The movie introduces the babies in a jungle pretending to be like The Wild Thornberrys, which happens to be a fake-out. Meanwhile, the adults are preparing for their vacation in the South China Seas. Stu has everyone's tickets for the Lipschitz Cruise. We then see that Susie is coming on vacation with them because her parents will be out of town. The Lipschitz cruise ship leaves without them and we Stu and Spike on a normal boat called the S.S. Nancy.
The adults get disgruntled and attempt to get on the cruise ship by sending signals and driving the boat there themselves. A large wave attacks them and it turns the ship upside- down. They get out of the rinky-dink tub, Betty opens up a life raft and they hop on there while the boat sinks. The family becomes stranded on a deserted island, and they begin disputing about how they're all gonna survive. Betty eventually becomes a leader after drawing a circle in the sand and she gets all the adults to work together as a team to find ways to survive on the island.
Meanwhile, the babies go their separate ways after Angelica scares them about how they're not gonna survive in the island. Spike runs into Eliza, and Spike starts to speak for the first time (since Eliza is capable of talking to animals) and Nigel Thornberry suffers amnesia and goes on adventures with the toddlers. Chuckie gets his clothes stolen from Donnie, and Chuckie ends up wearing his clothes as well. Angelica, since she is pretty much a b****, becomes good friends with Debbie, due to them sharing the same type of personality.
Nigel and the babies try and find the clouded leopard named Siri. The parents eventually encounter Mrs. Thornberry. Their attempt at finding the babies in the Bathosphere worked, but the fuel in there was empty, and Stu solved the problem, making him a hero at the end. The credits end with the children reuniting with their families and taking the Lipschitz Cruise back home, giving the movie a fantastic ending.
