Toothbrush, the baby elephant finds Martin and Chris Kratt, roaming about in a cave where bats live. Since Toothbrush has been separated from her family, the Kratt brothers aide her in searching for them. This way, she will be reunited with them again. A garder snake is spotted, when Jackie was cutting the grass. The snake likes being in dark areas, so she doesn't mow down, part of the grass.

After admiring the camouflaged coats and amazing night vision of two visiting black jaguar cubs, Martin and Chris build a pair of "Eye-Spy goggles", a contraption that lets them see the world as various animals do. Jackie replants the evergreen that was her Christmas tree and decorates it with apples and popcorn for the birds.

While the brothers are building a model of a dinosaur they call the ""Martinandchrisaurus,"" Zoboo tells them he thinks he saw a dinosaur on his way to Animal Junction. The mystery creature turns out to be a monitor lizard. Jackie breaks open a pellet from an owl's stomach to see its prey's bones and fur inside, then runs into the Kratts while visiting the Royal Ontario Museum to see dinosaur bones.

A flying squirrel glides in looking for a hole to live in, and a search around Animal Junction reveals lots of other animals, from foxes and rabbits to snakes and porcupines, already living in various holes. When a man starts to cut down a dead tree with a hole in it, Jackie stops him by explaining that it may be the home of an owl.

When two fellow ring-tailed lemurs come to visit, Zoboo is stunned to hear that many people don't know what a lemur is. The Kratt brothers offer to remedy things by declaring an international Lemur Day holiday, complete with party and cake. Jackie rescues two turtles who were heading for a busy highway.

The arrival of a couple of river otters prompts a swimming party, with black jaguars, soft-shelled turtles, penguins, and capybaras jumping in. Jackie and her dog Goldie join in with a swim in MudPuppy Pond, where they meet even more water creatures.

Chris, Martin, and Zoboo explore the good things about slime, from puppies showing affection by licking to the slick coatings that keep frogs from drying out and let earthworms slide through dirt. To help make MudPuppy Pond an even better home for her own favorite slimy buddies "mudpuppy salamanders", Jackie rakes dead leaves into the water.

During the snowstorm of the century, Martin, Chris, Zoboo, and Jackie shelter one very cold Japanese snow monkey and shovel paths for animals having trouble maneuvering through the white stuff.

A camp-out at Animal Junction gives everyone a chance to discover nocturnal animals, creatures who sleep during the day and are active at night. Binturongs, raccoons, owls, ringtails, and dormice are among those living the night life.

Many animals have unique features that help them climb, from the sticky pads on the bottoms of frogs' feet to the prehensile tail of the kinkajou. The Kratts lose a climbing contest to a band of coatis, whose sharp claws and long tails give them an advantage, while Jackie and the Animal Helpers rescue a kitten who has figured out how to climb up a tree—but not how to get back down to the ground.

Zoboo decides he wants to join a visiting pack of Arctic wolves, so he takes lessons in howling, hunting, and obeying the pack pecking order. But just when he's ready to go home with his new friends, someone explains how different from warm, sunny Animal Junction the wolves' home territory is, and he rethinks his decision. Meanwhile, Jackie rescues a spider who's been stranded in a neighbor's bathtub.

The Kratts help out a beaver who's looking for wood to build a dam, and Jackie and the Animal Helpers build nest boxes for Eastern bluebirds.

The discovery of a litter of eight puppies turns Chris, Martin, and Zoboo into puppysitters. When one of the puppies and a calf both wander off from their mothers, everyone at Animal Junction learns how important it is to keep a close watch on babies.

Martin and Chris follow the tracks of a lynx through the snow, and Jackie works on protecting her bird feeder from marauding squirrels.

"Fling" is the nickname the Kratts give to a white-fronted capuchin monkey, which they return to the wild. Jackie learns about the wild when she tries to build a terrarium for a frog.

Everyone has got an itch, whether it's from poison ivy, bugs, or burrs.

Rabbits, bloodhounds, springhares, and foxes weigh in as Chris and Martin want to hear every animal's range of hearing.

It's all about animal coats, from porcupine to lynx to duck.

Martin and Chris run like other animals, beginning with the emu, extending to the crab, the fisher, the gecko, and the cheetah.

Today, Animal Junction is full of baby creatures! A baby ring tailed lemur, lynx kittens, bobcat kittens, a sliver fox kit, and baby coatis all need to be taken care of. Chris and Martin build a creature playpen to keep them all in.

There are giant animals galore at Animal Junction: giraffe, elephant, camel, and capybaras among them. This leads the Kratt brothers to find the world's biggest deer, biggest lemur, and biggest cat. Trees are also given giant attention.

Chris and Martin find a bunch of pets at Animal Junction. They all belong to Jackie and her animal helpers. Zoboomafoo learns how to take care of ducklings, goldfish, a rabbit, puppies, kittens, a crab, and even a calf. We also learn that all pets need lots of love. Zoboo also learns which animals should be pets and which ones should be ""free and in the wild"".

Animal Junction finds itself the center of attention for bears, wolverines, and kinkajous.

The guys have a plan to plant grass seeds to attract the African Crowned Crane to Animal Junction. But, they have a time trying to keep the sheep and goats from eating all the grass beforehand. These creatures have amazing lids like horns on top of their heads.

Animal "music" spills into Animal Junction, performed by camels, wolves, and elk, far better than a sound effects machine.

You know what they say about all work and no play. Thus the Kratts take a break at Animal Junction, playing with lion cubs, serval kittens, ducklings and, yes, children.

Between the cheetah and the snail, the Kratts find a great deal about the speed of animals. Then there is the chameleon, which varies speed a good deal.

Everybody likes horses, so the Kratts spend time with a foal and her mother, a strong Belgian draft horse. Then the brothers learn what's different about zebras.

A bath for certain animals is not what one would think. Chris and Martin give a bath to dogs before stepping out of Animal Junction for the elephant bath.

Zoboomafoo welcomes his fellow jumping animals to Animal Junction, from kangaroos to frogs.