that Klonoa is not from Lunatea, a distraught Lolo asks if it's okay for her to cry, and the two embrace. Crying inside Klonoa's arms, Lolo begs him not to go but Klonoa consoles her, promising her that even though he doesn't belong in this world, they'll always be together, as long as she doesn't forget about the sadness of this moment. With a final thank you, Klonoa walks off to an uncertain future.
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