As a thank-you from Merlin and Morgan, Jack and Annie are sent on what should be a vacation at a luxurious resort in Cozumel, Mexico, but is, by mistake, an adventure with ancient Mayans, instead.
The magic treehouse takes Jack and Annie back two thousand years to ancient China where they must find the original copy of an old legend before the Imperial Library is burned down by the evil Dragon King.
Jack and Annie travel to a monastery in the Swiss Alps where, with the help of St. Bernard dogs and magic, they seek the second of four special objects necessary to break the spell on the wizard Merlin's beloved penguin, Penny.
The magic tree house transports Jack and Annie on a mission to the Ice Age where they encounter Cro-Magnons, cave bears, sabertooth tigers, and woolly mammoths.
Using their magic tree house, Jack and Annie travel back to the time of the American Revolution and help General George Washington during his famous crossing of the Delaware River.
Jack and Annie travel 500 years back in time to Florence, Italy, and spend a day helping Leonardo da Vinci in the hope of learning another secret of happiness.
Jack and Annie travel in their magic treehouse to the year 1621, where they celebrate the first Thanksgiving with the Pilgrims and Wampanoag Indians in the New Plymouth Colony.