The story continues one year after the events of the first film, following the young boy Lubicchi, who is still grieving the loss of his friend Poupelle, the man made of garbage who disappeared after helping bring stars back to the sky over Chimney Town. While trying to cope with this lingering sense of loss, Lubicchi is drawn into a new adventure when a mouse steals a cherished bracelet belonging to Poupelle. Giving chase, he falls into a fountain and is magically transported to a strange and surreal realm known as the Millennium Fortress.

In this mysterious world, time itself has been thrown into disorder, and at its center stands a clock tower whose hands are frozen forever at 11:59. The town is divided by conflict, with some wishing to protect the motionless tower and others hoping to repair it. Lubicchi learns that to find his way back home, he must succeed in a difficult task ordered by a queen named Nezumi: restart the great clock. His journey is guided by a grumpy cat he names Mofu, who becomes his new companion.

Within this land where time stands still, Lubicchi encounters Gus, an elderly watchmaker who has been faithfully waiting and believing in a promise made over a hundred years ago. The story also centers on Nagi, a plant transformed into a human girl with a beautiful singing voice, whose existence is deeply connected to the watchmaker's long-held vow. As Lubicchi helps these new friends, he finds the courage to believe in reunions again, learning the value of patient waiting rather than constantly chasing after what is lost. The central theme contrasts sharply with the first film's message of going forward to get what you want, instead focusing on the power and difficulty of waiting with unwavering faith.