In the land of Dor, everyone is happy, especially when Soup Day rolls around and chef Andre (voice of KEVIN KLINE), with the help of his vegetable and fruit-based friend Boldo (voice of STANLEY TUCCI), reveals his latest savory creation for the royal family. This time, however, epicurean rat Roscuro (voice of DUSTIN HOFFMAN) has arrived via a sailing ship and accidentally falls in the Queen's soup, leading to her shock and untimely demise.
As a result, the grieving King not only outlaws soup, but also makes rats illegal. That results in Roscuro and the rest of his kind being banished in Ratworld deep down inside the castle's dungeon where Gregory (voice of ROBBIE COLTRANE) guards over no one in particular and grouses about the slop brought to him by servant girl Miggory Sow (voice of TRACEY ULLMAN).
Back up top, Princess Pea (voice of EMMA WATSON) is despondent over her father's grief, the joy vanishing from the land and its people, and a perpetual cloudiness that yields no rain, leaving everyone miserable. That is, except for Despereaux (voice of MATTHEW BRODERICK), a tiny mousy with huge ears. His lack of fear worries his parents, Lester (voice of WILLIAM H. MACY) and Antoinette (voice of FRANCES CONROY), who think he should cower like his older brother, Furlough (voice of TONY HALE), and the rest of the Mouseworld population, and eat books rather than read them.
But that's exactly what he does -- entranced by a tale of a knight battling to save an unhappy princess -- but that and his overall nature end up getting him banished down to Ratworld where the sadistic rat leader, Botticelli (voice of CIARAN HINDS), entertains the masses by offering Despereaux to a huge cat.
Sensing a kindred spirit, Roscuro saves the plucky mouse, but when the rat goes to apologize to the Princess, she freaks out and tries to have him killed. That results in him aligning with Miggory, a farm girl turned servant with delusions of being the princess. From that point on, and like his literary hero and inspiration, Despereaux sets out to save the day and Princess Pea from her misery.