The film focuses on a small group of overzealous scientists who hope to use Dracula's desiccated—but still alive—body to discover the secret of immortality. Elizabeth Blaine, working at the New Orleans morgue, receives Dracula's 'corpse' from her friend and co-worker Luke following the events of Dracula 2000. (This is a departure from the epilogue of the first film, in which Mary Van Helsing explains in a voiceover that she had returned Dracula to London and assumed her father's duties as Dracula's keeper.)
The film takes place in an unidentified city (presumably New York City) in the modern day, and follows the characters of Rufus King (Thomas Downey) and Jacob Van Helsing (Rhett Giles), both of whom have been observing recent attacks made upon young teenagers in the city at night. Van Helsing correctly identifies that the attacks are being made by a group of vampires residing in the city. The vampires are led by a foreign seductress named Countess Bathorly (Christina Rosenberg), who hopes to use the humans to feed her growing vampire clan and to eventually seize control of the city, while at the same time using her growing power to gain the powers of "the Master". Discovering Bathorly's plan, Van Helsing and King begin to hunt down and destroy the vampires one by one, until they finally face the Countess herself and try to kill her once and for all, before her evil consumes the city and allows Dracula's curse to consume the human race.
Arthur Holmwood attempts to cure the syphilis with which he was born and which also caused the death of his father. Arthur receives his diagnosis soon after becoming engaged to Lucy Westenra. He contacts an occult group called the Brotherhood, which is being led by a man named Singleton. The Brotherhood claims that it can clean his polluted blood, but for a price.
Every year, all of the classic Hollywood monsters (consisting of Frankenstein's monster, his wife Repulsa, a Mummy, the Witch Sisters, Bone Jangles the Skeleton, Dr. Jekyll/Mr. Snyde, Swamp Thing, and Dragonfly) gather at Count Dracula's castle in Transylvania for the "Monster Road Rally", an ultimate road race similar to Wacky Races, awarding the winner with the "Monster of the Year" award as well as many other prizes only monsters would enjoy (and one prize — a trip to Hawaii — that none of the monsters want). This year, however, Dracula receives a postcard from the Wolfman stating that he has retired to Florida and will not be participating.
After hearing rumors from a TV newscaster (portrayed by Andrew Duncan) that Halloween may end and that he is being blamed, Dracula exclaims, "How dare they suggest such a thing? Halloween is my national holiday!" and he calls the world's most famous monsters—Warren the Werewolf aka Wolf Man (Jack Riley) of Budapest, the Mummy of Egypt (Robert Fitch), Frankenstein's monster (John Schuck), Zabaar the Zombie (Josip Elic) of Haiti, and the Witch - to his castle to make them scary again. Dracula believes that the problem is that the monsters have "exploited their monsterhood" to the point of being funny rather than scary, for example, Frankenstein's monster has let a movie influence him into tapdancing rather than scaring people. As it turns out, the rumor about Halloween coming to an end was started by the Witch herself; sick of jokes about how ugly she is, she no longer wishes to participate, and without her annual ride over the moon, there can be no Halloween. She has prepared a list of demands, which Dracula refuses to meet, so she rides off to her own castle.
Dark Prince: The True Story of Dracula tells the story of Vlad Dracula, the historical figure who gave Bram Stoker's Dracula his name. Vlad is a dispossessed noble, and a patriot who fights the occupation forces of the Turks hoping to avenge the murder of his father by Romanian nobles and the capture of his brother by the Ottoman sultan. The King of Hungary (Roger Daltrey) becomes Vlad's ally and, with his support, Vlad and his men attack the occupying Turks and turncoat Romanian boyars, and seizes the throne of Wallachia.
Flynn Carsen (Noah Wyle) travels to an auction house in England in order to bid on a priceless Ming vase on behalf of the Library. During the bidding war that ensues, he accidentally both outbids his competitor by going over budget and has a fight with his girlfriend on the phone. Once he has signed for the vase, he promptly breaks it open, revealing the philosopher's stone, the most powerful transmutational artifact in existence, known for changing any object instantly into gold. As his opponent bidder and henchman ambush him for the stone, he deftly defends it by combining historical knowledge and swordplay throughout the auction house, concurrently parrying his opponents' blows while the two debate the pricing of the items within. Once Flynn has won the duel, he proceeds to his hotel lobby, hoping to repair his relationship with his girlfriend, only to find that she has abandoned him after a string of disappointments.
Scooby-Doo, Shaggy, and Scrappy-Doo are on their way to a Miss Grimwood's Finishing School for Girls, where they have been hired as gym teachers. Once there, however, they find that it is actually a school for girl ghouls. The pupils include Sibella, the daughter of Count Dracula; Elsa Frankenteen, the daughter of Frankenstein's monster, Winnie, the daughter of The Wolfman; Phantasma (usually called Phanty for short), the daughter of a phantom, possibly The Phantom of the Opera; and Tanis, the daughter of The Mummy - all parodies/tributes to the Universal Monsters of the 1930s-40s. Other residents of the school are a floating white hand; an octopus, who is the school's butler; Legs, a spider that helps with the upcoming volleyball match; Miss Grimwood, the headmistress; and her pet dragon Matches (who dislikes Scooby at first, but later becomes friends, and has a strong friendship with Scrappy). Shaggy and Scooby want no part of this at first, but eventually they agree to stay as teachers.