In the kitchens of Redwall Abbey, Mattimeo, son of Matthias and Cornflower, fights Vitch, a mean little rat. Mattimeo is punished by his father for discourtesy to a guest. But Mattimeo's instincts about Vitch are validated when it transpires that Vitch is a spy for Slagar the fox - a slaver for the terrible underground Kingdom of Malkariss. Slagar gains entry to Redwall disguised as the leader of a troupe of magicians. At the great feast he is able to drug the drinks and capture Mattimeo and his friends: Tess, Tim, Sam Squirrel, and Cynthia Bankvole. They join a group of slaves among whom is Auma, little daughter of Orlando the badger - who even now is hunting the fox. As the slaves are taken away, Slagar is revealed to be Chickenhound - the treacherous fox from season one - seeking revenge against Matthias the Warrior.

Redwall Abbey awakes to find their young ones are gone. As they piece the previous night together, they realized that Mattimeo was right that Vitch was the slaver's spy. Desperate that he ignored his son's warnings, Matthias vows to pursue Slagar the Fox accompanied by Basil and the others. He is unaware that Orlando is already in far away pursuit. Slagar takes his slaves on circuitous routes, laying false trails to confuse the pursuers. The frightened slaves look to Mattimeo for leadership but he is not ready and responds badly. As his father sets off in entirely the wrong direction Mattimeo learns the true story of Chickenhound - and that he is now a hostage to Chickenhounds who only thirst for revenge on Matthias for his mother's death.

Mattimeo realizes that the slaves are headed south while their parents are following false trails. They must escape by themselves or not at all. It is a slow beginning of his transformation as a leader, but not yet in time to save them from the treachery of Scurl the frilled newt who steals their few belongings for false freedom. Way behind the slaves, the Redwall pursuers meet Cheek, an alert orphan otter. In return for food and kindness, he sets them on the right track. He joins the hunt under the wry protection of Basil Stag Hare. The group encounters and joins forces with Orlando and a group of hedgehogs who have also lost a young one to Slagar. At Redwall Abbey Abbot Mordalfus dreams of Martin the Warrior who tells him to "seek the founder in the stones, where the little folk go." Constance, Cornflower, Formole and the others begin a task on deciphering the cryptic clue to the destination of Slagar, who moves southwards fast towards the dark mountain.

Mattimeo and the slaves make their first attempt to escape. Mattimeo takes another step towards his birthright of leadership. Matthias and the others are now chasing them in the right direction. At Redwall Abbey, Baby Rollo unravels the dream clue and the Redwall company follow the little folk - the ants - and so begin their own strange journey of pursuit which leads them to more cryptic clues. They struggle to solve something in the riddle that will help them help Matthias in pursuit of their young ones. The past and the present move towards a combined destiny - but what? As Mattimeo and the company hide from Slagar, Matthias and his companions approach the very gorge where Slagar secretly awaits them.

Mattimeo and his companions race to the landslide beneath where their parents are buried. They are seen by Slagar who send rats to recapture them. Within the cave Matthias and the pursuers are close to suffocating while above them - unknown to them - Mattimeo digs frantically. Beneath Redwall Abbey, John father of the captured Tim and Tess helps decipher the ancient Loamscript - but it contains more questions than answers. They work on, aware that solving the riddle will give them an answer to where their young ones are being taken. The answer indicates the South - and Warbeak and her Sparra squadrons take copies of the partly solved riddle and fly South to try to find Matthias. Mattimeo is recaptured by Slagar and cruelly forced to abandon his dying father. It forces the last step in his transformation which chills even Slagar. Mattimeo has become a warrior. Matthias is then rescued by Log-a-log and his shrew army.

From Redwall Abbey, Warbeak and her sparra squadrons fly South bearing the riddle. They hope to find Matthias to help him for his quest. But they are unaware that their departure is observed by Ironbeak, an evil raven general who invades Redwall as soon as Warbeak is gone. They drive the citizens of Redwall into the cavern hole and make them prisoners in their own abbey. Slagar and his slaves ascend the huge Great South Cliffs and cut off the means of pursuit leaving Matthias unable to follow. They pass along through the Dark Forest and are attacked by the fearsome and terrifying Painted Ones. They survive to find that Slagar is about to cross a huge river beyond which a huge rat army awaits him and his slaves. Mattimeo is beyond help, Matthias is halted, and Redwall is under siege.

Safely across the river, Slagar awaits Stonefleck's army of rats. Below the cliffs, Matthias meets Sir Harry the owl who reveals a way to ascend them. Matthias and company ascend but also comes under attack in the Dark Forest almost losing Cheek before making their escape. Across the river Mattimeo leads an escape of his own but is immediately recaptured by Stonefleck's rats. Back at Redwall, Ambrose Spike and the others set traps for the invading birds and they engage in what is to be a long battle of wits and courage. The birds take Cornflower, Rollo, and Mrs. Churchmouse hostage and threaten to kill them unless Redwall surrenders. The stand-off temporarily resolved by the Abbot, but it leaves the captives in great danger. Matthias and the pursuers launch a raft to rescue Mattimeo but come under massive fire and take to the water, only to find it is alive with nibbling fish. Without any choice, they have to ride the river.

Matthias's raft drifts towards the rats on shore, watched in horror by Mattimeo and friends. In the roof of Redwall Abbey Baby Rollo, Mrs. Churchmouse, and Cornflower wait to be thrown down unless the abbey surrenders. Triumphant, Slagar drags the miserable slaves onwards as Warbeak desperately and unsuccessfully still seeks Matthias. At Redwall, little Sister May comes up with a potion to drug the birds with food. Cheek saves Matthias and the other by eating the nibbling fish and drift them to shore. As Abbot Mordalfus prepares to exchange hostages at Redwall, Warbeak joins Matthias at the river to defeat Stonefleck's rats. She delivers the deciphered message which will help to locate the young ones but is killed in battle trying to save the other Sparras. Matthias heads south, deeply saddened by the death of his old Redwall ally. Slagar will pay dearly for his evil.

Slagar reaches the abyss and forces the slaves across a rope bridge, cutting it away behind him. There is now no way for Matthias to pursue him. A full day and night behind the pursuers arrive at the abyss and are stopped dead, until Sir Harry comes their rescue by retrieving enough rope to cross the bottomless gorge. At Redwall Abbey the hostages are exchanged, but Ironbeak treacherously uses the diversion to take over a section of the abbey. The citizens of Redwall are trapped without water and are saved when Foremole digs a tunnel. The celebration is short when it is discovered that Ironbeak is attacking the Martin the Warrior Tapestry. Rushing to its rescue the citizens of Redwall are trapped; it was a baited ruse. Ahead of Mattimeo and the slaves are the Badger Head and Bell Rocks in a lifeless wasteland, which scares even Slagar and his rats. The terrible journey is approaching its climax.

As the slaves arrive at the ominous Badger Head and Bell rocks, Mattimeo bravely comfronts them and promises "I will not fail us." At Redwall the citizens defend the tapestry in a pitched battle and recapture it. Simultaneously Matthias arrives at the Loamhedge Abbey and meets an old rabbit who forecasts doom, giving him an amulet. Slagar craftly sets his henchrats against each other and prepares to take all the slave profits himself. While at Redwall Cornflower and Constance haunt the terrified birds with the 'ghost' of Martin in his armour. The king of Malkariss appears silently and orders the slaves anaesthetized. Slagar's rats attack each other and in the chaos are captured by Matthias who demands they help him pursue Slagar. In front of the statue of a polecat, he tells them this is where they will live and die.

Underground in the kingdom of Malkariss, Mattimeo and friends see the slaves building a huge city. Brave Tess refuses to be a slave and Mattimeo is brutally attacked when he tries to save her from punishment. The slaves are thrown into a dark cell. Matthias unravels the last secret of the Loamhedge parchment and and finds a way into Malkariss - the old rabbit's amulet is the key to enter! Redwall Abbey is also successfully fighting back with Martin's Ghost and Stryk, the enormous kite bird, crashed on the earth. While Slagar and Malkariss deal for power, Matthias and friends descend into the kingdom. A fierce battle ensures in which Log-a-Log saves Matthias's life but is mortally injured. To prevent more bloodshed Matthias challenges the rats to bring forth their champion for him to fight - none other than the ferocious Wearet the Slavemaster.

In the kingdom of Malkariss, Matthias fights the slavemaster, Wearet, and falls into the abyss. There he grimly hangs on the rope that previously lowered a mysterious basket. But as Mattimeo and friends are released by the dying Log-a-Log, the Wearet cuts the rope and Matthias falls into the basket - and meets Malkariss himself! In Redwall, Stryk recovers slowly and becomes a close friend of Cornflower, but Ironbeak uncovers the 'hauntings' are a ruse and cunningly imprisons Constance as he prepares his final attack. The defenders are revealed and weakened - and Ironbeak is sure of victory. Matthias faces the evil, pale polecat Malkariss - whose slaves, seeing Matthias courage, turn on him and stone him to death. Matthias looks up to the high-above battle to see his son Mattimeo and fights to get to him. But he fails to see Slagar the Fox taking deadly aim at him with his bolas - and Slagar has never been known to miss.

In the pit of the kingdom of Malkariss, Matthias fights off Slagar who escapes to daylight as Matthias joins his battling friends - now reinforced by the released slaves. As Matthias joyfully embraces Mattimeo an earthquake shakes the ground. The terrible Polecat statue topples and with it the kingdom of Malkariss starts to collapse. At Redwall, Ironbeak penetrates the barricade which protects the citizens of Redwall and takes them hostage. He attacks Sister May which enrages huge Stryk who fights an aerial duel with Ironbeak, as Constance breaks free and attacks the birds from behind. Ironbeak's army swiftly surrenders and Redwall is saved! The kingdom of Malkariss is now doomed - but not before Matthias and Orlando are safely ejected from the earthquake, only to face Slagar, the cause of all their grief and loss. Fleeing from their ferocious attack he falls into the depths of the collapsing underground city.

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.

Matthias sets off to find Asmodeus and recapture Martin's sword. Helped by the shrews of Mossflower he finally meets his foe in the deep caverns where he guards the warrior's sword - the object of Matthias' quest. In a terrible battle Matthias kills Asmodeus. At last the serpent is dead and the sword is his. Now he can truly be a protector of Redwall. But news of Cluny's assault reaches him and he realizes he is trapped deep underground.

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.