The plot begins with several problems occurring throughout Wizard City, host to the Ravenwood school. The player must aid other wizards in completing dangerous missions. After defeating Lord Nightshade, a Grim Reaper-like spirit that is responsible for the undead attacks on Wizard City, the player gains access to the location of Krokotopia, where the Kroks, an ancient race that enslaved Krokotopia centuries ago, have reawakened from a deep sleep and are now attacking the current residents of Krokotopia. Krokotopia is also the world that holds the ancient book called the Krokonomicon, and is needed by the player before Malistaire can get to it. When the Krokonomicon is later transported to another world, Marleybone, the player follows the lead. The Mayor of Marleybone doesn't allow you to take the Krokonomicon due to recent crimes, and the Krokonomicon is stolen by the master thief Meowiarty on behalf of Malistaire soon after. The player must find Meowiarty's lair, which is at the top of Big Ben. When Meowiarty is returned to prison, Malistaire then travels to Mooshu to get the key to Dragonspyre from Emperor Yoshihito, but when he refuses to hand it over, Malistare severely injures him and steals the key. It is then up to the wizard to heal the Emperor in order to get to Dragonspyre, but you must face the Oni in order to do it, including the Jade Oni who has taken over the Emperor's body. Once healed, the Emperor gives the player the Spiral key and informs him/her that Malistare is now in Dragonspyre, an ancient world destroyed by a giant dragon where he shall put his plan into action. With a little help from Malistare's brother Cyrus Drake, the wizard reaches the top of the volcano. When there, Cyrus tries to reason with his brother but fails, Malistare dubs himself the "Necromaster," attempting to resurrect his wife using the Krokonomicon to summon the Dragon Titan. When he is eventually defeated by the player, Malistaire and his wife finally gain peace.
Merle Ambrose calls on you to travel to the sunken world of Celestia to check on an expedition from Marleybone. You soon unravel a plot where agents of Morganthe and Morganthe herself - a vile sorceress - are planning to take the secrets of the Astral Magic in Celestia - the Sun, the Moon, and the Stars. You journey through Celestia, both helping the Marleybonian Expedition and discovering Morganthe's intentions in the world. You meet her after collecting the Star, Moon, and Sun relics in the Solarium, where she has you face one of her minions, Big Salgio, and then leaves you with a warning: "The Mirror will break, the Horn will call. From the Shadows I strike, and the Skies will fall." Your journey continues when you journey to the African-themed world of Zafaria. You and Inyanga Whitestripes, a friendly Zebra witch-doctor, try to search for a missing group of Ravenwood students studying in Zafaria. You soon realize that this is no normal disappearance - Morganthe is back! You first travel to the Savannah and resolve the issues involving the Lion tribes there. You then travel to the Zebra land of Zamunda where you meet Tse-Tse Snaketail, the supporting antagonist in this world. You also uncover a war that has broken out between the Zebras and the Elephants because the Elephants believe the Zebras are responsible for the disappearance of their prince, Tiziri Silvertusk. You then go to Stone Town and the Waterfront to find that Rasik Pridefall, the Zafarian council member for Elephants, is really an agent of Morganthe. Finally, you go to the Drum Jungle where you find the Prince and Morganthe. You track her to Mirror Lake and Shining Mountain where she escapes with her Deck of Shadows. She again repeats her riddle: "The Mirror will break, the Horn will call. From the Shadows I strike, and the Skies will fall. This implies that Mirror Lake was the "mirror" in the prophecy. Afterwards, Merle calls you again to recover the Sword of Kings in the world of Avalon, the home of Merle Ambrose and Morganthe. You go around Avalon rallying the knights of an organization known as the Silver Rose and meditating upon the shrines, a requirement to wielding the Sword of Kings, find the Lady of the Lake and defeat the evil Pendragon, Lord of the Wild Hunt a creature who has caused much havoc in Avalon. The quest of finding the knights and the shrines takes you to the village of Caer Lyon, the forests of the Weirwood, the yard of Castle Avalon, Lake Nimue, the Catacombs and Crystal Caves beneath Castle Avalon and the past of Castle Avalon itself where you confront a young version of Morganthe. Then you are deemed worthy to hold the Sword of Kings, which you get at Castle Avalon (also known as the Keep of Ganelon) in the present and use to slay the Pendragon, who then reveals to be King Artorius mutated by the Horned Crown (which Morganthe tricked him into wearing) and who you heal by obtaining the venom of two dragons. After you heal Artorius, he leads Avalon into a new golden age. Later The Lady of the Lake foresees a shadow washing across the Spiral and tells you to report back to Merle.