The book continues the story of the young house mouse Audrey and her friends as they attempt to banish the spirit of the evil cat Jupiter once and for all.

Several troubling events begin to occur: the psychic bats leave the house's attic, the Starwife's magical Starglass is stolen, and there are reports of a bloodthirsty rat army growing in the city.

The Deptford mice soon reach the horrifying conclusion that the spirit of Jupiter has returned to seek revenge by smothering the world in eternal winter, and they have no idea how to defeat him this time as he is already dead.

The city rats, now led by Jupiter's former lieutenant Morgan (who survived his fall into the sewer water at the end of the first book), prepare to go to Deptford and slaughter all the mice there.

With her magical silver acorn pendant, the Starwife casts the healing spell while simultaneously performing a ritual to transfer her powers to the unsuspecting Audrey.

According to Jarvis, "After the unfolding drama of the previous story I knew this one had to have a powerful beginning which dragged the reader onto a roller coaster ride that did not let up until the very last page.

"[1] Several parts of the Holeborn scenes were cut from the finished book due to issues of space, which Jarvis considered "a great pity as there were some old campaigners in the missing pieces who I was very fond of.

"[5] Charlotte Decker of Library Media Connection gave a positive review where she described The Final Reckoning as being "packed with action as the rats once again come under Jupiter's evil will and wage war upon the mice.