The Story takes place in the 16th century in France. It tells of Prince Fredrick, who lived with his kingly father (Michael Hordern) in a huge castle by the ocean, and was taught magical powers. His mother, the queen, has been dead for over a year, drowned at sea in a storm. One day, Freddie went horse riding in the forest with his father, but after his evil aunt, Messina (Billie Whitelaw), spooked the horse his father was riding, his father fell to his death from a great height. Freddie spotted a long, red cobra; he had never seen one of those in the forest before. Now an orphan, Frederick is taken in by Messina, who accedes to the throne, but only filling in the temporary position as regent, until the time Frederick comes of age to assume the responsibility as the next ruler when she must step down. Soon Freddie realises that the cobra he saw in the forest was Messina (who also was responsible for conjuring the storm that lead to his mother's death) and rather than killing the young prince, she and transformed him into a frog and tried to capture him. Soon, both fall from the castle window and into the raging ocean, and Freddie is saved in the jaws of a giant sea monster. Messina blurts out she will rule the world and destroy Freddie. The monster really turns out to be Nessie (Phyllis Logan), the Loch Ness monster. As Messina left, Nessie's tail became trapped by a boulder. She befriended Freddie, who in turn used his powers to free her tail from the boulder. Nessie took him near dry land, and notes that if Freddie ever needed her, he would whistle. Freddie then leaped into the night sky, and fell into a swamp full of frogs, where he would spend the rest of his childhood until he meets Winnie the Pooh, Ash Ketchum, Simba, and their friends.
Freddie eventually grows up to become a member of the French secret service, known as F.R.O.7. (Ben Kingsley) with Pooh and the others as part of an international spy team of the rebel alliance. They are then called to London by the British Secret Service, as some major famous buildings & Monuments in the United Kingdom are vanishing. By the time Freddie and our heroes arrive, Nelson's Column, Tower of London, Buckingham Palace, St. Pauls Cathedral, and Stonehenge are already missing. Freddie and the others meets the Brigadier G (Nigel Hawthorne), who seems to have trouble keeping himself and his comrades from getting tangled up in the phonecord.
Freddie and the gang are introduced to Daffers (Jenny Agutter), an English woman who is an expert in martial arts, and Scottie (John Sessions), a Scotsman who is an expert with weapons. Things take a turn for the worse as Canterbury Cathedral disappears. Freddie also meets Tribly, a sneaky member of the secret service.
During a trip to Ascot, Freddie and the others discovers that the villain capturing the buildings is called El Supremo (Brian Blessed), and he's working alongside Messina, who spends most of the film in her cobra form with extra help of Bowser Koopa's Professional Recruits Team Rocket, Dr. Facilier, The Grand Duke of Owls and Lord Rothbart. Freddie also finds out that El Supremo and Bowser's Thugs are planning to steal Big Ben next. Knowing Daffers and Scottie won't want to be taken, Freddie tells them the next target is Windsor Castle and they hide on Big Ben - and are promptly captured by a giant robotic snake.
They go to a secret island in Scotland and discover that El Supremo and Bowser's thugs plans to use the buildings, by shrinking them to a size of a trophy and using them as batteries to a giant crystal, which will send a powerful sleeping virus across the world (starting with the UK), which will put people to sleep, allowing him to invade and enslave them. Scottie then freaks out as the last required building is captured: Edinburgh Castle as part of Bowser's plots.
Freddie and Scottie are thrown into a pool of sea monsters, while Daffers is brainwashed into a mindless follower of El Supremo and Messina. El Supremo uses the crystal to send his sleeping virus all across Great Britain and the whole country shuts down.
Freddie whistles and Nessie appears to save them both from being eaten, and Scottie is saved from drowning. Nessie shows her family to Freddie, who then asks them to help defeat El Supremo by submerging the patrolling submarines. Freddie and Scottie save Daffers from the snake guards in disguise and the three return to stop El Supremo from conquering the world. They have to battle an army of soldiers, but in the process, Daffers and Scottie come too close to the crystal's energy and fall unconscious. Freddie manages to infilrate the crystal's energy with his mind powers and destroys it, but also falls unconscious. El Supremo and Messina arrive to kill Freddie, but he, Daffers and Scottie defeat El Supremo by shrinking him down to an ant's size and trapping him in a matchbox. Pooh, Ash, Simba, and thier friends started to fight their enemies. Timon defeats Rothbart by shooting an arrow at him. Pumbaa blasted off Team Rocket.
A final battle then ensues between Freddie and Messina, who attacks by shapeshifting into a gargoyle, hyena, scorpion and boa. But he uses his mind control to transform Messina into a buzzard and she flees Brigadier G and his team arrive in time, and Trilby is discovered to be a spy for the villains. Britain is restored to normal and Freddie heads off to deal with some bad guys in the United States.