When the Thornberrys visit Nigel's friend Jomo, they search for an elephant, Rebecca, that Nigel saved twenty years ago. As the family attends to an elephant stuck in a mudhole, Eliza bonds with Rebecca, only to learn that she is old and ready to die.
When Eliza tries to swim with the humpback whales, Darwin's clumsiness leads to an accident that causes the whales to stop their ritual singing. When Eliza tries to set things right, she is arrested for violating the Marine Mammal Protection Act.
The Thornberrys are in the Philipines to find the Angler Fish. While Nigel and Eliza travel the river to find it Debbie and Marianne stay behind to study for Debbie's final. While looking for the fish Nigel is stung by a poisonous fish and Eliza must go into a dark, mysterious bog to get the antitoxin.
When Eliza meets a group of temple monkeys, they con her into bringing all of her family's food. While Darwin tries to convince her otherwise, Eliza realizes that she's been duped and learns the value of Darwin's friendship.
The Thornberrys visit a cattle ranch in Argentina where Marianne's old high school buddy,Gabriella, lives. Eliza is also looking forward to meeting her pen pal Miguel for the first time. While Marianne and Gabriella reminisce about old times Debbie develops a crush on the foreman Antonio. They all go out on a cattle drive where Eliza discovers that Miguel is not quite the gaucho he has led everyone to believe.
Eliza and a Chinese girl, Arioka, secretly switch places so Eliza can ride across the desert on camels and Arioka can ride in the Commvee, but Arioka's parents change their plans and Eliza must figure a way ro get them back to the Thornberrys.
When the Thornberrys visit the Great Wall Of China, Eliza is shocked to find that a poacher has captured her panda friend Shi Shou and his mother. With the help of her e-mail pal, Ling, Eliza tries to rescue the pandas.
The Thornberrys are in the Florida Everglades to film the Endangered Snail Kite. It is also Nigel's birthday and Marianne and the girls have a brand new watch/compass for him. While Marianne and Nigel go off to film the girls and Darwin and Donnie explore the Everglades in an air boat. Debbie wants to keep track of their time and brings the new watch. Soon they get lost and while using the compass drop it overboard. A Swamp Witch and a hungry alligator will make getting it back very difficult.
The Thornberrys are in Mongolia for the Naadam Festival. The festival is held outdoors and features events such as horse racing, wrestling and archery. Eliza decides she wants to enter the horse racing contest and asks Marianne to help train her. Debbie becomes involved in the archery contest and Donnie enters the wrestling contest. Eliza picks a nice, reliable horse to ride but what she really wants is to ride one of the wild horses. But they are not reliable and she gets more than she bargained for when she mounts one.
The Thornberry's are in the Congo along the banks of the Congo River to film the African Clawless Otter where they are waiting for Tyler Tucker to join them. Tyler and Eliza are cousins and close in age and very competitive with each other. When the commvee is put out of commission they take a small steamer boat named Prudence up the river in search of the otter. Tyler is not aware of all the dangers that the wild can hold and soon has them heading straight for disaster.
While camping near a Masai village Eliza and her cousin Tyler compete to see who is the bravest. Their courage is truly put to the test when they are caught out on the Savannah during a lightning storm.
The Thornberrys are in Egypt to film the elusive Caracal cat. While Marianne and Nigel go off via camel to film Eliza, Tyler and Darwin go exploring. While wandering through the desert they fall into an ancient burial chamber. Eliza and Tyler will have to work together to avoid the booby traps that have been set to discourage grave robbers. Meanwhile Debbie is convinced she is a descendant of Cleopatra.
While on the island of Zanzibar Debbie pleads with her mom to go to Stone Town Market for some shopping. Marianne is reluctant to let her have the comvee but eventually gives in. Debbie, Eliza, Tyler and Darwin head to the market while Nigel, Marianne and Donnie go off to film in an ancient crater. Most of the shopping at the market is done by barter and they accidentally trade the comvee for a dress. The kids take off in pursuit of the merchant who is now driving their comvee to try and reach an understanding with him.
All set to celebrate his thirteenth birthday in the Savannah, Tyler can't wait to accompany Eliza on one of her adventures, but Eliza keeps ditching him so she can help the Elephant Phaedra figure out what's wrong with her cousin, Shango.
Eliza offers to help Nigel film manta rays. When a fisherman tells her that a dragon haunts the bay, Eliza, already spooked from reading too many ghost stories, is convinced that something is out there.
Debbie accidentally hurts fer father's feelings on New Year's Eve by ditching the family for a couple of eccentric, 30's-era volcano chasers, Mitzi and Merrick Dash. Eliza goes after her to reclaim her friend, Santusa the Llama.
The Thornberrys visit the "land of happiness" to film the black-necked crane migration dance, but due to tourist limits, only two of them can enter the city. After it is decided that Marianne and Debbie go, Eliza and Darwin sneak inside the border.
On April Fool's Day, Eliza and Marianne keep up their yearly tradition of pulling practical jokes on each other. When Tyler tries to top Eliza by pulling off a better prank, he takes it too far and ends up falling into quicksand.
The Thornberry's are in Japan near Mt. Fuji to film the Asian black bear when Marianne's parents visit to spend their 50th anniversary with them. Grandpa Frank has had health problems recently and has problems acting his age. Eliza, Darwin and Grandpa Frank go off to climb Mt. Fuji.