Matthias the mouse is orphaned when the vile rat Cluny the Scourge destroys his town. Adopted by the generous creatures of Redwall Abbey he grows up to admire their legendary protector, Martin the Warrior. But his peaceful young life is shattered when the Abbey is attacked by rats and Matthias meets their warlord - none other than Cluny! Matthias resolves to fight the tyrant that once again threatens his life - and his new family.

While Redwall prepares for a long siege, Cluny steals the symbolic tapestry of Martin the Warrior from within the abbey, and Matthias learns that Martin's great sword still exists - but nobody knows where. As Cluny's next attack is repulsed Matthias meets a new ally, Basil Stag Hare, and learns that his own destiny is inextricably linked to his hero Martin. Matthias will become Redwall's next protector - but only if his quest for the sword is successful.

Cluny uses two treacherous foxes, Sela the vixen and her son Chickenhound, to plant a false attack plan in Redwall, while Matthias and his mousemaid friend Cornflower unravel the mysterious motto, "I am that is." It is an anagram for "I Matthias" written years before he was born, another clue for the quest for Martin's sword. Cluny's real underground attack is inventively repulsed by hot porridge and Matthias sees the fearful snake Asmodeus for the first time and realizes that somehow their fates are horribly intertwined.

Following the complex clues which promise to lead to Martin's Sword, Matthias climbs high into the abbey roof - and the kingdom of the crazy King Bull Sparra. A feisty sparrow returns a kindness and addresses him as King Sparra flies to attack Asmodeus - who has Martin's Sword! The king returns in time to fight who narrowly escapes death. But at least Matthias knows where his sword quest must end in a battle against the vile snake!

A traveling circus comes to Redwall and Cluny uses it to try in infiltrate the abbey with his lieutenants, dressed as clowns. The mysterious circus star, Wild Ivy the Knifethrower, seemingly mesmerizes Matthias. But she is, in fact, an ally. As Cornflower is threatened with death by Cluny, Ivy turns her circus against the rats in an acrobatic battle of fire-eaters versus fur! And Wild Ivy has seen - that Matthias and Cornflower are destined to be together - if Redwall survives.

Cluny attempts to starve the abbey into submission as within Redwall pressure mounts as tempers flare. When Basil and Jess Squirrel seem to desert, Matthias wonders if surrender is close. He decided to try and rescue the stolen tapestry from Cluny in order to give courage to the citizens of Redwall - and discovers that Basil and Jess are attempting the same thing! They outwit Cluny, retrieve the precious tapestry of Martin, and renew the spirit of Redwall.

While Cluny plans to recapture the tapestry by burning down the abbey gates, Matthias determines to renew his search for Martin's sword but does not know where its keeper, Asmodeus, hides. He learns that only the fierce mouse-eating owl, Captain Snow, knows where he is. To ask him Matthias has to pass the gigantic marmalade cat, Squire Julian Gingivere, and the Shrew of Mossflower Wood! Matthias breaks off the search for the sword to return with his new allies to once again beat Cluny.

Conspiring with Matthias, Constance builds a huge crossbow and shoots Cluny - but Cluny uses a substitute and escapes her arrow. Unknown to Redwall, he plans an attack with a huge movable siege tower. The abbey is saved when courageous Cornflower single handedly burns it down. Only then does the abbey realize Cluny is still alive and only Cornflower stood between them and disaster. Matthias and Cornflower become even closer warrior friends.

Cluny captures a traveling spice salesmouse an holds his wife ransom against the mouse entering Redwall and capturing Cornflower. Torn between love and honor, he does as Cluny demands. But with Matthias' help the two outwit Cluny with expansive flair and rescue the mousemaids, riding back to safety in a spectacular underground waterborne escape.

Matthias' wild sparrow friend, Warbeak, attempts to reconnoiter Cluny's camp as he prepares yet another attack on the abbey. She is captured and Matthias has to attempt to rescue her before Cluny feeds her to Asmodeus the snake. Posing as Cluny, Basil helps rescue Warbeak and Matthias sees Asmodeus once more and resolves to find a way to kill him. he stands between Matthias and Martin's sword and battle is inevitable.

As Matthias is lost in Asmodeus' caverns, Cluny digs his way under Redwall, taking advantage of the exhausted citizens of Redwall. After using the sword to escape the caverns, Matthias and the shrews go on a terrifying river adventure and he returns with the shrews to defend Redwall - but not before he is almost trapped by Cluny and only just saved by Cornflower. Cluny flees at the sight of Martin the Warrior's "ghost" while Matthias at last gets to wear his hero's armor.

Cluny seizes the family of a dormouse and threatens to kill them unless their father, Plumpen, betrays Redwall and opens the gate to the now huge army of rats. The plan works and Redwall is finally captured. But Matthias challenges Cluny and in a final confrontation, he kills him. Cornflower and Matthias are at last married and Redwall returns to its idyllic lifestyle. Matthias has become like a hero he admired in his childhood.